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cmsc_r <- function(x, y, rescale = FALSE, xmin = NULL, xmax = NULL, ymin = NULL, ymax = NULL, comp = "si") { if (anyNA(x) || anyNA(y)) { x[is.na(y)] <- NA y[is.na(x)] <- NA if (all(is.na(x))) return(NA) } if (is.null(xmin)) xmin <- min(x, na.rm = T) if (is.null(xmax)) xmax <- max(x, na.rm = T) if (is.null(ymin)) ymin <- min(y, na.rm = T) if (is.null(ymax)) ymax <- max(y, na.rm = T) if (xmin > xmax) stop("xmin > xmax, please reset them!"); if (ymin > ymax) stop("ymin > ymax, please reset them!"); if (xmax < min(x, na.rm = T) || xmin > max(x, na.rm = T)) stop("[xmin, xmax] is beyond the range of x!"); if (ymax < min(y, na.rm = T) || ymin > max(y, na.rm = T)) stop("[ymin, ymax] is beyond the range of x!"); xymin <- min(xmin, ymin) xymax <- max(xmax, ymax) if (xymin == xymax) stop("global min equals to global max!"); maxmmin <- xymax - xymin if (rescale) { if (xmin == xmax) x[!is.na(x)] <- 1 else x <- (x - xmin) / (xmax - xmin) if (ymin == ymax) y[!is.na(y)] <- 1 else y <- (y - ymin) / (ymax - ymin) maxmmin <- 1 } sdx <- stats::sd(x, na.rm = T) sdy <- stats::sd(y, na.rm = T) s3 <- if (sdx == 0 && sdy == 0) { 1 } else if (sdx == 0 || sdy == 0) { 0 } else { stats::cor(x, y, use = "na.or.complete") } d2 <- ((sdx - sdy) / (maxmmin / 2))^2 if (d2 > 1) d2 <- 1 mx <- mean(x, na.rm = T) my <- mean(y, na.rm = T) d1 <- ((mx - my) / maxmmin)^2 if (d1 > 1) d1 <- 1 s2 <- 1 - d2 s1 <- 1 - d1 if (comp == "si") return(s1 * s2 * s3) if (comp == "s1") return(s1) if (comp == "s2") return(s2) if (comp == "s3") return(s3) stop("comp should be 'si' or 's1', 's2', 's3'!") }
test_that("works as expected", { files = list.files( test_file( '' ), full.names = TRUE )[1:4] files = files[ !grepl( '~[$]', files ) ] t = fldict( file.list = files ) expect_equal( length(t) > 0, TRUE ) })
setClass( Class="PairwiseComparisonMatrix", slots = c( valuesChar = "matrix", values = "matrix", variableNames = "character" ), validity=function(object) { if(nrow(object@valuesChar)!=ncol(object@valuesChar)){ return(paste("The pairwise comparison matrix is not a square matrix. Dimensions are - ncol = ", ncol(object@valuesChar), ", nrow = ", nrow(object@valuesChar), ".", sep = "")) } for(i in 1:nrow(object@valuesChar)){ if(!(object@valuesChar[i,i] == "1")){ return(paste("The elements on the main diagonal of the pairwise comparison matrix must be equal to 1. Position ", i, ",", i, " is not equal to 1.", sep = "")) } } for(i in 1:nrow(object@values)){ for(j in i:nrow(object@values)){ if (i!=j){ if (!isTRUE(all.equal(object@values[j,i], (1/object@values[i,j])))){ return(paste("The pairwise comparison matrix is not reciprocal. Elements [",i,",",j, "] and [",j,",",i,"] are not reciprocal. ", object@values[i,j], " is not reciprocal to ", object@values[j,i],". Because ", object@values[i,j], " != ", 1/object@values[j,i], sep = "")) } } } } if(max(object@values) > 9){ warning(paste("The maximal value in the pairwise comparison matrix should not be higher than 9, however,", "the value ", max(object@values), " was found.", sep = "")) } return(TRUE) } ) setGeneric("pairwiseComparisonMatrix", function(matrix) standardGeneric("pairwiseComparisonMatrix")) setMethod( f="pairwiseComparisonMatrix", signature(matrix = "matrix"), definition=function(matrix) { if(typeof(matrix)=="character"){ values = .parseCharacterMatrix(matrix) names = .getVariableNames(matrix) colnames(matrix) = NULL matrix = .textMatrixRepresentation(values) }else if(typeof(matrix)=="double"){ values = .parseDoubleMatrix(matrix) names = .getVariableNames(matrix) matrix = matrix(as.character(values), nrow = nrow(values), ncol=ncol(values)) colnames(matrix) = NULL matrix = .textMatrixRepresentation(values) } return(new("PairwiseComparisonMatrix", valuesChar = matrix, values = values, variableNames = names)) } ) setGeneric(".textMatrixRepresentation", function(matrix) standardGeneric(".textMatrixRepresentation")) setMethod( f=".textMatrixRepresentation", signature(matrix = "matrix"), definition=function(matrix) { values = matrix(data = "", nrow = nrow(matrix), ncol = ncol(matrix)) for (i in 1:nrow(matrix)){ for (j in 1:ncol(matrix)){ values[i, j] = as.character(fractions(matrix[i, j])) } } return(values) } ) setGeneric(".parseDoubleMatrix", function(matrix) standardGeneric(".parseDoubleMatrix")) setMethod( f=".parseDoubleMatrix", signature(matrix = "matrix"), definition=function(matrix) { values = matrix(data = 0, nrow = nrow(matrix), ncol = ncol(matrix)) for (i in 1:nrow(matrix)){ for (j in 1:ncol(matrix)){ if(is.na(matrix[i, j]) || matrix[i, j]==0){ values[i, j] = 0 }else{ values[i, j] = matrix[i, j] } } } if(all(values[upper.tri(values)] == 0)){ values[upper.tri(values)] = 1/t(values)[upper.tri(1/t(values))] } if(all(values[lower.tri(values)] == 0)){ values[lower.tri(values)] = 1/t(values)[lower.tri(1/t(values))] } return(values) } ) setGeneric(".parseCharacterMatrix", function(matrix) standardGeneric(".parseCharacterMatrix")) setMethod( f=".parseCharacterMatrix", signature(matrix = "matrix"), definition=function(matrix) { values = matrix(data = 0, nrow = nrow(matrix), ncol = ncol(matrix)) for (i in 1:nrow(matrix)){ for (j in 1:ncol(matrix)){ cell = gsub(" ", "", matrix[i,j]) if(cell == "" || is.na(cell)){ values[i, j] = 0 }else if(grepl("/", cell)){ numbers = unlist(strsplit(cell, "/")) if(suppressWarnings(is.na(as.numeric(numbers[1]))) || suppressWarnings(is.na(as.numeric(numbers[2])))){ stop(paste0("Element [", i, ",", j,"] is not a number - ", cell, ".")) } values[i,j] = as.numeric(numbers[1]) / as.numeric(numbers[2]) }else{ values[i,j] = as.numeric(cell) } } } if(all(values[upper.tri(values)] == 0)){ values[upper.tri(values)] = 1/t(values)[upper.tri(1/t(values))] } if(all(values[lower.tri(values)] == 0)){ values[lower.tri(values)] = 1/t(values)[lower.tri(1/t(values))] } return(values) } ) setGeneric(".getVariableNames", function(matrix) standardGeneric(".getVariableNames")) setMethod( f=".getVariableNames", signature(matrix = "matrix"), definition=function(matrix) { if(length(colnames(matrix))>0){ variableNames = colnames(matrix) }else if(length(rownames(matrix))>0){ variableNames = rownames(matrix) }else{ variableNames = c() for(i in 1:nrow(matrix)){ variableNames = c(variableNames, paste0("C_",i)) } } return(variableNames) } )
`cusp.nc.C` <- function (alpha, beta, subdivisions = 100, rel.tol = .Machine$double.eps^0.25, abs.tol = rel.tol, stop.on.error = TRUE, aux = NULL, keep.order = TRUE) { limit <- as.integer(subdivisions) if (limit < 1 || (abs.tol <= 0 && rel.tol < max(50 * .Machine$double.eps, 5e-29))) stop("invalid parameter values") lower <- -Inf upper <- Inf inf <- 2 bound <- 0 wk <- .External("cuspnc", as.double(alpha), as.double(beta), as.double(bound), as.integer(inf), as.double(abs.tol), as.double(rel.tol), limit = limit) wk }
b31gafr <- function(d, wth, l){ checkmate::assert_double(d, lower = 3.93e-2, upper = 1.27e5, finite = TRUE, any.missing = FALSE, min.len = 1) checkmate::assert_double(wth, lower = 0, upper = 1.275e4, finite = TRUE, any.missing = FALSE, min.len = 1) checkmate::assert_double(l, lower = 0, upper = 1.275e4, finite = TRUE, any.missing = FALSE, min.len = 1) 1e-3*trunc(1e3*.893*l/sqrt(d*wth)) }
test_that("returns the correct linting", { ops <- c( "+", "-", "=", "==", "!=", "<=", ">=", "<-", "<", ">", "->", "%%", "/", "*", "|", "||", "&", "&&", "%>%", "%Anything%", "%+%", NULL ) linter <- infix_spaces_linter() msg <- rex("Put spaces around all infix operators.") expect_lint("blah", NULL, linter) for (op in ops) { expect_lint(paste0("1 ", op, " 2"), NULL, linter) expect_lint(paste0("1 ", op, "\n2"), NULL, linter) expect_lint(paste0("1 ", op, "\n 2"), NULL, linter) expect_lint(paste0("1", op, "2"), msg, linter) if (!op %in% ops[1:2]) { expect_lint(paste0("1 ", op, "2"), msg, linter) } expect_lint(paste0("1", op, " 2"), msg, linter) } expect_lint("b <- 2E+4", NULL, linter) expect_lint("a <- 1e-3", NULL, linter) expect_lint("a[-1]", NULL, linter) expect_lint("a[-1 + 1]", NULL, linter) expect_lint("a[1 + -1]", NULL, linter) expect_lint("fun(a=1)", msg, linter) })
ggcorplot <- function(rpcaObj, pcs=c(1,2), loadings=TRUE, var_labels=FALSE, var_labels.names=NULL, alpha=1, top.n=NULL) { if (!requireNamespace('ggplot2', quietly = TRUE)) { stop("The package 'ggplot2' is needed for this function to work. Please install it.", call. = FALSE) } p = nrow(rpcaObj$rotation) stopifnot(length(pcs) == 2) if(max(pcs) > ncol(rpcaObj$rotation)) stop("Selected PC is not valid.") if(min(pcs) < 1) stop("Selected PC is not valid.") PC1 = paste("PC", pcs[1], sep="") PC2 = paste("PC", pcs[2], sep="") theta <- c(seq(-pi, pi, length = 360)) circle <- data.frame(x = cos(theta), y = sin(theta)) if(loadings==FALSE) rotation = rpcaObj$rotation[,pcs] if(loadings==TRUE) rotation = t(t(rpcaObj$rotation[,pcs]) * rpcaObj$eigvals[pcs]**0.5) df <- data.frame(rotation=rotation, row.names = 1:p) colnames(df) <- c( 'a', 'b') if(is.null(rownames(rpcaObj$rotation))) { df$"varName" <- as.character(1:p) } else { df$"varName" <- rownames(rpcaObj$rotation) } if(!is.null(var_labels.names)) df$"varName" <- var_labels.names df$abs <- sqrt(df$a**2 + df$b**2) variance = rpcaObj$sdev**2 explained_variance_ratio = round(variance / rpcaObj$var, 3) * 100 PC1 = paste("PC ", pcs[1], "(", explained_variance_ratio[pcs[1]] , "% explained var.)", sep="") PC2 = paste("PC ", pcs[2], "(", explained_variance_ratio[pcs[2]] , "% explained var.)", sep="") x <- NULL y <- NULL a <- NULL b <- NULL varName <- NULL g <- ggplot2::ggplot( circle , ggplot2::aes( x , y) ) + ggplot2::geom_path( size=0.5, colour="black" ) if(is.null(top.n)) top.n <- nrow(df) if(top.n>nrow(df)) top.n <- nrow(df) if(top.n < 50) { g <- g + ggplot2::geom_point(data = df[order(df$abs, decreasing=TRUE)[1:top.n], ], size = 4, mapping = ggplot2::aes(x = a, y = b, colour = varName ) ) + ggplot2::theme(legend.position = "none") } g <- g + ggplot2::geom_segment(data = df, ggplot2::aes(x = 0, y = 0, xend = a, yend = b ), arrow = grid::arrow(length = grid::unit(0.5, 'picas')), color = 'black' , size = 0.5, alpha = alpha) g <- g + ggplot2::coord_fixed(ratio=1) g <- g + ggplot2::ggtitle('Variables factor map (PCA)') g <- g + ggplot2::xlab(PC1) + ggplot2::ylab(PC2) g <- g + ggplot2::guides(colour=ggplot2::guide_legend(title=NULL)) g <- g + ggplot2::geom_vline(xintercept=0, linetype="dashed", color = "black") g <- g + ggplot2::geom_hline(yintercept=0, linetype="dashed", color = "black") if(var_labels == TRUE) { g <- g + ggplot2::geom_text(data = df[order(df$abs, decreasing=TRUE)[1:top.n], ], ggplot2::aes(label = varName, x = a, y = b, angle = 0, hjust = 0, vjust = 0), color = 'black', size = 4) } g <- g + ggplot2::theme_bw() g <- g + ggplot2::theme(panel.grid.major = ggplot2::element_blank(), panel.grid.minor = ggplot2::element_blank()) return( g ) }
' Authors Torsten Pook, [email protected] Copyright (C) 2017 -- 2020 Torsten Pook This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. ' get.age.point <- function(population, database=NULL, gen=NULL, cohorts=NULL, use.id=FALSE){ database <- get.database(population, gen, database, cohorts) n.animals <- sum(database[,4] - database[,3] +1) data <- rep(0, n.animals) before <- 0 names <- numeric(n.animals) for(row in 1:nrow(database)){ animals <- database[row,] nanimals <- database[row,4] - database[row,3] +1 if(nanimals>0){ data[(before+1):(before+nanimals)] <- population$breeding[[animals[1]]][[22+ animals[2]]][animals[3]:animals[4]] names[(before+1):(before+nanimals)] <- paste(if(animals[2]==1) "M" else "F", animals[3]:animals[4],"_", animals[1], sep="") before <- before + nanimals } } if(use.id){ names(data) <- get.id(population, database = database) } else{ names(data) <- names } return(data) }
psmMergeSplit_base <- function(partition, psm, logPosteriorPredictiveDensity = function(i, subset) 0.0, mass = 1.0, discount = 0.0, nUpdates = 1L, selectionWeights = NULL) { if (!is.function(logPosteriorPredictiveDensity)) { stop("Function argument 'logPosteriorPredictiveDensity' must be of type 'closure'") } if (discount < 0 | discount >= 1) { stop("Function argument 'discount' must be on the interval [0,1).") } if (mass <= -discount) { stop("Function argument 'mass' must be strictly greater than the negative of the function argument 'discount'.") } if (!is.integer(nUpdates)) { nUpdates <- as.integer(nUpdates) if (nUpdates < 1) { stop("Function argument 'nUpdates' must be a positive integer.") } } if (!isCanonical(partition)) { partition <- asCanonical(partition) } nItems <- length(partition) if (is.null(selectionWeights)) { samplePair <- function() sample(nItems, 2, replace = FALSE) } else { samplePair <- function() { as.integer(selectionWeights[sample(nrow(selectionWeights), 1, prob = selectionWeights[,3]), 1:2]) } } psmWeights <- function(k, set) { wt <- c(0,0) clusterSizes <- sapply(set, length) t <- sum(clusterSizes) num <- sapply(1:2, function(x) sum(psm[set[[x]], k])) wts <- num / sum(num) wts } mkLogPriorRatio <- function(d) { if (d == 0) { function(doSplit) { if (doSplit) { log(mass) + lfactorial(n_si_split - 1) + lfactorial(n_sj_split - 1) - lfactorial(n_si -1) } else { lfactorial(n_si_merge - 1) - log(mass) - lfactorial(n_si - 1) - lfactorial(n_sj - 1) } } } else { function(doSplit) { if (doSplit) { log(mass + d*q) + lgamma(n_si_split - d) + lgamma(n_sj_split - d) - lgamma(1-d) - lgamma(n_si - d) } else { lgamma(n_si_merge - d) + lgamma(1-d) - log(mass + d*(q-1)) - lgamma(n_si - d) - lgamma(n_sj - d) } } } } logPriorRatio <- mkLogPriorRatio(discount) accept <- 0 for (u in 1:nUpdates) { q <- length(unique(partition)) ijPair <- samplePair() clusterForI <- clusterWithItem(ijPair[1], partition) clusterForJ <- clusterWithItem(ijPair[2], partition) doSplit <- clusterForI$which == clusterForJ$which if (doSplit) { s <- which(partition == clusterForI$which) clusterForJ$which <- max(unique(partition)) + 1 s <- s[!s %in% ijPair] s_i <- ijPair[1] s_j <- ijPair[2] n_s <- length(s) if (n_s > 0) { if (n_s > 1) { permuteS <- sample(s) } else { permuteS <- s } q_k <- numeric(n_s) for (k in 1:n_s) { wts <- psmWeights(permuteS[k], list(s_i, s_j)) if (sum(wts) == 0) wts <- c(1,1) chooseThisCluster <- sample(1:2, 1, prob = wts) if (chooseThisCluster == 1) { s_i <- sort(c(s_i, permuteS[k])) } else { s_j <- sort(c(s_j, permuteS[k])) } q_k[k] <- wts[chooseThisCluster]/sum(wts) } } else { q_k <- 1 } proposedPartition <- partition proposedPartition[s_i] <- clusterForI$which proposedPartition[s_j] <- clusterForJ$which si_split <- clusterWithItem(ijPair[1], proposedPartition)$cluster n_si_split <- length(si_split) ik_split <- sapply(1:n_si_split, function(i) logPosteriorPredictiveDensity(si_split[i], si_split[0:(i-1)])) sj_split <- clusterWithItem(ijPair[2], proposedPartition)$cluster n_sj_split <- length(sj_split) jk_split <- sapply(1:n_sj_split, function(j) logPosteriorPredictiveDensity(sj_split[j], sj_split[0:(j-1)])) si <- clusterWithItem(ijPair[1], partition)$cluster n_si <- length(si) ik <- sapply(1:n_si, function(i) logPosteriorPredictiveDensity(si[i], si[0:(i-1)])) pRatio <- logPriorRatio(doSplit) lRatio <- sum(ik_split) + sum(jk_split) - sum(ik) qRatio <- -sum(log(q_k)) mhRatio <- qRatio + pRatio + lRatio if (log(runif(1)) < mhRatio) { partition <- asCanonical(proposedPartition) accept <- accept + 1 } } else { s <- union(clusterForI$cluster, clusterForJ$cluster) proposedPartition <- partition proposedPartition[s] <- partition[ijPair[1]] s_split <- s[!s %in% ijPair] s_i <- ijPair[1] s_j <- ijPair[2] n_s <- length(s_split) if (n_s > 0) { if (n_s > 1) { permuteS <- sample(s_split) } else { permuteS <- s_split } q_k <- numeric(n_s) for (k in 1:n_s) { wts <- psmWeights(permuteS[k], list(s_i, s_j)) if (sum(wts) == 0) wts <- c(1,1) chooseThisCluster <- sample(1:2, 1, prob = wts) if (chooseThisCluster == 1) { s_i <- c(s_i, permuteS[k]) } else { s_j <- c(s_j, permuteS[k]) } q_k[k] <- wts[chooseThisCluster]/sum(wts) } } else { q_k <- 1 } si_merge <- sort(union(clusterForI$cluster, clusterForJ$cluster)) n_si_merge <- length(si_merge) ik_merge <- sapply(1:n_si_merge, function(i) logPosteriorPredictiveDensity(si_merge[i], si_merge[0:(i-1)])) si <- clusterForI$cluster n_si <- length(si) ik <- sapply(1:n_si, function(i) logPosteriorPredictiveDensity(si[i], si[0:(i-1)])) sj <- clusterForJ$cluster n_sj <- length(sj) jk <- sapply(1:n_sj, function(j) logPosteriorPredictiveDensity(sj[j], sj[0:(j-1)])) pRatio <- logPriorRatio(doSplit) lRatio <- sum(ik_merge) - sum(ik) - sum(jk) qRatio <- sum(log(q_k)) mhRatio <- pRatio + lRatio + qRatio if (log(runif(1)) < mhRatio) { partition <- asCanonical(proposedPartition) accept <- accept + 1 } } } list(partition = partition, accept = accept/nUpdates) }
CIG <- function (design, select.catlg = catlg, nfac=NULL, static = FALSE, layout = layout.auto, label = "num", plot = TRUE, ...) { ll <- list(...) if ("vertex.label" %in% names(ll)) vertex.label <- ll$vertex.label if ("catlg" %in% class(design)) { if (length(design) > 1) stop("design must not contain more than one catlg entry") design <- design[[1]] } else { if (is.matrix(design) || (is.character(design) & length(design)>1) || is(design,"formula")){ if (is(design,"formula")){ fn <- row.names(attr(terms(formula(design)), "factors")) design <- estimable.check(design, length(fn), fn) names(design) <- c("clear.2fis","nfac") if (!exists("vertex.label", inherits=FALSE)) vertex.label <- fn else if (!length(vertex.label)==length(fn)) warning("vertex.label has wrong length") design$res <- 4 } if (is.matrix(design)){ if (!nrow(design)==2) stop("matrix design must have two rows.") if (any (design[1,]==design[2,])) stop("entries in the same column of matrix design must be different") fn <- unique(design) if (!is.null(nfac) && all(fn %in% 1:nfac)) fn <- 1:nfac if (!exists("vertex.label", inherits=FALSE)) vertex.label <- fn else if (!length(vertex.label)==length(fn)) warning("vertex.label has wrong length") if (is.character(design)) design <- list(clear.2fis=matrix(sapply(design, function(obj) which(fn==obj)), nrow=2), nfac=length(fn),res=4) else design <- list(clear.2fis=design, nfac=length(fn), res=4) } if (is.character(design) && length(design)>1){ if (!all(nchar(design)==2)) stop("character vector design must have length 2 entries only") if (is.null(nfac)) nfac <- max(which(Letters %in% unique(unlist(strsplit(design,""))))) design <- estimable.check(design,nfac,NULL) if (!exists("vertex.label", inherits=FALSE)) vertex.label <- Letters[1:design$nfac] else if (!length(vertex.label)==design$nfac) warning("vertex.label has wrong length") names(design) <- c("clear.2fis","nfac") if (any (design$clear.2fis[1,]==design$clear.2fis[2,])) stop("characters in the same element of vector design must be different") design$res <- 4 } } else{ if (!"catlg" %in% class(select.catlg)) stop("select.catlg must be a catalogue") if (!(is.character(design) && length(design) == 1)) stop("design must be a design name") if (!(design %in% names(select.catlg))) stop("design must be a design name that occurs in select.catlg") design <- select.catlg[[design]] } } if (!exists("vertex.label", inherits=FALSE)) { vertex.label <- 1:design$nfac if (!label == "num") vertex.label <- Letters[vertex.label] } go2 <- graph.empty(n = design$nfac, directed = FALSE) if (!length(design$clear.2fis) == 0) go2 <- add.edges(go2, design$clear.2fis) if (design$res < 4) warning("the design is of resolution less than IV") if (plot) { if (!static) { id <- tkplot(go2, vertex.label = vertex.label, ...) invisible(list(graph = go2, coords = tkplot.getcoords(id))) } else { invisible(go2) plot(go2, layout = layout, vertex.label = vertex.label, ...) } } else return(go2) } CIGstatic <- function(graph, id, label = "num", xlim = c(-1, 1), ylim = c(1, -1), ...){ if ("list" %in% class(graph)) if (names(graph)[1] == "graph") graph <- graph$graph if (!exists("vertex.label", inherits = FALSE)) { vertex.label <- 1:graph[[1]][[1]][2] if (!label == "num") vertex.label <- Letters[vertex.label] } coords <- tkplot.getcoords(id) plot(graph, layout = coords, vertex.label = vertex.label, xlim = xlim, ylim = ylim, ...) }
treespace <- function(x, method="treeVec", nf=NULL, lambda=0, return.tree.vectors=FALSE, processors=1, ...){ if(!inherits(x, "multiPhylo")) stop("x should be a multiphylo object") num_trees <- length(x) if(num_trees<3) { stop("treespace expects at least three trees. The function treeDist is suitable for comparing two trees.") } dots <- list(...) if(!is.null(dots$return.lambda.function)) stop("return.lambda.function is not compatible with treespace. Consider using multiDist instead.") if(!is.null(dots$save.memory)) stop("save.memory is not compatible with treespace. Consider using multiDist instead.") if(is.null(names(x))) names(x) <- 1:num_trees else if(length(unique(names(x)))!=num_trees){ warning("duplicates detected in tree labels - using generic names") names(x) <- 1:num_trees } lab <- names(x) for (i in 1:num_trees) { if (!setequal(x[[i]]$tip.label,x[[1]]$tip.label)) { stop(paste0("Tree ",lab[[i]]," has different tip labels from the first tree.")) } } if (method=="treeVec") { df <- t(mcmapply(treeVec, x, lambda=lambda, MoreArgs=dots, mc.cores=processors)) D <- as.dist(rdist(df)) } else if(method %in% c("Abouheif","sumDD")){ df <- t(mcmapply(adephylo::distTips, x, method=method, MoreArgs=dots, mc.cores=processors)) D <- as.dist(rdist(df)) } else if(method=="patristic"){ D <- path.dist(x, use.weight=TRUE) } else if(method=="nNodes"){ D <- path.dist(x, use.weight=FALSE) } else if(method=="RF"){ D <- RF.dist(x) if (!ade4::is.euclid(D)) { warning("Distance matrix is not Euclidean; making it Euclidean using ade4::cailliez") D <- ade4::cailliez(D, print=FALSE) } } else if(method=="wRF"){ D <- wRF.dist(x) if (!ade4::is.euclid(D)) { warning("Distance matrix is not Euclidean; making it Euclidean using ade4::cailliez") D <- ade4::cailliez(D, print=FALSE) } } else if(method=="KF"){ D <- KF.dist(x) } else if(method=="BHV"){ D <- dist.multiPhylo(x) if (!ade4::is.euclid(D)) { warning("Distance matrix is not Euclidean; making it Euclidean using ade4::cailliez") D <- ade4::cailliez(D, print=FALSE) } } attr(D,"Labels") <- lab pco <- dudi.pco(D, scannf=is.null(nf), nf=nf) if (return.tree.vectors==TRUE) { out <- list(D=D, pco=pco, vectors=df) } else { out <- list(D=D, pco=pco) } return(out) }
tbl_layout_feature <- function(features, contig_layout){ print("TODO: check start < end") layout <- features %>% select(cid=1,fstart=2,fend=3,fstrand=4, everything()) contig_info <- contig_layout %>% mutate( gcoffset=goffset+coffset, gcstrand=gstrand*cstrand) %>% select(cid, gid, gix, gcoffset, gcstrand) layout %>% inner_join(contig_info) %>% mutate( fstrand=fstrand*gcstrand, foffset=gcoffset) %>% select(cid, gid, gix, foffset, fstart, fend, fstrand, everything()) }
plot_errors <- function(dataIn, plotType = c('boxplot')) UseMethod('plot_errors') plot_errors.errprof <- function(dataIn, plotType = c('boxplot')){ if(!plotType %in% c('boxplot', 'bar', 'line')) stop('plotType must be boxplot, bar, or line') if(plotType == 'boxplot'){ toplo <- attr(dataIn, 'errall') toplo <- melt(toplo) percs <- dataIn$MissingPercent toplo$L2 <- factor(toplo$L2, levels = unique(toplo$L2), labels = percs) names(toplo) <- c('Error value', 'Percent of missing observations', 'Methods') p <- ggplot(toplo, aes(x = `Percent of missing observations`, y = `Error value`)) + ggtitle(dataIn$Parameter) + geom_boxplot(aes(fill = Methods)) + theme_bw() return(p) } toplo <- data.frame(dataIn[-1]) toplo <- melt(toplo, id.var = 'MissingPercent') toplo$MissingPercent <- factor(toplo$MissingPercent) names(toplo) <- c('Percent of missing observations', 'Methods', 'Error value') if(plotType == 'bar'){ p <- ggplot(toplo, aes(x = `Percent of missing observations`, y = `Error value`)) + ggtitle(dataIn$Parameter) + geom_bar(aes(fill = Methods), stat = 'identity', position = 'dodge') + theme_bw() return(p) } if(plotType == 'line'){ p <- ggplot(toplo, aes(x = `Percent of missing observations`, y = `Error value`, group = Methods)) + ggtitle(dataIn$Parameter) + geom_line() + geom_point(aes(fill = Methods), shape = 21, size = 5, alpha = 0.75) + theme_bw() return(p) } }
go_indica_fi <- function( time_0 = NA, time_t = NA, timeName = NA, workDF = NA , indicaT = NA, indiType = c('highBest','lowBest')[1], seleMeasure = "all", seleAggre = 'EU27', x_angle = 45, data_res_download = FALSE, auth = 'A.Student', dataNow = Sys.time(), outFile = NA, outDir = NA, pdf_out = FALSE, workTB = NULL, selfContained = FALSE ){ if(is.na(workDF) & (!is.null(workTB))){ curTB <- workTB }else if(!is.na(workDF) & is.null(workTB)){ curTB <- get(workDF,envir = .GlobalEnv) workTB <- curTB }else{ stop("Error while specifying data.") } if( any(!stats::complete.cases(curTB))){ obj_out <- convergEU_glb()$tmpl_out obj_out$err <- paste("Error: one or more missing values (NAs) in the dataframe. ", "Please perform imputation of missing values (NA) before making fiches.") return(obj_out) } sourceFilecss <- system.file("extdata", "EUF.css", package = "convergEU") sourceFile1 <- system.file("extdata", "indica_fi_2.Rmd", package = "convergEU") sourceFile2 <- system.file("extdata", "eurofound.jpg", package = "convergEU") sourceFile71 <- system.file("extdata", "indica_fi_2_sigma.Rmd", package = "convergEU") sourceFile72 <- system.file("extdata", "indica_fi_2_beta.Rmd", package = "convergEU") sourceFile73 <- system.file("extdata", "indica_fi_2_nobeta.Rmd", package = "convergEU") sourceFile74 <- system.file("extdata", "indica_fi_2_delta.Rmd", package = "convergEU") sourceFile75 <- system.file("extdata", "indica_fi_2_gamma.Rmd", package = "convergEU") if (is.na(outFile)) { outFile2 <- paste0("indica-fie-",seleAggre,"-", indicaT, "-", time_0,"-",time_t, ".html") outFile <- paste0("indica-fi-",seleAggre,"-", indicaT, "-", time_0,"-",time_t) }else{ outFile2 <- paste0(outFile,".html") } if (is.na(outDir)) { outDir <- file.path(getwd(),"out_dir_counvergEU") } resDE <- dir.exists(outDir) if (!resDE) { dir.create(outDir, FALSE) } outPF <- file.path(outDir,outFile2) outFcss <- file.path(outDir,"EUF.css") sourcePF1 <- file.path(outDir,"indica_fi_2.Rmd") sourcePF2 <- file.path(outDir,"eurofound.jpg") sourcePF71 <- file.path(outDir,"indica_fi_2_sigma.Rmd") sourcePF72 <- file.path(outDir,"indica_fi_2_beta.Rmd") sourcePF73 <- file.path(outDir,"indica_fi_2_nobeta.Rmd") sourcePF74 <- file.path(outDir,"indica_fi_2_delta.Rmd") sourcePF75 <- file.path(outDir,"indica_fi_2_gamma.Rmd") file.copy(from = sourceFile1, to = sourcePF1, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile2, to = sourcePF2, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile71, to = sourcePF71, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile72, to = sourcePF72, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile73, to = sourcePF73, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile74, to = sourcePF74, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFile75, to = sourcePF75, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); file.copy(from = sourceFilecss, to = outFcss, overwrite = TRUE, recursive = FALSE, copy.mode = TRUE, copy.date = FALSE); if(selfContained){ myOutOpt <- list(self_contained = TRUE, mathjax ="default") }else{ myOutOpt <- list(self_contained = FALSE, mathjax = 'local') } rmarkdown::render(sourcePF1, params = list( dataNow = dataNow, workingDF = workDF, time_0 = time_0, time_t = time_t, timeName = timeName, indiType = indiType, indicaT = indicaT, seleMeasure = seleMeasure, seleAggre = seleAggre, x_angle = x_angle, data_res_download = data_res_download, auth = auth, outFile = outFile, outDir = outDir, pdf_out = FALSE, workTB = workTB ), output_options = myOutOpt, output_file = outPF, encoding = "UTF-8") }
gpScaleBiasGradient <- function(model) { g = list() if (model$learnScales) { g = 1/model$scale * drop(model$innerProducts-1) fhandle <- get(model$scaleTransform$func, mode="function") g = g * fhandle(model$scale, "gradfact") } return (g) }
relocate.dtplyr_step <- function(.data, ..., .before = NULL, .after = NULL) { sim_data <- simulate_vars(.data) to_move <- tidyselect::eval_select(expr(c(...)), sim_data) if (length(to_move) == 0) { return(.data) } .before <- enquo(.before) .after <- enquo(.after) has_before <- !quo_is_null(.before) has_after <- !quo_is_null(.after) if (has_before && has_after) { abort("Must supply only one of `.before` and `.after`.") } else if (has_before) { where <- min(unname(tidyselect::eval_select(.before, sim_data))) if (!where %in% to_move) { to_move <- c(to_move, where) } } else if (has_after) { where <- max(unname(tidyselect::eval_select(.after, sim_data))) if (!where %in% to_move) { to_move <- c(where, to_move) } } else { where <- 1L if (!where %in% to_move) { to_move <- union(to_move, where) } } lhs <- setdiff(seq2(1, where - 1), to_move) rhs <- setdiff(seq2(where + 1, ncol(.data)), to_move) new_vars <- .data$vars[unique(c(lhs, to_move, rhs))] out <- step_colorder(.data, new_vars) step_group(out, .data$groups) } relocate.data.table <- function(.data, ..., .before = NULL, .after = NULL) { .data <- lazy_dt(.data) relocate(.data, ..., .before = {{ .before }}, .after = {{ .after }}) }
downsample_time_data <- function(data, pupil, timebin_size, option = c('mean', 'median')){ if('PupillometryR' %in% class(data) == FALSE){ stop('Dataframe is not of class PupillometryR. Did you forget to run make_pupillometryr_data? Some tidyverse functions associated with dplyr and tidyr can also interfere with this functionality.') } if(is.null(option)) option = 'mean' options <- attr(data, 'PupillometryR') subject <- options$Subject trial <- options$Trial time <- options$Time condition <- options$Condition other <- options$Other pupil <- deparse(substitute(pupil)) data[["Timebin"]] <- floor(data[[time]] / timebin_size) if(option == 'median'){ message('Calculating median pupil size in each timebin \n') data2 <- data %>% group_by(!!sym(subject), !!sym(trial), !!sym(condition), !!sym(other), Timebin) %>% summarise(!!sym(pupil) := median(!!sym(pupil))) %>% ungroup() %>% mutate(!!sym(time) := Timebin * timebin_size) }else{ message('Calculating mean pupil size in each timebin \n') data2 <- data %>% group_by(!!sym(subject), !!sym(trial), !!sym(condition), !!sym(other), Timebin) %>% summarise(!!sym(pupil) := mean(!!sym(pupil))) %>% ungroup() %>% mutate(!!sym(time) := Timebin * timebin_size) } class(data2) <- c(class(data)) attr(data2, 'PupillometryR') <- options return(data2) } calculate_missing_data <- function(data, pupil){ if('PupillometryR' %in% class(data) == FALSE){ stop('Dataframe is not of class PupillometryR. Did you forget to run make_pupillometryr_data? Some tidyverse functions associated with dplyr and tidyr can also interfere with this functionality.') } options <- attr(data, 'PupillometryR') subject <- options$Subject trial <- options$Trial time <- options$Time condition <- options$Condition other <- options$Other pupil <- deparse(substitute(pupil)) data_trial <- data %>% group_by(!!sym(subject), !!sym(trial)) %>% mutate(Missing = ifelse(is.na(!!sym(pupil)), 1, 0)) %>% summarise(Missing = sum(Missing) /length(Missing)) %>% ungroup() return(data_trial) } clean_missing_data <- function(data, pupil, trial_threshold = 1, subject_trial_threshold = 1){ if('PupillometryR' %in% class(data) == FALSE){ stop('Dataframe is not of class PupillometryR. Did you forget to run make_pupillometryr_data? Some tidyverse functions associated with dplyr and tidyr can also interfere with this functionality.') } options <- attr(data, 'PupillometryR') subject <- options$Subject trial <- options$Trial time <- options$Time condition <- options$Condition other <- options$Other pupil <- deparse(substitute(pupil)) if(subject_trial_threshold == 1){ if(trial_threshold > 1){ stop('Please input trial threshold as a proportion') } data_trial <- data %>% group_by(!!sym(subject), !!sym(trial)) %>% mutate(Missing = ifelse(is.na(!!sym(pupil)), 1, 0)) %>% summarise(SumMissing = sum(Missing), PropMissing = sum(Missing)/length(Missing)) %>% ungroup() data_trial2 <- data_trial[data_trial[['PropMissing']] < trial_threshold,] data_bad <- data_trial[data_trial[['PropMissing']] > trial_threshold,] data_trial <- data_trial %>% mutate(Remove = ifelse(PropMissing > trial_threshold, 1, 0)) bad_num <- length(data_bad[['PropMissing']]) message(paste('Removing trials with a proportion missing >', trial_threshold, '\n ...removed', bad_num, 'trials \n')) data_out <- left_join(data_trial2, data, by = c(subject, trial)) data_out$SubjProp <- 1 }else{ if(subject_trial_threshold > 1){ stop('Please input subject trial threshold as a proportion') } if(trial_threshold > 1){ stop('Please input trial threshold as a proportion') } data_trial <- data %>% group_by(!!sym(subject), !!sym(trial)) %>% mutate(Missing = ifelse(is.na(!!sym(pupil)), 1, 0)) %>% summarise(SumMissing = sum(Missing), PropMissing = sum(Missing)/length(Missing)) %>% ungroup() data_trial2 <- data_trial[data_trial$PropMissing < trial_threshold,] data_bad <- data_trial[data_trial$PropMissing > trial_threshold,] bad_num <- length(data_bad[['PropMissing']]) data_trial <- data_trial %>% mutate(Remove = ifelse(PropMissing > trial_threshold, 1, 0)) message(paste('Removing trials with a proportion missing >', trial_threshold, '\n ...removed', bad_num, 'trials \n')) data_part <- data_trial %>% group_by(!!sym(subject)) %>% summarise(SubjProp = sum(Remove)/length(Remove)) %>% ungroup() data_part2 <- data_part[data_part[['SubjProp']] < subject_trial_threshold,] data_bad2 <- data_part[data_part[['SubjProp']] > subject_trial_threshold,] part_num <- length(data_bad2[['SubjProp']]) message(paste('Removing subjects with a proportion of missing trials >', subject_trial_threshold, '\n ...removed', part_num, 'subjects \n')) data_out2 <- left_join(data_trial2, data, by = c(subject, trial)) data_out <- left_join(data_part2, data_out2, by = subject) } data_out <- data_out %>% select(-SubjProp, -PropMissing, -SumMissing) class(data_out) <- c(class(data)) attr(data_out, 'PupillometryR') <- options return(data_out) }
writeExpectTest <- function(expr, filename="", ...) { tfile <- tempfile() on.exit(unlink(tfile)) exsub <- deparse(substitute(expr)) result <- paste(deparse(dput(expr, file=tfile)), collapse="\n") output <- paste0("expect_equal(", exsub, ",\n", result, "\n)") cat(output, file=filename, ...) }
ParamStMoE <- setRefClass( "ParamStMoE", fields = list( X = "numeric", Y = "numeric", n = "numeric", phiBeta = "list", phiAlpha = "list", K = "numeric", p = "numeric", q = "numeric", df = "numeric", alpha = "matrix", beta = "matrix", sigma2 = "matrix", lambda = "matrix", delta = "matrix", nu = "matrix" ), methods = list( initialize = function(X = numeric(), Y = numeric(1), K = 1, p = 3, q = 1) { X <<- X Y <<- Y n <<- length(Y) phiBeta <<- designmatrix(x = X, p = p) phiAlpha <<- designmatrix(x = X, p = q) df <<- (q + 1) * (K - 1) + (p + 1) * K + K + K + K K <<- K p <<- p q <<- q alpha <<- matrix(0, q + 1, K - 1) beta <<- matrix(NA, p + 1, K) sigma2 <<- matrix(NA, 1, K) lambda <<- matrix(NA, ncol = K) delta <<- matrix(NA, ncol = K) nu <<- matrix(NA, ncol = K) }, initParam = function(segmental = FALSE) { "Method to initialize parameters \\code{alpha}, \\code{beta} and \\code{sigma2}. If \\code{segmental = TRUE} then \\code{alpha}, \\code{beta} and \\code{sigma2} are initialized by clustering the response \\code{Y} uniformly into \\code{K} contiguous segments. Otherwise, \\code{alpha}, \\code{beta} and \\code{sigma2} are initialized by clustering randomly the response \\code{Y} into \\code{K} segments." if (!segmental) { klas <- sample(1:K, n, replace = TRUE) for (k in 1:K) { Xk <- phiBeta$XBeta[klas == k,] yk <- Y[klas == k] beta[, k] <<- solve(t(Xk) %*% Xk) %*% t(Xk) %*% yk sigma2[k] <<- sum((yk - Xk %*% beta[, k]) ^ 2) / length(yk) } } else { nk <- round(n / K) - 1 klas <- rep.int(0, n) for (k in 1:K) { i <- (k - 1) * nk + 1 j <- (k * nk) yk <- matrix(Y[i:j]) Xk <- phiBeta$XBeta[i:j, ] beta[, k] <<- solve(t(Xk) %*% Xk, tol = 0) %*% (t(Xk) %*% yk) muk <- Xk %*% beta[, k, drop = FALSE] sigma2[k] <<- t(yk - muk) %*% (yk - muk) / length(yk) klas[i:j] <- k } } Z <- matrix(0, nrow = n, ncol = K) Z[klas %*% ones(1, K) == ones(n, 1) %*% seq(K)] <- 1 tau <- Z res <- IRLS(phiAlpha$XBeta, tau, ones(nrow(tau), 1), alpha) alpha <<- res$W lambda <<- -1 + 2 * rand(1, K) delta <<- lambda / sqrt(1 + lambda ^ 2) nu <<- 50 * rand(1, K) }, MStep = function(statStMoE, calcAlpha = FALSE, calcBeta = FALSE, calcSigma2 = FALSE, calcLambda = FALSE, calcNu = FALSE, verbose_IRLS = FALSE) { "Method which implements the M-step of the EM algorithm to learn the parameters of the StMoE model based on statistics provided by the object \\code{statStMoE} of class \\link{StatStMoE} (which contains the E-step)." reg_irls <- 0 if (calcAlpha) { res_irls <- IRLS(phiAlpha$XBeta, statStMoE$tik, ones(nrow(statStMoE$tik), 1), alpha, verbose_IRLS) reg_irls <- res_irls$reg_irls alpha <<- res_irls$W } if (calcBeta) { for (k in 1:K) { TauikWik <- (statStMoE$tik[, k] * statStMoE$wik[, k]) %*% ones(1, p + 1) TauikX <- phiBeta$XBeta * (statStMoE$tik[, k] %*% ones(1, p + 1)) betak <- solve((t(TauikWik * phiBeta$XBeta) %*% phiBeta$XBeta), tol = 0) %*% (t(TauikX) %*% ((statStMoE$wik[, k] * Y) - (delta[k] * statStMoE$E1ik[, k]))) beta[, k] <<- betak } } if (calcSigma2) { for (k in 1:K) { sigma2[k] <<- sum(statStMoE$tik[, k] * (statStMoE$wik[, k] * ((Y - phiBeta$XBeta %*% beta[, k]) ^ 2) - 2 * delta[k] * statStMoE$E1ik[, k] * (Y - phiBeta$XBeta %*% beta[, k]) + statStMoE$E2ik[, k])) / (2 * (1 - delta[k] ^ 2) * sum(statStMoE$tik[, k])) } } if (calcLambda) { for (k in 1:K) { try(lambda[k] <<- uniroot(f <- function(lmbda) { return((lmbda / sqrt(1 + lmbda ^ 2)) * (1 - (lmbda ^ 2 / (1 + lmbda ^ 2))) * sum(statStMoE$tik[, k]) + (1 + (lmbda ^ 2 / (1 + lmbda ^ 2))) * sum(statStMoE$tik[, k] * statStMoE$dik[, k] * statStMoE$E1ik[, k] / sqrt(sigma2[k])) - (lmbda / sqrt(1 + lmbda ^ 2)) * sum(statStMoE$tik[, k] * ( statStMoE$wik[, k] * (statStMoE$dik[, k] ^ 2) + statStMoE$E2ik[, k] / (sqrt(sigma2[k]) ^ 2) )) ) }, c(-100, 100), extendInt = "yes")$root, silent = TRUE) delta[k] <<- lambda[k] / sqrt(1 + lambda[k] ^ 2) } } if (calcNu) { for (k in 1:K) { try(nu[k] <<- suppressWarnings(uniroot(f <- function(nnu) { return(-psigamma((nnu) / 2) + log((nnu) / 2) + 1 + sum(statStMoE$tik[, k] * (statStMoE$E3ik[, k] - statStMoE$wik[, k])) / sum(statStMoE$tik[, k])) }, c(0, 100))$root), silent = TRUE) } } return(reg_irls) } ) )
hhpdf <- function(file, ...) {invisible(NULL)} hhdev.off <- function(...) {invisible(NULL)} hhcapture <- function(file, text, echo=TRUE, print.eval=TRUE) { source(textConnection(text), echo=TRUE, print.eval=TRUE, keep.source=TRUE, max.deparse.length=500) } hhcode <- function(file, text) { cat(text) } hhpng <- function(file, ...) {invisible(NULL)} hhlatex <- function(file="", ...) { file.tex <- Hmisc::latex(file="", ...) invisible(NULL) }
data(ttrc) rownames(ttrc) <- ttrc$Date ttrc$Date <- NULL input <- list( all=ttrc[1:250,], top=ttrc[1:250,], mid=ttrc[1:250,] ) input$top[1:10,] <- NA input$mid[9:20,] <- NA iAll <- ttrc[1:250,] iTop <- iAll; iTop[1:10,] <- NA iMid <- iAll; iMid[9:20,] <- NA hl <- c('High','Low') hlc <- c('High','Low','Close') cl <- 'Close' load(system.file("unitTests/output.misc.rda", package="TTR")) test.ROC.continuous <- function() { roc <- ROC(iAll[,cl], type='continuous') checkEqualsNumeric( roc, output$allROCc ) checkEquals( attributes(roc), attributes(output$allROCc) ) } test.ROC.discrete <- function() { roc <- ROC(input$all$Close, type='discrete') checkEqualsNumeric( roc, output$allROCd ) checkEquals( attributes(roc), attributes(output$allROCd) ) } test.momentum <- function() { mom <- momentum(input$all$Close) checkEqualsNumeric( mom, output$allMom ) checkEquals( attributes(mom), attributes(output$allMom) ) } test.CLV <- function() { ia <- iAll[,hlc]; rownames(ia) <- NULL it <- iTop[,hlc]; rownames(it) <- NULL oa <- as.data.frame(output$allCLV); rownames(oa) <- rownames(ia) ot <- as.data.frame(output$topCLV); rownames(ot) <- rownames(it) checkEqualsNumeric( CLV(ia), output$allCLV ) checkEquals( attributes(CLV(ia)), attributes(output$allCLV) ) checkEqualsNumeric( CLV(it), output$topCLV ) checkEquals( attributes(CLV(it)), attributes(output$topCLV) ) } test.EMV <- function() { ia <- iAll[,hl]; rownames(ia) <- NULL emv.all <- EMV(ia, input$all$Volume) checkEqualsNumeric( emv.all, output$allEMV ) checkEquals( attributes(emv.all), attributes(output$allEMV) ) } test.KST <- function() { checkEqualsNumeric( KST(input$all$Close), output$allKST ) checkEquals( attributes(KST(input$all$Close)), attributes(output$allKST) ) }
setGeneric(name="cancel",def=function(.Object){standardGeneric("cancel")}) setMethod(f = "cancel",signature(.Object = "geojob"),definition = function(.Object){ setJobState() .Object@id <- "<no active job>" return(.Object) }) setMethod(f = "cancel",signature(.Object = "missing"),definition = function(.Object){ setJobState() })
uM2pool <- function(m2, n_x, n_y) { m2*(n_x + n_y)/(n_x + n_y - 2) } uM3pool <- function(m3, n_x, n_y) { m3*n_x*n_y*(n_x + n_y)/(n_x^2*n_y + n_x*n_y^2 - 6*n_x*n_y + 2*n_x + 2*n_y) } uM2pow2pool <- function(m2, m4, n_x, n_y) { n_x*n_y*(-m2^2*(n_x^2 + 2*n_x*n_y + n_y^2)*(n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 6*n_x^2*n_y - 3*n_x^2 + 6*n_x*n_y^2 - 3*n_y^2) + m4*n_x*n_y*(n_x + n_y)*(n_x^2*n_y + n_x*n_y^2 - 4*n_x*n_y + n_x + n_y))/(3*(n_x^2*n_y + n_x*n_y^2 - 4*n_x*n_y + n_x + n_y)*(4*n_x^2*n_y^2 - 5*n_x^2*n_y + 3*n_x^2 - 5*n_x*n_y^2 + 3*n_y^2) - (n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 6*n_x^2*n_y - 3*n_x^2 + 6*n_x*n_y^2 - 3*n_y^2)*(n_x^3*n_y + 2*n_x^2*n_y^2 - 5*n_x^2*n_y + n_x*n_y^3 - 5*n_x*n_y^2 + 12*n_x*n_y - 3*n_x - 3*n_y)) } uM4pool <- function(m2, m4, n_x, n_y) { n_x*n_y*(3*m2^2*(n_x^2 + 2*n_x*n_y + n_y^2)*(4*n_x^2*n_y^2 - 5*n_x^2*n_y + 3*n_x^2 - 5*n_x*n_y^2 + 3*n_y^2) - m4*n_x*n_y*(n_x + n_y)*(n_x^3*n_y + 2*n_x^2*n_y^2 - 5*n_x^2*n_y + n_x*n_y^3 - 5*n_x*n_y^2 + 12*n_x*n_y - 3*n_x - 3*n_y))/(3*(n_x^2*n_y + n_x*n_y^2 - 4*n_x*n_y + n_x + n_y)*(4*n_x^2*n_y^2 - 5*n_x^2*n_y + 3*n_x^2 - 5*n_x*n_y^2 + 3*n_y^2) - (n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 6*n_x^2*n_y - 3*n_x^2 + 6*n_x*n_y^2 - 3*n_y^2)*(n_x^3*n_y + 2*n_x^2*n_y^2 - 5*n_x^2*n_y + n_x*n_y^3 - 5*n_x*n_y^2 + 12*n_x*n_y - 3*n_x - 3*n_y)) } uM2M3pool <- function(m2, m3, m5, n_x, n_y) { n_x^2*n_y^2*(m2*m3*(n_x^2 + 2*n_x*n_y + n_y^2)*(n_x^4*n_y^3 + n_x^3*n_y^4 - 10*n_x^3*n_y^3 + 10*n_x^3*n_y^2 - 10*n_x^3*n_y + 4*n_x^3 + 10*n_x^2*n_y^3 - 10*n_x*n_y^3 + 4*n_y^3) - m5*n_x*n_y*(n_x + n_y)*(n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 5*n_x^2*n_y - 2*n_x^2 + 5*n_x*n_y^2 - 2*n_y^2))/(10*(n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 5*n_x^2*n_y - 2*n_x^2 + 5*n_x*n_y^2 - 2*n_y^2)*(-2*n_x^3*n_y^3 + 5*n_x^3*n_y^2 - 8*n_x^3*n_y + 4*n_x^3 + 5*n_x^2*n_y^3 - 8*n_x*n_y^3 + 4*n_y^3) + (n_x^4*n_y^3 + n_x^3*n_y^4 - 10*n_x^3*n_y^3 + 10*n_x^3*n_y^2 - 10*n_x^3*n_y + 4*n_x^3 + 10*n_x^2*n_y^3 - 10*n_x*n_y^3 + 4*n_y^3)*(n_x^4*n_y^2 + 2*n_x^3*n_y^3 - 12*n_x^3*n_y^2 + 2*n_x^3*n_y + n_x^2*n_y^4 - 12*n_x^2*n_y^3 + 60*n_x^2*n_y^2 - 42*n_x^2*n_y + 20*n_x^2 + 2*n_x*n_y^3 - 42*n_x*n_y^2 + 20*n_y^2)) } uM5pool <- function(m2, m3, m5, n_x, n_y) { n_x^2*n_y^2*(10*m2*m3*(n_x^2 + 2*n_x*n_y + n_y^2)*(-2*n_x^3*n_y^3 + 5*n_x^3*n_y^2 - 8*n_x^3*n_y + 4*n_x^3 + 5*n_x^2*n_y^3 - 8*n_x*n_y^3 + 4*n_y^3) + m5*n_x*n_y*(n_x + n_y)*(n_x^4*n_y^2 + 2*n_x^3*n_y^3 - 12*n_x^3*n_y^2 + 2*n_x^3*n_y + n_x^2*n_y^4 - 12*n_x^2*n_y^3 + 60*n_x^2*n_y^2 - 42*n_x^2*n_y + 20*n_x^2 + 2*n_x*n_y^3 - 42*n_x*n_y^2 + 20*n_y^2))/(10*(n_x^3*n_y^2 + n_x^2*n_y^3 - 8*n_x^2*n_y^2 + 5*n_x^2*n_y - 2*n_x^2 + 5*n_x*n_y^2 - 2*n_y^2)*(-2*n_x^3*n_y^3 + 5*n_x^3*n_y^2 - 8*n_x^3*n_y + 4*n_x^3 + 5*n_x^2*n_y^3 - 8*n_x*n_y^3 + 4*n_y^3) + (n_x^4*n_y^3 + n_x^3*n_y^4 - 10*n_x^3*n_y^3 + 10*n_x^3*n_y^2 - 10*n_x^3*n_y + 4*n_x^3 + 10*n_x^2*n_y^3 - 10*n_x*n_y^3 + 4*n_y^3)*(n_x^4*n_y^2 + 2*n_x^3*n_y^3 - 12*n_x^3*n_y^2 + 2*n_x^3*n_y + n_x^2*n_y^4 - 12*n_x^2*n_y^3 + 60*n_x^2*n_y^2 - 42*n_x^2*n_y + 20*n_x^2 + 2*n_x*n_y^3 - 42*n_x*n_y^2 + 20*n_y^2)) }
cdm_ll_numerical_differentiation <- function(ll0, ll1, ll2, h) { d1 <- ( ll1 - ll2 ) / ( 2 * h ) d2 <- ( ll1 + ll2 - 2*ll0 ) / h^2 res <- list( d1=d1, d2=d2) return(res) }
.ptime <- proc.time() unname(extSoftVersion()["PCRE"]) unname(pcre_config()["stack"]) if(pcre_config()["stack"]) { op <- options(warn = 1) for (n in c(seq(5000L, 10000L, 1000L), 20000L, 50000L, 100000L)) { print(n) x <- paste0(rep("a", n), collapse="") print(grepl("(a|b)+", x, perl = TRUE)) } options(op) } if(!pcre_config()["JIT"]) { message("The rest of these tests are pointless without JIT support") q("no") } txt2 <- c("The", "licenses", "for", "most", "software", "are", "designed", "to", "take", "away", "your", "freedom", "to", "share", "and", "change", "it.", "", "By", "contrast,", "the", "GNU", "General", "Public", "License", "is", "intended", "to", "guarantee", "your", "freedom", "to", "share", "and", "change", "free", "software", "--", "to", "make", "sure", "the", "software", "is", "free", "for", "all", "its", "users") grep("[gu]", txt2, perl = TRUE) st <- function(expr) sum(system.time(expr)[1:2]) st(for(i in 1:1e4) grep("[gu]", txt2, perl = TRUE)) options(PCRE_use_JIT = TRUE) st(for(i in 1:1e4) grep("[gu]", txt2, perl = TRUE)) txt3 <- rep(txt2, 10) options(PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep("[gu]", txt3, perl = TRUE)) options(PCRE_use_JIT = TRUE) st(for(i in 1:1e3) grep("[gu]", txt3, perl = TRUE)) pat <- "([^[:alpha:]]|a|b)+" long_string <- paste0(rep("a", 1023), collapse="") N <- 10 options(PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep(pat, rep(long_string, N), perl = TRUE)) options(PCRE_use_JIT = TRUE) st(for(i in 1:1e3) grep(pat, rep(long_string, N), perl = TRUE)) txt <- rep("a test of capitalizing", 50) options(PCRE_use_JIT = FALSE) st(for(i in 1:1e4) gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl = TRUE)) options(PCRE_use_JIT = TRUE) st(for(i in 1:1e4) gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl = TRUE)) if(grepl("^10", extSoftVersion()["PCRE"])) { cat("Time elapsed: ", proc.time() - .ptime,"\n") q() } options(PCRE_study = FALSE, PCRE_use_JIT = FALSE) st(for(i in 1:1e4) grep("[gu]", txt2, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = FALSE) st(for(i in 1:1e4) grep("[gu]", txt2, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = TRUE) st(for(i in 1:1e4) grep("[gu]", txt2, perl = TRUE)) txt3 <- rep(txt2, 10) options(PCRE_study = FALSE, PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep("[gu]", txt3, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep("[gu]", txt3, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = TRUE) st(for(i in 1:1e3) grep("[gu]", txt3, perl = TRUE)) pat <- "([^[:alpha:]]|a|b)+" long_string <- paste0(rep("a", 1023), collapse="") N <- 10 options(PCRE_study = FALSE, PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep(pat, rep(long_string, N), perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = FALSE) st(for(i in 1:1e3) grep(pat, rep(long_string, N), perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = TRUE) st(for(i in 1:1e3) grep(pat, rep(long_string, N), perl = TRUE)) txt <- rep("a test of capitalizing", 50) options(PCRE_study = FALSE, PCRE_use_JIT = FALSE) st(for(i in 1:1e4) gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = FALSE) st(for(i in 1:1e4) gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl = TRUE)) options(PCRE_study = TRUE, PCRE_use_JIT = TRUE) st(for(i in 1:1e4) gsub("(\\w)(\\w*)", "\\U\\1\\L\\2", txt, perl = TRUE)) cat("Time elapsed: ", proc.time() - .ptime,"\n")
expected <- eval(parse(text="TRUE")); test(id=0, code={ argv <- eval(parse(text="list(structure(list(srcfile = \"/home/lzhao/tmp/RtmptukZK0/R.INSTALL2ccc3a5cba55/nlme/R/lmList.R\", frow = 612L, lrow = 612L), .Names = c(\"srcfile\", \"frow\", \"lrow\"), row.names = c(NA, -1L)))")); do.call(`is.list`, argv); }, o=expected);
context("sofa_deletedb") sofa_createdb("deldbtesting") test_that("sofa_deletedb returns a character of length 1", { expect_that(length(sofa_deletedb("deldbtesting")), equals(1)) }) sofa_createdb("deldbtesting") test_that("sofa_deletedb returns the right characters", { expect_that(sofa_deletedb("deldbtesting"), matches("")) }) sofa_createdb("deldbtesting") test_that("sofa_deletedb returns the correct class", { expect_that(sofa_deletedb('deldoctesting'), is_a("character")) expect_that(sofa_deletedb('deldoctesting_absent'), is_a("character")) })
mybnn <- function(train,test,ratio){ n = dim(train)[1] weight = rep(0,n) for(i in 1:n){ weight[i] = ratio*(1-ratio)^(i-1)/(1-(1-ratio)^n) } if(is.vector(test) == TRUE){ if(dim(train)[2] - 1 == 1){ test.mat = as.matrix(test) }else{ test.mat = t(as.matrix(test)) } }else{ test.mat = test } if(dim(test.mat)[2] != (dim(train)[2]-1)) stop("training data and test data have different dimensions") label = apply(test.mat,1,function(x) mywnn(train,x,weight)) return(label) }
NULL GeomMarkCircle <- ggproto('GeomMarkCircle', GeomShape, setup_data = function(self, data, params) { if (!is.null(data$filter)) { self$removed <- data[!data$filter, c('x', 'y', 'PANEL')] data <- data[data$filter, ] } data }, draw_panel = function(self, data, panel_params, coord, expand = unit(5, 'mm'), radius = expand, n = 100, label.margin = margin(2, 2, 2, 2, 'mm'), label.width = NULL, label.minwidth = unit(50, 'mm'), label.hjust = 0, label.buffer = unit(10, 'mm'), label.fontsize = 12, label.family = '', label.fontface = c('bold', 'plain'), label.fill = 'white', label.colour = 'black', label.lineheight = 1, con.colour = 'black', con.size = 0.5, con.type = 'elbow', con.linetype = 1, con.border = 'one', con.cap = unit(3, 'mm'), con.arrow = NULL) { if (nrow(data) == 0) return(zeroGrob()) coords <- coord$transform(data, panel_params) if (!is.integer(coords$group)) { coords$group <- match(coords$group, unique(coords$group)) } coords <- coords[order(coords$group), ] first_idx <- !duplicated(coords$group) first_rows <- coords[first_idx, ] label <- NULL ghosts <- NULL if (!is.null(coords$label) || !is.null(coords$description)) { label <- first_rows is_ghost <- which(self$removed$PANEL == coords$PANEL[1]) if (length(is_ghost) > 0) { ghosts <- self$removed[is_ghost, ] ghosts <- coord$transform(ghosts, panel_params) ghosts <- list(x = ghosts$x, y = ghosts$y) } } circEncGrob(coords$x, coords$y, default.units = 'native', id = coords$group, expand = expand, radius = radius, n = n, label = label, ghosts = ghosts, mark.gp = gpar( col = first_rows$colour, fill = alpha(first_rows$fill, first_rows$alpha), lwd = first_rows$size * .pt, lty = first_rows$linetype ), label.gp = gpar( col = label.colour, fill = label.fill, fontface = label.fontface, fontfamily = label.family, fontsize = label.fontsize, lineheight = label.lineheight ), con.gp = gpar( col = con.colour, fill = con.colour, lwd = con.size * .pt, lty = con.linetype ), label.margin = label.margin, label.width = label.width, label.minwidth = label.minwidth, label.hjust = label.hjust, label.buffer = label.buffer, con.type = con.type, con.border = con.border, con.cap = con.cap, con.arrow = con.arrow ) }, default_aes = aes(fill = NA, colour = 'black', alpha = 0.3, size = 0.5, linetype = 1, filter = NULL, label = NULL, description = NULL) ) geom_mark_circle <- function(mapping = NULL, data = NULL, stat = 'identity', position = 'identity', expand = unit(5, 'mm'), radius = expand, n = 100, label.margin = margin(2, 2, 2, 2, 'mm'), label.width = NULL, label.minwidth = unit(50, 'mm'), label.hjust = 0, label.fontsize = 12, label.family = '', label.lineheight = 1, label.fontface = c('bold', 'plain'), label.fill = 'white', label.colour = 'black', label.buffer = unit(10, 'mm'), con.colour = 'black', con.size = 0.5, con.type = 'elbow', con.linetype = 1, con.border = 'one', con.cap = unit(3, 'mm'), con.arrow = NULL, ..., na.rm = FALSE, show.legend = NA, inherit.aes = TRUE) { layer( data = data, mapping = mapping, stat = stat, geom = GeomMarkCircle, position = position, show.legend = show.legend, inherit.aes = inherit.aes, params = list( na.rm = na.rm, expand = expand, radius = radius, n = n, label.margin = label.margin, label.width = label.width, label.minwidth = label.minwidth, label.fontsize = label.fontsize, label.family = label.family, label.lineheight = label.lineheight, label.fontface = label.fontface, label.hjust = label.hjust, label.fill = label.fill, label.colour = label.colour, label.buffer = label.buffer, con.colour = con.colour, con.size = con.size, con.type = con.type, con.linetype = con.linetype, con.border = con.border, con.cap = con.cap, con.arrow = con.arrow, ... ) ) } circEncGrob <- function(x = c(0, 0.5, 1, 0.5), y = c(0.5, 1, 0.5, 0), id = NULL, id.lengths = NULL, expand = 0, radius = 0, n = 100, label = NULL, ghosts = NULL, default.units = 'npc', name = NULL, mark.gp = gpar(), label.gp = gpar(), con.gp = gpar(), label.margin = margin(), label.width = NULL, label.minwidth = unit(50, 'mm'), label.hjust = 0, label.buffer = unit(10, 'mm'), con.type = 'elbow', con.border = 'one', con.cap = unit(3, 'mm'), con.arrow = NULL, vp = NULL) { if (is.null(id)) { if (is.null(id.lengths)) { id <- rep(1, length(x)) } else { id <- rep(seq_along(id.lengths), id.lengths) if (length(id) != length(x)) { stop('id.lengths must sum up to the number of points', call. = FALSE) } } } include <- unlist(lapply(split(seq_along(x), id), function(i) { xi <- x[i] yi <- y[i] if (length(unique(xi)) == 1) { return(i[c(which.min(yi), which.max(yi))]) } if (length(unique(yi)) == 1) { return(i[c(which.min(xi), which.max(xi))]) } i[chull(xi, yi)] })) mark <- shapeGrob( x = x[include], y = y[include], id = id[include], id.lengths = NULL, expand = expand, radius = radius, default.units = default.units, name = name, gp = mark.gp, vp = vp ) if (!is.null(label)) { label <- lapply(seq_len(nrow(label)), function(i) { grob <- labelboxGrob(label$label[i], 0, 0, label$description[i], gp = label.gp, pad = label.margin, width = label.width, min.width = label.minwidth, hjust = label.hjust ) if (con.border == 'all') { grob$children[[1]]$gp$col <- con.gp$col grob$children[[1]]$gp$lwd <- con.gp$lwd grob$children[[1]]$gp$lty <- con.gp$lty } grob }) labeldim <- lapply(label, function(l) { c( convertWidth(grobWidth(l), 'mm', TRUE), convertHeight(grobHeight(l), 'mm', TRUE) ) }) ghosts <- lapply(ghosts, unit, default.units) } else { labeldim <- NULL } gTree( mark = mark, n = n, label = label, labeldim = labeldim, buffer = label.buffer, ghosts = ghosts, con.gp = con.gp, con.type = con.type, con.cap = as_mm(con.cap, default.units), con.border = con.border, con.arrow = con.arrow, name = name, vp = vp, cl = 'circ_enc' ) } makeContent.circ_enc <- function(x) { mark <- x$mark x_new <- convertX(mark$x, 'mm', TRUE) y_new <- convertY(mark$y, 'mm', TRUE) circles <- enclose_points(round(x_new, 2), round(y_new, 2), mark$id) circles$id <- seq_len(nrow(circles)) circles <- circles[rep(circles$id, each = x$n), ] points <- 2 * pi * (seq_len(x$n) - 1) / x$n circles$x <- circles$x0 + cos(points) * circles$r circles$y <- circles$y0 + sin(points) * circles$r circles <- unique(circles) mark$x <- unit(circles$x, 'mm') mark$y <- unit(circles$y, 'mm') mark$id <- circles$id if (inherits(mark, 'shape')) mark <- makeContent(mark) if (!is.null(x$label)) { polygons <- Map(function(x, y) list(x = x, y = y), x = split(as.numeric(mark$x), mark$id), y = split(as.numeric(mark$y), mark$id) ) labels <- make_label( labels = x$label, dims = x$labeldim, polygons = polygons, ghosts = x$ghosts, buffer = x$buffer, con_type = x$con.type, con_border = x$con.border, con_cap = x$con.cap, con_gp = x$con.gp, anchor_mod = 2, arrow = x$con.arrow ) setChildren(x, do.call(gList, c(list(mark), labels))) } else { setChildren(x, gList(mark)) } }
get_conservation_scores <- function(variantsTable, conservationBwPath) { Chr <- Pos <- Ref <- NULL coords <- variantsTable %>% transmute(chrom = Chr, start = Pos, end = as.numeric(start+nchar(Ref))-1) if (all(str_starts(coords[[1]], "chr")) == FALSE) { coords[!str_starts(coords[[1]], "chr"),1] <- str_c("chr", coords[[1]][!str_starts(coords[[1]], "chr")]) } scores_out <- c() for (i in 1:nrow(coords)) { scores_df <- data.frame(pos = seq(coords[[i,2]], coords[[i,3]])) scores_vec <- rtracklayer::import.bw(con = conservationBwPath, which = GRanges(paste0(coords[[i, 1]], ":", coords[[i,2]], "-", coords[[i,3]]))) if (length(scores_vec) == 0) { scores_out <- append(scores_out, paste(rep("NA", nrow(scores_df)), collapse = ";")) next } final_score <- data.frame(pos = start(scores_vec), conservation = round(scores_vec$score, 3)) scores_df <- left_join(scores_df, final_score, by=c("pos"="pos")) scores_out <- append(scores_out, paste(scores_df$conservation, collapse = ";")) } return (scores_out) }
updateSd <- function(X.new, integration.points.oldsd, model, precalc.data, integration.points ){ d <- model@d n <- model@n X.new <- t(X.new) krig <- predict_nobias_km(object=model, newdata=as.data.frame(X.new), type="UK", se.compute=TRUE, cov.compute=TRUE) mk <- krig$mean sk <- krig$sd F.newdata <- krig$F.newdata c.newdata <- krig$c Sigma.r <- krig$cov kn = computeQuickKrigcov(model, integration.points, X.new, precalc.data, F.newdata, c.newdata) chol.Sigma.r <- NULL chol.Sigma.r <- try(chol(Sigma.r),TRUE) if(!is.numeric(chol.Sigma.r)) return(list(error=TRUE)) lambda_nplus.r <- kn %*% chol2inv(chol.Sigma.r) predict_var <- pmax(0,integration.points.oldsd^2 - rowSums(lambda_nplus.r * kn)) predict_sd <- sqrt(predict_var) return(predict_sd) }
"petri_dishes"
pava.sa <- function(y,w=NULL,decreasing=FALSE,long.out=FALSE,stepfun=FALSE) { if(decreasing) y <- rev(y) n <- length(y) if(is.null(w)) w <- rep(1,n) else if(decreasing) w <- rev(w) r <- rep(1,n) repeat { stble <- TRUE i <- 1 while(i < n) { if(y[i] > y[i+1]) { stble <- FALSE www <- w[i] + w[i+1] ttt <- (w[i]*y[i] + w[i+1]*y[i+1])/www y[i+1] <- ttt w[i+1] <- www y <- y[-i] w <- w[-i] r[i+1] <- r[i] + r[i+1] r <- r[-i] n <- n-1 } i <- i+1 } if(stble) break } y <- rep(y,r) if(decreasing) y <- rev(y) if(long.out | stepfun) { if(decreasing) r <- rev(r) tr <- rep(tapply(1:length(y),rep(1:length(r),r),min),r) } if(long.out) { if(decreasing) w <- rev(w) w <- rep(w,r) lout <- list(y=y,w=w,tr=tr) } if(stepfun) { knots <- 1+which(diff(tr)!=0) y0 <- c(y[1],y[knots]) h <- stepfun(knots,y0) } ntype <- 1+sum(c(long.out,stepfun)*(1:2)) switch(ntype,y,lout,h,c(lout,list(h=h))) }
expected <- eval(parse(text="structure(c(1.00192158474469, 0.500611696028749, 0.332967709798622, 0.249529151583945, 0.199859932368632, 0.166171774633113, 0.143725080104588, 0.126847385576286, 0.111726067153096, 0.500611696028749, 0.33253138023914, 0.249894545257491, 0.200854308505617, 0.166937485699285, 0.142293779520833, 0.124647353499376, 0.110137293143018, 0.0998824472204338, 0.332967709798622, 0.249894545257491, 0.199825768542762, 0.166651515553326, 0.142257314562146, 0.12462530226749, 0.11031627347356, 0.0988990038212295, 0.0904793912005313, 0.249529151583945, 0.200854308505617, 0.166651515553326, 0.143436707679878, 0.124928204062841, 0.111342021505031, 0.100047337927152, 0.090875357601969, 0.0835813207368242, 0.199859932368632, 0.166937485699285, 0.142257314562146, 0.124928204062841, 0.110898989913376, 0.0998749310316349, 0.0908543225642293, 0.0833287409605183, 0.0765033842774308, 0.166171774633113, 0.142293779520833, 0.12462530226749, 0.111342021505031, 0.0998749310316349, 0.0915211007463971, 0.0833424511320793, 0.0769931402253433, 0.0707755214962486, 0.143725080104588, 0.124647353499376, 0.11031627347356, 0.100047337927152, 0.0908543225642293, 0.0833424511320793, 0.0770880372305834, 0.0718651376951712, 0.0666164897993546, 0.126847385576286, 0.110137293143018, 0.0988990038212295, 0.090875357601969, 0.0833287409605183, 0.0769931402253433, 0.0718651376951713, 0.0676106605311985, 0.063324574978029, 0.111726067153096, 0.0998824472204338, 0.0904793912005313, 0.0835813207368242, 0.0765033842774308, 0.0707755214962486, 0.0666164897993546, 0.063324574978029, 0.0613649549614623), .Dim = c(9L, 9L))")); test(id=0, code={ argv <- eval(parse(text="list(structure(c(-1.22589324018138, -0.740548974281808, -0.54768368397833, -0.441021701509591, -0.370068251595057, -0.319690799411412, -0.282987166340516, -0.254112864677485, -0.230083320312515, 0.203647970189376, -0.0305516337408725, -0.0825170335109532, -0.0984577177107505, -0.100129992839015, -0.0988979642888749, -0.0945771185256416, -0.0902309571831907, -0.0871241228998968, -0.00955870050771132, 0.0197754782700907, 0.0125304440435148, 0.00419858922572787, -0.00191073996840182, -0.0061756059258365, -0.00956682744689523, -0.0127366531032827, -0.0131079781713544, 0.000214464770644159, -0.000956552371122151, 5.72249143534175e-05, 0.00029865136977495, 0.00077852017665313, 0.00142425180877207, 0.000491677810053133, -0.000120006753650731, -0.00247588122373662, 4.2574997724815e-05, -0.000297064220851874, 0.000399761711902461, 5.67830351414009e-05, -0.00026523273781528, 0.000320119491527155, -0.00026454073650643, -0.000195756422133707, 0.000192249930248858, -4.94461924222768e-07, 2.80125995838013e-05, -0.000119138513940463, 0.000151917649712048, -7.31975645151543e-05, 4.92140187851149e-05, -1.13604576670922e-05, -3.74519303853871e-05, 9.55915555684852e-06), .Dim = c(9L, 6L)), structure(c(-0.709851441473678, -0.428813651666777, -0.317135326144804, -0.255372882626744, -0.214287405483635, -0.185116425598763, -0.163863247924954, -0.147143631578904, -0.133229363887123, 0.633337192677659, -0.0950143815681878, -0.256624734846691, -0.306199636924392, -0.311400346924765, -0.307568786499592, -0.294131125799441, -0.280614734641737, -0.270952601985731, -0.28505721606605, 0.58973945020027, 0.373679821042009, 0.125209295460755, -0.0569816174886273, -0.184167401344961, -0.285299575647986, -0.379829336915808, -0.390902901787376, 0.0675695685124445, -0.301372718615498, 0.0180293609967187, 0.0940935153626058, 0.245281648154537, 0.448726753036158, 0.154908693733931, -0.0378094944843564, -0.780054577138554, 0.056333641054865, -0.393064241503382, 0.528949712019966, 0.0751331835725979, -0.350946016360591, 0.423570111428232, -0.350030386168567, -0.259017559788085, 0.254377901167792, -0.00226968135332679, 0.128583560874789, -0.546870143699694, 0.697333080468545, -0.335991790571385, 0.225902410856869, -0.0521468239901137, -0.171912019667483, 0.0438784789244046), .Dim = c(9L, 6L)))")); .Internal(tcrossprod(argv[[1]], argv[[2]])); }, o=expected);
library(mfdb) library(unittest, quietly = TRUE) helpers <- c('utils/helpers.R', 'tests/utils/helpers.R') ; source(helpers[file.exists(helpers)]) mdb <- fake_mdb() even <- function (x) x %% 2 == 0 cap <- function(code) { grep("\\d{4}-\\d{2}-\\d{2}", capture.output({ x <- code cat("Return Value:\n") str(x) }), value = TRUE, invert = TRUE) } ok_group("sanitise_col", local({ ok(cmp(sanitise_col(mdb, data.frame(aaaa=1,b=2,aa=3), 'aaaa'), 1), "Picked correct column (aaaa)") ok(cmp(sanitise_col(mdb, data.frame(aaaa=1,b=2,aa=3), 'aa'), 3), "Picked correct column (aa)") ok(cmp(sanitise_col(mdb, data.frame(aaaa=9,b=8,aa=7), 'AaAa'), 9), "Case is insensitive (AaAa)") ok(cmp(sanitise_col(mdb, data.frame(aaaa=9,b=8,aa=7), 'Aa'), 7), "Case is insensitive (Aa)") ok(cmp_error(sanitise_col(mdb, data.frame(a=9,b=8,c=7), 'bueller'), 'bueller'), "Complained about missing column when no default supplied") ok(cmp(sanitise_col(mdb, data.frame(a=9,b=8,c=7), 'x', default = 99), 99), "No column x, used default") ok(cmp(sanitise_col(mdb, data.frame(a=9,b=8,x=7), 'x', default = 99), 7), "Column overrode default") ok(cmp( sanitise_col(mdb, data.frame(gerald = c(2,4,6,8), freda = c(1,2,3,5)), 'gerald', test = even), c(2,4,6,8)), "All of gerald passes test") ok(cmp_error( sanitise_col(mdb, data.frame(gerald = c(2,4,6,8), freda = c(1,2,3,5)), 'freda', test = even), "freda"), "Freda does not") ok(cmp_error( sanitise_col(mdb, data.frame(gerald = c(2,4,6,8), freda = c(1,2,3,5)), 'freda', test = even), "1,3,5$"), "Which items that don't match are mentioned") ok(cmp_error( sanitise_col(mdb, data.frame(freda = c(1:150)), 'freda', test = even), paste(c(seq(1, 50 * 2 - 1, 2), " \\.\\.\\.$"), collapse=",")), "Give up complaining after 50 items") }, asNamespace('mfdb')))
"addDscal" <- function (modellist, dscal) { if(length(dscal) != 0) { for(i in 1:length(dscal)){ if(length(dscal[[i]]$perclp) == 0) dscal[[i]]$perclp <- FALSE modellist[[dscal[[i]]$to]]@dscalspec <- dscal[[i]] modellist[[dscal[[i]]$to]]@drel <- dscal[[i]]$value } } modellist }
SquareSpike <- function(baseline, peak, period, duty_cycle, trend, duration, resolution) { if(peak < baseline) { stop("peak must be larger than baseline!") } if(duration <= resolution ) { stop("duration must be longer than resolution!") } if((abs(duration/resolution - round(duration/resolution))) > 1e-10) { stop("duration must be a multiple of resolution!") } if((abs(period/resolution - round(period/resolution))) > 1e-10) { stop("period must be a multiple of resolution!") } if(duration <= 0 || resolution <= 0 || peak <= 0 || period <= 0) { ID=matrix(ncol=1,nrow=6) rownames(ID)=c("duration","resolution","peak","period") ID[,1]=c(duration,resolution,peak,period) Ind=which(ID[,1]<=0) stop(paste0(rownames(ID)[Ind]," must be larger than 0! ")) } if(baseline < 0) { stop("baseline must be larger than or equal to 0!") } if(duty_cycle <= 0 || duty_cycle > 1) { stop("duty cycle must be larger than 0 and smaller or equal to 1!") } if(trend <=0) { stop("trend must be larger than 0!") } Osc=matrix(ncol=2,nrow=length(seq(0,duration,resolution))) colnames(Osc)=c("time","osc") Osc[,1]=seq(0,duration,resolution) active=period*duty_cycle Osc[,2]=baseline for (i in 1:(nrow(Osc)*resolution/period)) { Osc[round((((i-1)*(period/resolution))+2):(((i-1)*(period/resolution))+active/resolution)),2]=peak peak=peak*trend if(peak <= baseline) { peak=baseline } } if ((nrow(Osc)-(((i)*(period/resolution)))) <= (active/resolution)) { Osc[round((((i)*(period/resolution))+1):nrow(Osc)),2]=peak } else { Osc[round((((i)*(period/resolution))+1):(((i)*(period/resolution))+active/resolution)),2]=peak } Osc[round((((i)*(period/resolution))+1)),2] = baseline return(Osc) }
packagename = "DSAIDE" helperdir = "auxiliary/helperfunctions" figuredir = "media" appdocdir = "appinformation" filenames = c("get_settings.R","write_tasktext.R") files_to_source = paste(here::here(),helperdir,filenames,sep="/") sapply(files_to_source, source)
span( h4("Step 2: Adding the random interaction term"), conditionalPanel( condition = "0", uiOutput("Mod8Step2_hidden") ), p(paste0("Step 1 above layered on the random slopes for each $",NOT$env,"$ variable, and these served to tip the population mean plane in various directions in environmental space, much like a circus performer spinning plates at various heights and with variable skill. However, the population mean plane could be warped due to an interaction between the two $",NOT$env,"$ variables. Because it appears that such warping is adaptive in real organisms, this would imply that individual variation in the extent of warping is possible. Here we add that last random effect term to the phenotypic equation.")), p(paste0("This now expands the phenotypic equation to include three slope terms, $",EQ1$dev1,"$, $",EQ1$dev2,"$, and $",EQ1$dev12,"$, which are the individual deviation from the population slope with respect to $",NOT$env,"_{1}$, $",NOT$env,"_{2}$, and the interaction between the two $",NOT$env,"$ variables, respectively. The full equation is thus:")), p(paste0("$$", NOT$trait.1,"_{",NOT$time,NOT$ind,"} = ",EQ1$mean0," + ",EQ1$dev0," + (",EQ1$mean1,"+",EQ1$dev1,")",NOT$env,"_{1",NOT$time,NOT$ind,"} + (",EQ1$mean2,"+",EQ1$dev2,")",NOT$env,"_{2",NOT$time,NOT$ind,"} + (",EQ1$mean12,"+",EQ1$dev12,")",NOT$env,"_{1",NOT$time,NOT$ind,"}",NOT$env,"_{2",NOT$time,NOT$ind,"} + ",NOT$error,"_{",NOT$time,NOT$ind,"}$$")), p("As above, the addition of another random effect expands the variance-covariance once again. It now is an ugly beast, but if you move through it systematically, you will see it is just a ledger sheet that accounts for every possibility:"), p(paste0("$$", "\\begin{pmatrix} ",EQ1$dev0," \\\\ ",EQ1$dev1," \\\\ ",EQ1$dev2," \\\\ ",EQ1$dev12," \\end{pmatrix}", "\\sim MVN(0, \\Omega_{",NOT$devI,NOT$devS,"}): \\Omega_{",NOT$devI,NOT$devS,"}= ", "\\begin{pmatrix} Var(",NOT$devI,") & Cov_{",NOT$devI,EQ3$dev1,"} & Cov_{",NOT$devI,EQ3$dev2,"} & Cov_{",NOT$devI,EQ3$dev12,"} \\\\ Cov_{",NOT$devI,EQ3$dev1,"} & Var(",EQ3$dev1,") & Cov_{",EQ3$dev1,EQ3$dev2,"} & Cov_{",EQ3$dev1,EQ3$dev12,"} \\\\ Cov_{",NOT$devI,EQ3$dev2,"} & Cov_{",EQ3$dev1,EQ3$dev2,"} & Var(",EQ3$dev2,") & Cov_{",EQ3$dev2,EQ3$dev12,"} \\\\ Cov_{",NOT$devI,EQ3$dev12,"} & Cov_{",EQ3$dev1,EQ3$dev12,"} & Cov_{",EQ3$dev2,EQ3$dev12,"} & Var(",EQ3$dev12,") \\end{pmatrix}", "$$")), p("We will simulate data with these terms, and assess two consequences of random slopes in two dimensions. First, we will ask where variation due to the interaction term ends up in a model that lacks that term. Second, we will try to visualize where variation caused by variation in warping is more likely to be seen."), p(paste0("As the phenotypic equation is getting more complex, we will increase the number of sampled individuals to 500. As before, each individual is measured 20 times for both $",NOT$env,"$ variables and both environments are random and unshared.")), p("Below, specify some parameter values:"), getSliderInput("Mod8Step2_Vi", Modules_VAR$Vi), getSliderInput("Mod8Step2_Ve", Modules_VAR$Vm), getSliderInput("Mod8Step2_B1", Modules_VAR$B1.1), getSliderInput("Mod8Step2_B2", Modules_VAR$B2.1), getSliderInput("Mod8Step2_B12", Modules_VAR$B1122), getSliderInput("Mod8Step2_Vs1", Modules_VAR$Vsx.1), getSliderInput("Mod8Step2_Vs2", Modules_VAR$Vsx.2), getSliderInput("Mod8Step2_Vs12", Modules_VAR$Vsx.12), getSliderInput("Mod8Step2_CorIS1", Modules_VAR$CorIS1), getSliderInput("Mod8Step2_CorIS2", Modules_VAR$CorIS2), getSliderInput("Mod8Step2_CorIS12", Modules_VAR$CorIS12), getSliderInput("Mod8Step2_CorS1S2", Modules_VAR$CorS1S2), getSliderInput("Mod8Step2_CorS1S12", Modules_VAR$CorS1S12), getSliderInput("Mod8Step2_CorS2S12", Modules_VAR$CorS2S12), p("As before, it might be easiest to start with 0 covariances (represented as correlations) and add them in individually so you can more easily see what each does."), p("Once the data are simulated, we can analyze them with lme4 as was done in the random regression module. For example, we can use the following equation in which the individual specific interaction term is omitted:"), p(paste0("$$", NOT$trait.1,"_{",NOT$time,NOT$ind,"} = ",EQ1$mean0," + ",EQ1$dev0," + (",EQ1$mean1,"+",EQ1$dev1,")",NOT$env,"_{1",NOT$time,NOT$ind,"} + (",EQ1$mean2,"+",EQ1$dev2,")",NOT$env,"_{2",NOT$time,NOT$ind,"} + (",EQ1$mean12,")",NOT$env,"_{1",NOT$time,NOT$ind,"}",NOT$env,"_{2",NOT$time,NOT$ind,"} + ",NOT$error,"_{",NOT$time,NOT$ind,"}$$")), displayRCode(" LMM1 <- lme4::lmer(Phenotype ~ 1 + X1*X2 (1 + X1 + X2|Individual) + (0 + X2|Individual), data = sampled_data)"), p("And we will compare those results with the full model:"), p(paste0("$$", NOT$trait.1,"_{",NOT$time,NOT$ind,"} = ",EQ1$mean0," + ",EQ1$dev0," + (",EQ1$mean1,"+",EQ1$dev1,")",NOT$env,"_{1",NOT$time,NOT$ind,"} + (",EQ1$mean2,"+",EQ1$dev2,")",NOT$env,"_{2",NOT$time,NOT$ind,"} + (",EQ1$mean12,"+",EQ1$dev12,")",NOT$env,"_{1",NOT$time,NOT$ind,"}",NOT$env,"_{2",NOT$time,NOT$ind,"} + ",NOT$error,"_{",NOT$time,NOT$ind,"}$$")), displayRCode("LMM2 <- lme4::lmer(Phenotype ~ 1 + X1*X2 (1+X1*X2|Individual), data = sampled_data)"), actionButton("Mod8Step2_Run", label = Modules_VAR$Run$label, icon = Modules_VAR$Run$icon, class = "runButton"), runningIndicator(), sim_msg(), p("Statistical output:"), uiOutput("Mod8Step2_summary_table"), p("As usual, omission of a key parameter causes variation to be placed elsewhere in the equation, in this case mostly in the residual."), p(paste0("A 3-d plot of the population mean (below) provides you with a visual orientation to the average phenotype across the environmental space created by the two $",NOT$env,"$ variables. We have also plotted the values different individuals will express at the corners of the graph where they would experience an extreme in both $",NOT$env,"$ distributions.")), p(plotlyOutput("Mod8Step2_3D")), p("Run this simulation several times with different values for the interaction term and the covariance terms. Where does the interaction term create the most phenotypic variance and how do covariances affect this?"), p(HTML("<b>Conclusion:</b> The effect of interactions between environments on phenotypes has three important characteristics. First, it seems biologically likely given the complexity of the environment and it in fact exists in many traits. Second, these effects can be modelled using mixed models, including the random effects of individual on the response to each environment and in theory on the interaction term itself. The third characteristic is that these models are exceedingly complex. At this point, you don't have in your mental pocket the full phenotypic equation. There are many more complexities to explore, but you now have all the basic tools. The SQuID platform can now be explored so you can assess what sampling regimes and experimental designs will allow you to effectively measure the attributes of most interest.")), div(class = "line"), actionLink("Mod8Step2GotoStep1", label = "<< Previous Step (1)", class= "linkToModuleSteps"), )
library(CHAID) library(rsample) library(plyr) library(dplyr) attrition %>% select_if(is.factor) %>% ncol attrition %>% select_if(is.numeric) %>% ncol attrition %>% select_if(function(col) length(unique(col)) <= 5 & is.integer(col)) %>% head attrition %>% select_if(function(col) length(unique(col)) <= 10 & is.integer(col)) %>% head income = floor(runif(1000, 50, 100)) gender = sample(c('M','F'), size=1000, replace=T, prob=c(.6,.4)) married = sample(c('Married','Single', 'Divorce'), size=1000, replace=T, prob=c(.3,.4,.3)) buy = sample(c('Buy','DontBuy'), size=1000, replace=T, prob=c(.6,.4)) df = data.frame(income, gender, married, buy) head(df) str(df) fcols = c('income','gender', 'married', 'buy') df[fcols] = lapply(df[fcols], factor) lapply(df,class) table(df$gender, df$buy) chaidmodel_1 = chaid(buy ~ gender + married + income, data=df) print(chaidmodel_1) plot(chaidmodel_1) ctrl_1 = chaid_control(minsplit = 10, minprob = 0.01) chaidmodel_2 = chaid(buy ~ incomee + gender + married, data=df, control = ctrl_1) plot(chaidmodel_2) print(chaidmodel_2) chaidmodel = chaid(buy ~ ., data=df) ?chaid require(rsample) data(attrition) str(attrition) names(attrition)
ancestral.pml <- function(object, type = "marginal", return = "prob") { call <- match.call() pt <- match.arg(type, c("marginal", "joint", "ml", "bayes")) tree <- object$tree INV <- object$INV inv <- object$inv data <- getCols(object$data, tree$tip.label) data_type <- attr(data, "type") if (is.null(attr(tree, "order")) || attr(tree, "order") != "postorder") { tree <- reorder(tree, "postorder") } nTips <- length(tree$tip.label) node <- tree$edge[, 1] edge <- tree$edge[, 2] m <- length(edge) + 1 w <- object$w g <- object$g l <- length(w) nr <- attr(data, "nr") nc <- attr(data, "nc") dat <- vector(mode = "list", length = m * l) result <- vector(mode = "list", length = m) dim(dat) <- c(l, m) x <- attributes(data) label <- as.character(1:m) nam <- tree$tip.label label[seq_along(nam)] <- nam x[["names"]] <- label tmp <- length(data) if (return != "phyDat") { result <- new2old.phyDat(data) } else { result[1:nTips] <- data } eig <- object$eig bf <- object$bf el <- tree$edge.length P <- getP(el, eig, g) nr <- as.integer(attr(data, "nr")) nc <- as.integer(attr(data, "nc")) node <- as.integer(node - min(node)) edge <- as.integer(edge - 1) nTips <- as.integer(length(tree$tip.label)) mNodes <- as.integer(max(node) + 1) contrast <- attr(data, "contrast") eps <- 1.0e-5 ind1 <- which(apply(contrast, 1, function(x) sum(x > eps)) == 1L) ind2 <- which(contrast[ind1, ] > eps, arr.ind = TRUE) pos <- ind2[match(seq_len(ncol(contrast)), ind2[, 2]), 1] nco <- as.integer(dim(contrast)[1]) for (i in 1:l) dat[i, (nTips + 1):m] <- .Call('LogLik2', data, P[i, ], nr, nc, node, edge, nTips, mNodes, contrast, nco) parent <- tree$edge[, 1] child <- tree$edge[, 2] nTips <- min(parent) - 1 for (i in 1:l) { for (j in (m - 1):1) { if (child[j] > nTips) { tmp2 <- (dat[[i, parent[j]]] / (dat[[i, child[j]]] %*% P[[i, j]])) dat[[i, child[j]]] <- (tmp2 %*% P[[i, j]]) * dat[[i, child[j]]] } } } for (j in unique(parent)) { tmp <- matrix(0, nr, nc) if (inv > 0) tmp <- as.matrix(INV) * inv for (i in 1:l) { tmp <- tmp + w[i] * dat[[i, j]] } if ((pt == "bayes") || (pt == "marginal")) tmp <- tmp * rep(bf, each = nr) tmp <- tmp / rowSums(tmp) if (return == "phyDat") { if (data_type == "DNA") { tmp <- p2dna(tmp) tmp <- fitchCoding2ambiguous(tmp) } else { tmp <- pos[max.col(tmp)] } } result[[j]] <- tmp } attributes(result) <- x attr(result, "call") <- call result } ancestral2phyDat <- function(x) { eps <- 1.0e-5 contr <- attr(x, "contrast") ind1 <- which(apply(contr, 1, function(x) sum(x > eps)) == 1L) ind2 <- which(contr[ind1, ] > eps, arr.ind = TRUE) pos <- ind2[match(seq_len(ncol(contr)), ind2[, 2]), 1] res <- lapply(x, function(x, pos) pos[max.col(x)], pos) attributes(res) <- attributes(x) return(res) } fitchCoding2ambiguous <- function(x, type = "DNA") { y <- c( 1L, 2L, 4L, 8L, 8L, 3L, 5L, 9L, 6L, 10L, 12L, 7L, 11L, 13L, 14L, 15L, 15L, 15L ) fmatch(x, y) } fitchCoding2ambiguous2 <- function(x, type = "DNA") { y <- c(1L, 2L, 4L, 8L, 8L, 3L, 5L, 9L, 6L, 10L, 12L, 7L, 11L, 13L, 14L, 15L) dna <- c( "a", "c", "g", "t", "t", "m", "r", "w", "s", "y", "k", "v", "h", "d", "b", "n" ) rna <- c( "a", "c", "g", "u", "u", "m", "r", "w", "s", "y", "k", "v", "h", "d", "b", "n" ) res <- switch(type, "DNA" = dna[fmatch(x, y)], "RNA" = rna[fmatch(x, y)] ) res } ancestral.pars <- function(tree, data, type = c("MPR", "ACCTRAN"), cost = NULL, return = "prob") { call <- match.call() type <- match.arg(type) if (type == "ACCTRAN") { res <- ptree(tree, data, return = return) attr(res, "call") <- call } if (type == "MPR") { res <- mpr(tree, data, cost = cost, return = return) attr(res, "call") <- call } res } pace <- ancestral.pars mpr.help <- function(tree, data, cost = NULL) { tree <- reorder(tree, "postorder") if (!inherits(data, "phyDat")) { stop("data must be of class phyDat") } levels <- attr(data, "levels") l <- length(levels) if (is.null(cost)) { cost <- matrix(1, l, l) cost <- cost - diag(l) } weight <- attr(data, "weight") p <- attr(data, "nr") kl <- TRUE i <- 1 dat <- prepareDataSankoff(data) for (i in seq_along(dat)) storage.mode(dat[[i]]) <- "double" tmp <- fit.sankoff(tree, dat, cost, returnData = "data") p0 <- tmp[[1]] datf <- tmp[[2]] datp <- pnodes(tree, datf, cost) nr <- attr(data, "nr") nc <- attr(data, "nc") node <- tree$edge[, 1] edge <- tree$edge[, 2] node <- as.integer(node - 1L) edge <- as.integer(edge - 1L) res <- .Call('sankoffMPR', datf, datp, as.numeric(cost), as.integer(nr), as.integer(nc), node, edge) root <- getRoot(tree) res[[root]] <- datf[[root]] res } mpr <- function(tree, data, cost = NULL, return = "prob") { data <- subset(data, tree$tip.label) att <- attributes(data) type <- att$type nr <- att$nr nc <- att$nc res <- mpr.help(tree, data, cost) l <- length(tree$tip.label) m <- length(res) label <- as.character(1:m) nam <- tree$tip.label label[seq_along(nam)] <- nam att[["names"]] <- label ntips <- length(tree$tip.label) contrast <- att$contrast eps <- 5e-6 rm <- apply(res[[ntips + 1]], 1, min) RM <- matrix(rm, nr, nc) + eps fun <- function(X) { rs <- rowSums(X) X / rs } for (i in 1:ntips) res[[i]] <- contrast[data[[i]], , drop = FALSE] for (i in (ntips + 1):m) res[[i]][] <- as.numeric(res[[i]] < RM) if (return == "prob") { if (return == "prob") res <- lapply(res, fun) } attributes(res) <- att fun2 <- function(x) { x <- p2dna(x) fitchCoding2ambiguous(x) } if (return != "prob") { if (type == "DNA") { res <- lapply(res, fun2) attributes(res) <- att } else { res <- ancestral2phyDat(res) } res[1:ntips] <- data } res } plotAnc <- function(tree, data, i = 1, site.pattern = TRUE, col = NULL, cex.pie = par("cex"), pos = "bottomright", ...) { y <- subset(data, select = i, site.pattern = site.pattern) CEX <- cex.pie xrad <- CEX * diff(par("usr")[1:2]) / 50 levels <- attr(data, "levels") nc <- attr(data, "nc") y <- matrix(unlist(y[]), ncol = nc, byrow = TRUE) l <- dim(y)[1] dat <- matrix(0, l, nc) for (i in 1:l) dat[i, ] <- y[[i]] plot(tree, label.offset = 1.1 * xrad, plot = FALSE, ...) lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv) XX <- lastPP$xx YY <- lastPP$yy xrad <- CEX * diff(lastPP$x.lim * 1.1) / 50 par(new = TRUE) plot(tree, label.offset = 1.1 * xrad, plot = TRUE, ...) if (is.null(col)) col <- hcl.colors(nc) if (length(col) != nc) { warning("Length of color vector differs from number of levels!") } BOTHlabels( pie = y, XX = XX, YY = YY, adj = c(0.5, 0.5), frame = "rect", pch = NULL, sel = seq_along(XX), thermo = NULL, piecol = col, col = "black", bg = "lightblue", horiz = FALSE, width = NULL, height = NULL, cex = cex.pie ) if (!is.null(pos)) legend(pos, legend=levels, text.col = col) } acctran2 <- function(tree, data) { if(!is.binary(tree)) tree <- multi2di(tree) tree <- reorder(tree, "postorder") edge <- tree$edge data <- subset(data, tree$tip.label) f <- init_fitch(data, FALSE, FALSE, m=2L) psc_node <- f$pscore_node(edge) tmp <- reorder(tree)$edge tmp <- tmp[tmp[,2]>Ntip(tree), ,drop=FALSE] f$traverse(edge) if(length(tmp)>0)f$acctran_traverse(tmp) psc <- f$pscore_acctran(edge) el <- psc parent <- unique(edge[,1]) desc <- Descendants(tree, parent, "children") for(i in seq_along(parent)){ x <- psc_node[parent[i]] -sum(psc[desc[[i]]]) if(x>0) el[desc[[i]] ] <- el[desc[[i]] ] + x/length(desc[[i]]) } tree$edge.length <- el[edge[,2]] tree } acctran <- function(tree, data) { if (inherits(tree, "multiPhylo")) { compress <- FALSE if (!is.null(attr(tree, "TipLabel"))){ compress <- TRUE tree <- .uncompressTipLabel(tree) } res <- lapply(tree, acctran2, data) class(res) <- "multiPhylo" if (compress) res <- .compressTipLabel(res) return(res) } acctran2(tree, data) } ptree <- function(tree, data, return = "prob") { tree <- reorder(tree, "postorder") edge <- tree$edge att <- attributes(data) nr <- att$nr type <- att$type m <- max(edge) nTip <- Ntip(tree) f <- init_fitch(data, FALSE, FALSE, m=2L) f$traverse(edge) tmp <- reorder(tree)$edge tmp <- tmp[tmp[,2]>Ntip(tree),] if(length(tmp)>0)f$acctran_traverse(tmp) res <- vector("list", m) att$names <- c(att$names, as.character((nTip+1):m)) if(return == "phyDat"){ res[1:nTip] <- data[1:nTip] if(type=="DNA"){ for(i in (nTip+1):m) res[[i]] <- f$getAnc(i)[1:nr] } } if(return == "phyDat"){ res[1:nTip] <- data[1:nTip] if(type=="DNA"){ for(i in (nTip+1):m) res[[i]] <- f$getAncAmb(i)[1:nr] } else stop("This is only for nucleotide sequences supported so far") } else { fun <- function(X) { rs <- rowSums(X) X / rs } contrast <- att$contrast for(i in seq_len(nTip)) res[[i]] <- contrast[data[[i]], , drop=FALSE] for(i in (nTip+1):m) res[[i]] <- f$getAnc(i)[1:nr, , drop=FALSE] res <- lapply(res, fun) } attributes(res) <- att res }
rearrr_fn_ <- function(data, origin_fn, check_fn, allowed_types, force_df, min_dims){ stop("'rearrr_fn' should not be called. Is used for documentation only.") }
new_ml_model_bisecting_kmeans <- function(pipeline_model, formula, dataset, features_col) { m <- new_ml_model_clustering( pipeline_model = pipeline_model, formula = formula, dataset = dataset, features_col = features_col, class = "ml_model_bisecting_kmeans" ) model <- m$model m$summary <- model$summary m$centers <- model$cluster_centers() %>% do.call(rbind, .) %>% as.data.frame() %>% rlang::set_names(m$feature_names) m$cost <- suppressWarnings( possibly_null( ~ pipeline_model %>% ml_stage(1) %>% ml_transform(dataset) %>% model$compute_cost() )() ) m } print.ml_model_bisecting_kmeans <- function(x, ...) { preamble <- sprintf( "K-means clustering with %s %s", nrow(x$centers), if (nrow(x$centers) == 1) "cluster" else "clusters" ) cat(preamble, sep = "\n") print_newline() ml_model_print_centers(x) print_newline() cat( "Within Set Sum of Squared Errors = ", if (is.null(x$cost)) "not computed." else x$cost ) }
plot.scdf <- function(...) { plotSC(...) } plotSC <- function(data, dvar, pvar, mvar, ylim = NULL, xlim = NULL, xinc = 1, lines = NULL, marks = NULL, phase.names = NULL, xlab = NULL, ylab = NULL, main = "", case.names = NULL, style = getOption("scan.plot.style"), ...) { dots <- list(...) op <- par(no.readonly = TRUE) on.exit(par(op)) if (missing(dvar)) dvar <- scdf_attr(data, .opt$dv) else scdf_attr(data, .opt$dv) <- dvar if (missing(pvar)) pvar <- scdf_attr(data, .opt$phase) else scdf_attr(data, .opt$phase) <- pvar if (missing(mvar)) mvar <- scdf_attr(data, .opt$mt) else scdf_attr(data, .opt$mt) <- mvar data_list <- .prepare_scdf(data) N <- length(data_list) if (N > 1) par(mfrow = c(N, 1)) if (is.list(style)) { ref.style <- "default" if ("style" %in% names(style)) ref.style <- style$style style <- c(style, style_plotSC(ref.style)) style <- style[unique(names(style))] } if (is.character(style)) style <- style_plotSC(style) sty_names <- c("fill", "fill.bg", "frame", "grid", "lwd", "pch", "text.ABlag", "type") if (any(names(dots) %in% sty_names)) { stop("Using style parameters directly as arguments (like 'fill') is deprectated. ", "Please use the 'stlye' argument to provide these parameters. ", "E.g., style = list(fill = 'blue', pch = 19)") } annotations <- style$annotations if (is.na(style$frame)) style$bty <- "n" par("bg" = style$col.bg) par("col" = style$col) par("family" = style$font) par("cex" = style$cex) par("cex.lab" = style$cex.lab) par("cex.axis" = style$cex.axis) par("las" = style$las) par("bty" = style$bty) par("col.lab" = style$col.text) par("col.axis" = style$col.text) if (isTRUE(style$frame == "")) style$frame <- NA if (isTRUE(style$grid == "")) style$grid <- FALSE if (isTRUE(style$fill.bg == "")) style$fill.bg <- FALSE if (identical(class(marks), c("sc_outlier"))) marks <- list(positions = marks$dropped.mt) if (!is.null(case.names)) names(data_list) <- case.names case.names <- names(data_list) if (is.null(xlab)) xlab <- mvar if (is.null(ylab)) ylab <- dvar if (is.null(xlab)) xlab <- "Measurement time" if (is.null(ylab)) ylab <- "Score" if (xlab == "mt") xlab <- "Measurement time" lines <- .prepare_arg_lines(lines) values.tmp <- unlist(lapply(data_list, function(x) x[, dvar])) mt.tmp <- unlist(lapply(data_list, function(x) x[, mvar])) if (is.null(ylim)) ylim <- c(min(values.tmp, na.rm = TRUE), max(values.tmp, na.rm = TRUE)) if (is.null(xlim)) xlim <- c(min(mt.tmp, na.rm = TRUE), max(mt.tmp, na.rm = TRUE)) par(mgp = c(2, 1, 0)) for(case in 1:N) { data <- data_list[[case]] design <- .phasestructure(data, pvar) y.lim <- ylim if (is.na(ylim[2])) y.lim[2] <- max(data[, dvar]) if (is.na(ylim[1])) y.lim[1] <- min(data[, dvar]) if (N == 1) { if (main != "") par(mai = c(style$mai[1:2], style$mai[3] + 0.4, style$mai[4])) if (main == "") par(mai = style$mai) plot( data[[mvar]], data[[dvar]], type = "n", xlim = xlim, ylim = y.lim, ann = FALSE, yaxt = "n", xaxt = "n", ... ) xticks_pos <- seq(xlim[1], xlim[2], 1) axis(side = 1, at = xticks_pos, labels = FALSE) text( x = seq(xlim[1], xlim[2], xinc), y = par("usr")[3], cex = style$cex.axis, labels = seq(xlim[1], xlim[2], xinc), srt = 0, pos = 1, offset = style$cex.axis, xpd = TRUE ) yticks_pos <- axTicks(2, usr = c(y.lim[1], ylim[2])) axis(side = 2, at = yticks_pos, labels = NA) text( x = par("usr")[1], y = yticks_pos, labels = yticks_pos, offset = style$cex.axis, srt = 0, pos = 2, cex = style$cex.axis, xpd = TRUE ) if (style$ylab.orientation == 0) mtext(text = ylab, side = 2, line = 2, las = 0, cex = style$cex.lab) if (style$ylab.orientation == 1) { mtext( text = ylab, side = 2, line = 2, las = 1, at = max(y.lim), cex = style$cex.lab ) } mtext(text = xlab, side = 1, line = 2, las = 0, cex = style$cex.lab) } if (N > 1 && case != N) { if (case == 1) { if (main != "") { par(mai = c(style$mai[1] * 2 / 6, style$mai[2], style$mai[3] * 3, style$mai[4])) } if (main == "") { par(mai = c(style$mai[1] * 2 / 6, style$mai[2], style$mai[3] * 3, style$mai[4])) } } else { par(mai = c(style$mai[1] * 4 / 6, style$mai[2], style$mai[3] * 2, style$mai[4])) } plot( data[[mvar]], data[[dvar]], xaxt = "n", yaxt = "n", type = "n", xlim = xlim, ylim = y.lim, ann = FALSE, ... ) yticks_pos <- axTicks(2, usr = c(y.lim[1], ylim[2])) axis(side = 2, at = yticks_pos, labels = NA) text( x = par("usr")[1], y = yticks_pos, labels = yticks_pos, offset = style$cex.axis, srt = 0, pos = 2, cex = style$cex.axis, xpd = TRUE ) if (style$ylab.orientation == 0) mtext(ylab, side = 2, line = 2, las = 0, cex = style$cex.lab) if (style$ylab.orientation == 1) mtext(ylab, side = 2, line = 2, las = 1, at = max(y.lim), cex = style$cex.lab) } if (N > 1 && case == N) { par(mai = style$mai) plot( data[[mvar]], data[[dvar]], type = "n", xlim = xlim, ylim = y.lim, ann = FALSE, xaxp = c(xlim[1], xlim[2], xlim[2] - xlim[1]), yaxt = "n", xaxt = "n", ... ) xticks_pos <- seq(xlim[1], xlim[2], 1) axis(side = 1, at = xticks_pos, labels = FALSE) text( x = seq(xlim[1], xlim[2], xinc), y = par("usr")[3], cex = style$cex.axis, labels = seq(xlim[1], xlim[2], xinc), srt = 0, pos = 1, offset = style$cex.axis, xpd = TRUE ) yticks_pos <- axTicks(2, usr = c(y.lim[1], ylim[2])) axis(side = 2, at = yticks_pos, labels = NA) text( x = par("usr")[1], y = yticks_pos, labels = yticks_pos, offset = style$cex.axis, srt = 0, pos = 2, cex = style$cex.axis, xpd = TRUE ) if (style$ylab.orientation == 0) mtext(ylab, side = 2, line = 2, las = 0, cex = style$cex.lab) if (style$ylab.orientation == 1) mtext(ylab, side = 2, line = 2, las = 1, at = max(y.lim), cex = style$cex.lab) mtext(xlab, side = 1, line = 2, las = 0, cex = style$cex.lab) } usr <- par("usr") if(class(style$fill.bg) == "character") { style$col.fill.bg <- style$fill.bg style$fill.bg <- TRUE } if (isTRUE(style$fill.bg)){ type_phases <- unique(design$values) col <- rep(style$col.fill.bg, length = length(type_phases)) for(i in seq_along(design$values)) { x <- data[design$start[i]:design$stop[i], mvar] y <- data[design$start[i]:design$stop[i], dvar] xmin <- min(x, na.rm = TRUE) xmax <- max(x, na.rm = TRUE) + 0.5 if (i == length(design$values)) xmax <- usr[2] if (i > 1) xmin <- xmin - 0.5 if (i == 1) xmin <- usr[1] .col <- col[which(type_phases == design$values[i])[1]] rect(xmin, usr[3], xmax, usr[4], col = .col, border = NA) } } if(class(style$grid) == "character") { style$col.grid <- style$grid style$grid <- TRUE } if (isTRUE(style$grid)) grid(NULL, NULL, col = style$col.grid, lty = style$lty.grid, lwd = style$lwd.grid) if (!is.na(style$frame)) rect(usr[1],usr[3],usr[2],usr[4], col = NA, border = style$frame) if (is.na(style$frame) && isTRUE(style$fill.bg)) rect(usr[1],usr[3],usr[2],usr[4], col = NA, border = style$col.fill.bg) if (is.na(style$frame) && !isTRUE(style$fill.bg)) rect(usr[1],usr[3],usr[2],usr[4], col = NA, border = par("bg")) if (style$fill == "" || is.na(style$fill)) style$fill <- FALSE if(class(style$fill) == "character") { style$col.fill <- style$fill style$fill <- TRUE } if (isTRUE(style$fill)) { for(i in 1:length(design$values)) { x <- data[design$start[i]:design$stop[i], mvar] y <- data[design$start[i]:design$stop[i], dvar] for(i in 1:length(x)) { x_values <- c(x[i], x[i+1], x[i+1], x[i]) y_values <- c(y.lim[1], y.lim[1], y[i+1], y[i]) polygon(x_values, y_values, col = style$col.fill, border = NA) } } } for(i in 1:length(design$values)) { x <- data[design$start[i]:design$stop[i], mvar] y <- data[design$start[i]:design$stop[i], dvar] if (style$col.lines != "") { lines( x, y, type = "l", pch = style$pch, lty = style$lty, lwd = style$lwd, col = style$col.lines, ... ) } if (style$col.dots != "") { lines( x, y, type = "p", pch = style$pch, lty = style$lty, lwd = style$lwd, col = style$col.dots, ... ) } } if (case == 1) title(main) if (!is.null(marks)) { marks.cex <- 1 marks.col <- "red" marks.pch <- style$pch if (any(names(marks) == "positions")) { marks.pos <- marks[[which(names(marks) == "positions")]] } else {stop("Positions of marks must be defined.")} if (any(names(marks) == "cex")) { marks.cex <- marks[[which(names(marks) == "cex")]] } if (any(names(marks) == "col")) { marks.col <- marks[[which(names(marks) == "col")]] } if (any(names(marks) == "pch")) { marks.pch <- marks[[which(names(marks) == "pch")]] } if (class(marks.pos) == "numeric") { mks <- marks.pos } else { mks <- marks.pos[[case]] } marks.x <- data[data[,mvar] %in% mks,mvar] marks.y <- data[data[,mvar] %in% mks,dvar] points(x = marks.x, y = marks.y, pch = marks.pch, cex = marks.cex, col = marks.col) } if (!is.null(annotations)) { annotations.cex <- 1 annotations.round <- 1 annotations.col <- "black" annotations.pos <- 3 annotations.offset <- 0.5 if (any(names(annotations) == "cex")) { annotations.cex <- annotations[[which(names(annotations) == "cex")]] } if (any(names(annotations) == "col")) { annotations.col <- annotations[[which(names(annotations) == "col")]] } if (any(names(annotations) == "round")) { annotations.round <- annotations[[which(names(annotations) == "round")]] } if (any(names(annotations) == "pos")) { annotations.pos <- annotations[[which(names(annotations) == "pos")]] } if (any(names(annotations) == "offset")) { annotations.offset <- annotations[[which(names(annotations) == "offset")]] } annotations.label <- round(data[,dvar], annotations.round) text( x = data[,mvar], y = data[,dvar], label = annotations.label, col = annotations.col, pos = annotations.pos, offset = annotations.offset, cex = annotations.cex, ... ) } if (!is.null(lines)) { for(i_lines in seq_along(lines)) { line <- lines[[i_lines]] if (is.null(line[["lty"]])) line[["lty"]] <- "dashed" if (is.null(line[["lwd"]])) line[["lwd"]] <- 2 if (is.null(line[["col"]])) line[["col"]] <- "black" lty.line <- line[["lty"]] lwd.line <- line[["lwd"]] col.line <- line[["col"]] if (line[["type"]] == "trend") { for(i in 1:length(design$values)) { x <- data[design$start[i]:design$stop[i], mvar] y <- data[design$start[i]:design$stop[i], dvar] reg <- lm(y~x) lines( x = c(min(x), max(x)), y = c( reg$coefficients[1] + min(x) * reg$coefficients[2], reg$coefficients[1] + max(x) * reg$coefficients[2] ), lty = lty.line, col = col.line, lwd = lwd.line ) } } if (line[["type"]] == "median") { for(i in 1:length(design$values)) { x <- data[design$start[i]:design$stop[i], mvar] y <- data[design$start[i]:design$stop[i], dvar] lines( x = c(min(x), max(x)), y = c(median(y, na.rm = TRUE), median(y, na.rm = TRUE)), lty = lty.line, col = col.line, lwd = lwd.line ) } } if (line[["type"]] == "mean") { if (is.null(line[["trim"]])) line[["trim"]] <- 0.1 lines.par <- line[["trim"]] for(i in 1:length(design$values)) { x <- data[design$start[i]:design$stop[i],mvar] y <- data[design$start[i]:design$stop[i],dvar] lines( x = c(min(x), max(x)), y = c( mean(y, trim = lines.par, na.rm = TRUE), mean(y, trim = lines.par, na.rm = TRUE) ), lty = lty.line, col = col.line, lwd = lwd.line ) } } if (line[["type"]] == "trendA") { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) reg <- lm(y~x) lines( x = c(min(x), maxMT), y = c( reg$coefficients[1] + min(x) * reg$coefficients[2], reg$coefficients[1] + maxMT * reg$coefficients[2] ), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "trendA_bisplit") { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) md1 <- c(median(y[1:floor(length(y)/2)], na.rm = FALSE), median(x[1:floor(length(x)/2)], na.rm = FALSE)) md2 <- c(median(y[ceiling(length(y)/2+1):length(y)], na.rm = FALSE), median(x[ceiling(length(x)/2+1):length(x)], na.rm = FALSE)) md <- rbind(md1, md2) reg <- lm(md[,1]~md[,2]) lines( x = c(min(x), maxMT), y = c( reg$coefficients[1] + min(x) * reg$coefficients[2], reg$coefficients[1] + maxMT * reg$coefficients[2] ), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "trendA_trisplit") { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) md1 <- c( median(y[1:floor(length(y) / 3)], na.rm = FALSE), median(x[1:floor(length(x) / 3)], na.rm = FALSE) ) md2 <- c( median(y[ceiling(length(y) / 3 * 2 + 1):length(y)], na.rm = FALSE), median(x[ceiling(length(x) / 3 * 2 + 1):length(x)], na.rm = FALSE) ) md <- rbind(md1, md2) reg <- lm(md[,1] ~ md[,2]) lines( x = c(min(x), maxMT), y = c( reg$coefficients[1] + min(x) * reg$coefficients[2], reg$coefficients[1] + maxMT * reg$coefficients[2] ), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "loreg") { if (is.null(line[["f"]])) line[["f"]] <- 0.5 lines.par <- line[["f"]] reg <- lowess(data[,dvar] ~ data[,mvar], f = lines.par) lines(reg, lty = lty.line, col = col.line, lwd = lwd.line) } if (line[["type"]] %in% c("maxA", "pnd")) { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) lines( x = c(min(x), maxMT), y = c(max(y), max(y)), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "minA") { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) lines( x = c(min(x), maxMT), y = c(min(y), min(y)), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "medianA") { x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) lines( x = c(min(x), maxMT), y = c(median(y, na.rm = TRUE), median(y, na.rm = TRUE)), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "meanA") { if (is.null(line[["trim"]])) line[["trim"]] <- 0.1 lines.par <- line[["trim"]] x <- data[design$start[1]:design$stop[1],mvar] y <- data[design$start[1]:design$stop[1],dvar] maxMT <- max(data[,mvar]) lines( x = c(min(x), maxMT), y = c( mean(y, trim = lines.par, na.rm = TRUE), mean(y, trim = lines.par, na.rm = TRUE) ), lty = lty.line, col = col.line, lwd = lwd.line ) } if (line[["type"]] == "plm") { pr <- plm(data_list[case]) y <- fitted(pr$full.model) lines(data[[mvar]], y, lty = lty.line, col = col.line, lwd = lwd.line) } if (line[["type"]] == "plm.ar") { if (is.null(line[["ar"]])) line[["ar"]] <-2 lines.par <- line[["ar"]] pr <- plm(data_list[case], AR = lines.par) y <- fitted(pr$full.model) lines(data[[mvar]], y, lty = lty.line, col = col.line, lwd = lwd.line) } if (line[["type"]] == "movingMean") { if (is.null(line[["lag"]])) line[["lag"]] <- 1 lines.par <- line[["lag"]] y <- .moving_average(data[, dvar],lines.par, mean) lines(data[, mvar], y, lty = lty.line, col = col.line, lwd = lwd.line) } if (line[["type"]] == "movingMedian") { if (is.null(line[["lag"]])) line[["lag"]] <- 1 lines.par <- line[["lag"]] y <- .moving_average(data[, dvar],lines.par, median) lines(data[, mvar], y, lty = lty.line, col = col.line, lwd = lwd.line) } } } if (is.null(phase.names)) { case_phase_names <- design$values } else { case_phase_names <- phase.names } for(i in 1:length(design$values)) { mtext( text = case_phase_names[i], side = 3, at = (data[design$stop[i], mvar] - data[design$start[i], mvar]) / 2 + data[design$start[i], mvar], cex = style$cex.text, ... ) } if (is.null(style$text.ABlag)) { for(i in 1:(length(design$values) - 1)) { abline( v = data[design$stop[i] + 1, mvar] - 0.5, lty = style$lty.seperators, lwd = style$lwd.seperators, col = style$col.seperators ) } } if (!is.null(style$text.ABlag)) { for(i in 1:(length(design$values) - 1)) { tex <- paste(unlist(strsplit(style$text.ABlag[i], "")), collapse = "\n") text( x = data[design$stop[i] + 1, mvar] - 0.5, y = (y.lim[2] - y.lim[1]) / 2 + y.lim[1], labels = tex, cex = 0.8, ...) } } if (length(case.names) == N) { args <- c( list(text = case.names[case]), style$names, cex = style$cex.text, at = min(xlim) ) args <- args[!duplicated(names(args))] do.call(mtext, args) } } } .prepare_arg_lines <- function(lines) { types <- list( "mean", "median", "pnd", "maxA", "minA", "medianA", "trend", "trendA", "plm", "plm.ar", "trendA_bisplit", "trendA_trisplit", "loreg", "movingMean", "movingMedian" ) if (class(lines) != "list") { lines <- lapply(lines, function(x) x) } if(!all(sapply(lines, is.list))) { lines <- list(lines) } if (length(lines) == 1) { tmp_args <- unlist(lines[[1]]) id <- which(tmp_args %in% names(types)) if (length(id) > 1) { warning("More than one line type detected in one list element!") for (i in 2:length(id)) { lines <- c(lines, list(lines[[1]][id[i]])) lines[[1]] <- lines[[1]][-id[i]] } } tmp_args <- names(lines[[1]]) id <- which(tmp_args %in% names(types)) if (length(id) > 1) { warning("More than one line type detected in one list element!") for (i in 2:length(id)) { lines <- c(lines, list(lines[[1]][id[i]])) lines[[1]] <- lines[[1]][-id[i]] } } } for (i in seq_along(lines)) { arg_names <- names(lines[[i]]) if (is.null(arg_names)) { names(lines[[i]]) <- rep("", length(lines[[i]])) arg_names <- names(lines[[i]]) } if (any(arg_names == "mean")) { id <- which(arg_names == "mean") lines[[i]] <- c(lines[[i]], trim = as.numeric(unname(lines[[i]][id]))) lines[[i]][id] <- names(lines[[i]])[id] names(lines[[i]])[id] <- "type" } if (any(arg_names == "loreg")) { id <- which(arg_names == "loreg") lines[[i]] <- c(lines[[i]], f = as.numeric(unname(lines[[i]][id]))) lines[[i]][id] <- names(lines[[i]])[id] names(lines[[i]])[id] <- "type" } if (any(arg_names == "movingMedian")) { id <- which(arg_names == "movingMedian") lines[[i]] <- c(lines[[i]], lag = as.numeric(unname(lines[[i]][id]))) lines[[i]][id] <- names(lines[[i]])[id] names(lines[[i]])[id] <- "type" } if (any(arg_names == "movingMean")) { id <- which(arg_names == "movingMean") lines[[i]] <- c(lines[[i]], lag = as.numeric(unname(lines[[i]][id]))) lines[[i]][id] <- names(lines[[i]])[id] names(lines[[i]])[id] <- "type" } if (any(arg_names == "plm.ar")) { id <- which(arg_names == "plm.ar") lines[[i]] <- c(lines[[i]], ar = as.numeric(unname(lines[[i]][id]))) lines[[i]][id] <- names(lines[[i]])[id] names(lines[[i]])[id] <- "type" } id <- which(arg_names == "") if(length(id) > 1) { stop("undefined lines argument(s)") } if(length(id) == 1) { names(lines[[i]])[id] <- "type" } } lines }
context("test-wait") test_that("wait(): both pipes work with a promise as an argument", { value <- runif(1) pr <- promises::promise_resolve(value) with_magrittr_pipe <- pr %>% wait(0.1) expect_identical(hold(with_magrittr_pipe), value) with_promises_pipe <- pr %...>% wait(0.1) expect_identical(hold(with_promises_pipe), value) }) test_that("wait() also works with a non-promise object", { value <- runif(1) pr <- wait(value, 0.1) expect_is(pr, "promise") expect_identical(hold(pr), value) }) test_that("timeout() works with a non promise argument", { value <- runif(1) pr <- timeout(x = value, delay = 0.1) expect_is(pr, "promise") expect_error(hold(pr), regexp = "0\\.1") }) test_that("timeout() returns the value of the promise when it is fulfilled before the delay expires", { value <- runif(1) pr <- timeout(wait(x = value, delay = 0.1), delay = 10) expect_is(pr, "promise") expect_identical(hold(pr), value) }) test_that("timeout() returns a promise which is rejected when the delay expires", { value <- runif(1) pr <- timeout(wait(x = value, delay = 10), delay = 0.1) expect_is(pr, "promise") expect_error(hold(pr), regexp = "0\\.1") })
predict_ic50s <- function( protein_sequence, peptide_length, mhcnuggets_options, peptides_path = create_temp_peptides_path() ) { if (peptide_length > 15) { stop( "'peptide_length' must be 15 at most. \n", "Actual value: ", peptide_length ) } n <- nchar(protein_sequence) - peptide_length + 1 peptides <- rep(NA, n) for (i in seq_len(n)) { peptides[i] <- substr(protein_sequence, i, i + peptide_length - 1) } testthat::expect_true(all(nchar(peptides) == peptide_length)) mhcnuggetsr::predict_ic50( peptides = peptides, mhcnuggets_options = mhcnuggets_options ) }
"userfs" <- function(s) { if (missing(s)) return (13) f.res <- s f.res }
table_import <- function(file,sep=F,format_corrector=F,...){ x<-data.frame(1:2) if(sep==F){sep=c(";",",","\t",":"," ") } for(i in 1:length(sep)){ x<-read.table(file,sep=sep[i],...) i<-i+1 if(ncol(x)>1){break} } if(ncol(x)==1){cat("specify separator")} if(format_corrector){x<-format_corrector(x)} return(x) }
taf.bootstrap <- function(software=TRUE, data=TRUE, clean=TRUE, force=FALSE, taf=NULL, quiet=FALSE) { if (isTRUE(taf)) software <- data <- clean <- force <- TRUE if (!dir.exists("bootstrap")) { warning( "'bootstrap' folder does not exists.\n", "Are you sure you are in the correct working directory?" ) return(invisible(NULL)) } if (!quiet) msg("Bootstrap procedure running...") if (force) clean(c("bootstrap/software", "bootstrap/library", "bootstrap/data")) out <- list(SOFTWARE.bib = FALSE, DATA.bib = FALSE) if (dir.exists("bootstrap/initial/config")) { if (clean) clean("config") warning("'bootstrap/initial/config' is deprecated.\n", "Use DATA.bib entry instead.") cp("bootstrap/initial/config", "bootstrap") } if (software && file.exists("bootstrap/SOFTWARE.bib")) { out[["SOFTWARE.bib"]] <- process.bibfile( "software", clean = clean, quiet = quiet ) } if (data && file.exists("bootstrap/DATA.bib")) { out[["DATA.bib"]] <- process.bibfile( "data", clean = clean, quiet = quiet ) } rmdir(c("bootstrap/data", "bootstrap/library", "bootstrap/software"), recursive = TRUE) rmdir("bootstrap/library:", recursive = TRUE) if (!quiet) msg("Bootstrap procedure done") invisible(out) }
dist.condi <- function(ind1, ind2, cs, dat, type = NULL, rob = FALSE, R = 499) { d <- sum( cs>0 ) x1 <- dat[, ind1] x2 <- dat[, ind2 ] if ( d == 0 ) { mod <- energy::dcov.test(x1, x2, R = R) dof <- 1 stat <- mod$statistic pvalue <- log( mod$p.value ) } else{ z <- dat[, cs] mod <- energy::pdcor.test(x1, x2, z, R) stat <- mod$statistic dof <- NCOL(z) pvalue <- log( mod$p.value ) } result <- c(stat, pvalue, dof) names(result) <- c('test', 'logged.p-value', 'df') result }
d_f_j1_a0_abq_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e7 + 2 * (.e6 * .e3) .e9 <- sqrt(.e8) .e10 <- 2 * .e3 .e11 <- .e4 + .e9 .e12 <- .e11/.e10 .e13 <- r0 - .e12 .e14 <- tij - t0 .e15 <- .e10 + 2 * (.e9/.e13) .e16 <- .e4/.e9 .e18 <- exp(2 * (.e9 * .e14)) .e20 <- .e15 * .e18 - .e10 .e21 <- .e3 * .e13 .e22 <- .e16 + 1 .e23 <- 2 * .e16 .e24 <- 0.5 * geno_a .e25 <- .e22 * .e9 .e27 <- .e25/.e21 + .e23 .e28 <- .e27/.e13 .e31 <- .e15 * .e4 * .e14/.e9 .e32 <- 1 - .e24 .e33 <- .e6/.e9 .e34 <- .e28 + 2 * .e31 .e35 <- 2 * .e21 .e36 <- 0.5 * .e33 .e41 <- .e32 * .e4/.e9 .e42 <- .e12 + 2 * (.e9/.e20) .e43 <- .e3/.e9 .e44 <- 0.5 * .e16 .e46 <- .e23 - 2 * (.e34 * .e18 * .e9/.e20) .e47 <- .e8 * .e9 .e48 <- .e15 * .e6 .e49 <- .e15 * .e3 .e50 <- .e22/.e10 .e52 <- .e4/.e8 .e53 <- .e33 - .e11/.e3 .e54 <- .e36 - .e12 .e55 <- .e50 + .e46/.e20 .e56 <- .e22/.e9 .e57 <- .e21^2 .e59 <- .e41 + 1 - .e24 .e61 <- .e48 * .e14/.e9 .e63 <- .e49 * .e14/.e9 .e65 <- .e4 * .e6/.e47 .e66 <- 0.5 + .e44 .e67 <- 2 * .e43 .e72 <- .e59 * .e9/.e35 + .e41 .e76 <- .e66 * .e9/.e35 + .e44 .e82 <- 0.5 - 0.5 * (.e7/.e8) .e83 <- 1 - (.e32 * .e7/.e8 + .e24) .e85 <- 2 * ((.e54 * .e9/.e35 + .e36)/.e13) .e86 <- 2 * ((.e43 + 1/(2 * .e13))/.e13) .e87 <- 2 * ((1/.e13 + .e67)/.e13) .e88 <- 2 + 2 * ((.e53 * .e9/.e35 + .e33)/.e13) .e90 <- .e28 + .e22 * .e3 * .e9/.e57 .e93 <- (.e61 + 1 + .e85) * .e18 - 1 .e94 <- .e56 - .e52 .e99 <- .e31 + 2 * (.e76/.e13) .e101 <- (.e88 + 2 * .e61) * .e18 - 2 .e102 <- .e4 * .e3 .e104 <- 2 * (.e72/.e13) + 2 * (.e32 * .e15 * .e4 * .e14/.e9) .e105 <- .e86 + 2 * .e63 .e106 <- .e87 + 4 * .e63 .e107 <- .e34 * .e6 .e108 <- .e34 * .e3 .e118 <- .e41 - .e104 * .e18 * .e9/.e20 .e125 <- .e48/.e8 .e126 <- .e49/.e8 .e127 <- .e102/.e47 .e128 <- .e33 - .e101 * .e9/.e20 .e130 <- .e43 - .e105 * .e18 * .e9/.e20 .e132 <- 0.5 * .e56 - 0.5 * .e52 .e133 <- .e44 - .e99 * .e18 * .e9/.e20 .e134 <- .e36 - .e93 * .e9/.e20 .e135 <- 2 * (.e82/.e9) .e136 <- 2 * (.e83/.e9) .e137 <- 2 * .e65 .e138 <- 2 * (.e3 * .e9) .e139 <- .e67 - .e106 * .e18 * .e9/.e20 c(a0 = -(0.5 * ((.e83/.e138 + (.e136 - (.e104 * .e46 + 2 * ((((.e90 * .e59/2 + (.e94 * .e32 * .e4 + 1 - .e24)/.e13)/.e3 + .e136)/.e13 + (2 * (.e34 * .e32 * .e4) + 2 * (.e83 * .e15 + 2 * (.e72 * .e4/.e13))) * .e14/.e9) * .e9 + .e34 * .e118)) * .e18/.e20)/.e20 - (.e59/.e10 + 2 * (.e118/.e20)) * .e55/.e42) * .e32/.e42)), a2 = -(0.5 * (geno_a * (.e82/.e138 + (.e135 - (.e99 * .e46 + 2 * ((((.e90 * .e66/2 + (.e132 * .e4 + 0.5)/.e13)/.e3 + .e135)/.e13 + (.e34 * .e4 + 2 * (.e82 * .e15 + 2 * (.e76 * .e4/.e13))) * .e14/.e9) * .e9 + .e34 * .e133)) * .e18/.e20)/.e20 - .e55 * (.e66/.e10 + 2 * (.e133/.e20))/.e42) * .e32/.e42)), b0 = 0.5 * ((((.e106 * .e46 + 2 * ((((.e28 + (.e25/.e57 - 4 * .e52) * .e3)/.e9 + (2 * .e56 - 2 * .e52)/.e13)/.e13 + (2 * ((.e87 - 2 * .e126) * .e4) + 4 * .e108) * .e14/.e9) * .e9 + .e34 * .e139)) * .e18/.e20 + 4 * .e127)/.e20 + .e55 * (1/.e9 + 2 * (.e139/.e20))/.e42 + .e4/.e47) * .e32 * (1 - 0.5 * geno_b) * .e5/.e42), b2 = 0.5 * (geno_b * (((.e105 * .e46 + 2 * ((((.e90/2 - 2 * (.e102/.e8))/.e9 + .e94/.e13)/.e13 + (2 * .e108 + 2 * ((.e86 - .e126) * .e4)) * .e14/.e9) * .e9 + .e34 * .e130)) * .e18/.e20 + 2 * .e127)/.e20 + .e55 * (1/(2 * .e9) + 2 * (.e130/.e20))/.e42 + .e4/(2 * .e47)) * .e32 * .e5/.e42), q0 = 0.5 * ((((.e101 * .e46 + 2 * (((((.e27 * .e53/2 + .e94 * .e6)/.e21 - (.e22 * (r0 - (.e53/2 + .e12)) * .e9/.e57 + .e137))/.e13 + (2 * .e107 + 2 * ((.e88 - .e125) * .e4)) * .e14/.e9) * .e9 + .e34 * .e128) * .e18))/.e20 + .e137)/.e20 + .e55 * (.e53/.e10 + 2 * (.e128/.e20))/.e42 + (.e22/.e3 + .e65)/.e10) * .e32 * (1 - 0.5 * geno_q)/.e42), q2 = 0.5 * (geno_q * (((.e93 * .e46 + 2 * (((((.e27 * .e54/2 + .e132 * .e6)/.e21 - (.e22 * (0.5 * .e13 - .e54/2) * .e9/.e57 + .e65))/.e13 + (.e107 + 2 * ((1 + .e85 - 0.5 * .e125) * .e4)) * .e14/.e9) * .e9 + .e34 * .e134) * .e18))/.e20 + .e65)/.e20 + .e55 * (.e54/.e10 + 2 * (.e134/.e20))/.e42 + (.e50 + 0.5 * .e65)/.e10) * .e32/.e42)) } d_f_j1_a2_abq_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e7 + 2 * (.e6 * .e3) .e9 <- sqrt(.e8) .e10 <- 2 * .e3 .e11 <- .e4 + .e9 .e12 <- .e11/.e10 .e13 <- r0 - .e12 .e14 <- tij - t0 .e15 <- .e10 + 2 * (.e9/.e13) .e16 <- .e4/.e9 .e18 <- exp(2 * (.e9 * .e14)) .e20 <- .e15 * .e18 - .e10 .e21 <- .e3 * .e13 .e22 <- .e16 + 1 .e23 <- 2 * .e21 .e24 <- .e22 * .e9 .e25 <- .e6/.e9 .e27 <- .e24/.e23 + .e16 .e30 <- .e15 * .e4 * .e14/.e9 .e31 <- .e27/.e13 .e32 <- .e31 + .e30 .e33 <- 0.5 * .e25 .e34 <- .e3/.e9 .e35 <- 0.5 * .e16 .e39 <- .e12 + 2 * (.e9/.e20) .e40 <- .e16 - 2 * (.e32 * .e18 * .e9/.e20) .e41 <- .e8 * .e9 .e42 <- .e15 * .e6 .e43 <- .e15 * .e3 .e45 <- .e25 - .e11/.e3 .e46 <- .e33 - .e12 .e47 <- 2 * .e13 .e48 <- 4 * .e3 .e50 <- .e42 * .e14/.e9 .e52 <- .e43 * .e14/.e9 .e53 <- .e4 * .e6 .e54 <- .e4/.e8 .e55 <- 0.5 + .e35 .e56 <- 2 * .e34 .e58 <- .e40/.e20 + .e22/.e48 .e59 <- .e22/.e9 .e60 <- .e23^2 .e66 <- .e55 * .e9/.e23 + .e35 .e68 <- .e53/.e41 .e70 <- 0.5 - 0.5 * (.e7/.e8) .e72 <- 2 * ((.e46 * .e9/.e23 + .e33)/.e13) .e73 <- 2 * ((.e34 + 1/.e47)/.e13) .e74 <- 2 * ((1/.e13 + .e56)/.e13) .e75 <- 2 + 2 * ((.e45 * .e9/.e23 + .e25)/.e13) .e78 <- (.e50 + 1 + .e72) * .e18 - 1 .e79 <- .e30 + 2 * (.e66/.e13) .e81 <- (.e75 + 2 * .e50) * .e18 - 2 .e82 <- .e4 * .e3 .e83 <- .e73 + 2 * .e52 .e84 <- .e74 + 4 * .e52 .e85 <- .e32 * .e6 .e86 <- .e32 * .e3 .e89 <- .e31 + 2 * (.e22 * .e3 * .e9/.e60) .e95 <- .e22/.e48^2 .e96 <- .e59 - .e54 .e98 <- .e8 * .e3 * .e9 .e99 <- .e70/.e9 .e106 <- .e42/.e8 .e107 <- .e43/.e8 .e108 <- .e82/.e41 .e109 <- .e25 - .e81 * .e9/.e20 .e110 <- .e34 - .e83 * .e18 * .e9/.e20 .e112 <- 0.5 * .e59 - 0.5 * .e54 .e113 <- 0.5 * .e68 .e114 <- .e35 - .e79 * .e18 * .e9/.e20 .e115 <- .e33 - .e78 * .e9/.e20 .e116 <- 2 * .e54 .e117 <- .e56 - .e84 * .e18 * .e9/.e20 c(a2 = -(0.5 * (geno_a^2 * ((.e99 - (.e79 * .e40 + 2 * ((((.e89 * .e55/2 + (.e112 * .e4 + 0.5)/.e47)/.e3 + .e99)/.e13 + (((.e27 + 2 * .e66)/.e13 + .e30) * .e4 + .e70 * .e15) * .e14/.e9) * .e9 + .e32 * .e114)) * .e18/.e20)/.e20 + .e70/(4 * (.e3 * .e9)) - .e58 * (.e55/.e10 + 2 * (.e114/.e20))/.e39)/.e39)), b0 = 0.5 * (geno_a * (((.e40 * .e84 + 2 * ((((.e31 + (2 * (.e24/.e60) - .e116) * .e3)/.e9 + (2 * .e59 - .e116)/.e47)/.e13 + ((.e74 - 2 * .e107) * .e4 + 4 * .e86) * .e14/.e9) * .e9 + .e32 * .e117)) * .e18/.e20 + 2 * .e108)/.e20 + .e58 * (1/.e9 + 2 * (.e117/.e20))/.e39 + .e4/(2 * .e41)) * (1 - 0.5 * geno_b) * .e5/.e39), b2 = 0.5 * (geno_a * geno_b * (((.e40 * .e83 + 2 * ((((.e89/2 - .e82/.e8)/.e9 + .e96/.e47)/.e13 + ((.e73 - .e107) * .e4 + 2 * .e86) * .e14/.e9) * .e9 + .e32 * .e110)) * .e18/.e20 + .e108)/.e20 + .e58 * (1/(2 * .e9) + 2 * (.e110/.e20))/.e39 + .e4/(4 * .e41)) * .e5/.e39), q0 = 0.5 * (geno_a * (((.e81 * .e40 + 2 * (((((.e27 * .e45/2 + .e96 * .e6/2)/.e21 - (.e68 + 2 * (.e22 * (r0 - (.e45/2 + .e12)) * .e9/.e60)))/.e13 + ((.e75 - .e106) * .e4 + 2 * .e85) * .e14/.e9) * .e9 + .e32 * .e109) * .e18))/.e20 + .e68)/.e20 + .e58 * (.e45/.e10 + 2 * (.e109/.e20))/.e39 + .e53/(4 * .e98) + 4 * .e95) * (1 - 0.5 * geno_q)/.e39), q2 = 0.5 * (geno_a * geno_q * (((.e78 * .e40 + 2 * (((((.e27 * .e46/2 + .e112 * .e6/2)/.e21 - (.e113 + 2 * (.e22 * (0.5 * .e13 - .e46/2) * .e9/.e60)))/.e13 + (.e85 + (1 + .e72 - 0.5 * .e106) * .e4) * .e14/.e9) * .e9 + .e32 * .e115) * .e18))/.e20 + .e113)/.e20 + .e58 * (.e46/.e10 + 2 * (.e115/.e20))/.e39 + .e53/(8 * .e98) + 2 * .e95)/.e39)) } d_f_j1_b0_bq_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e6 * .e3 .e9 <- .e4^2 + 2 * .e7 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e15 <- tij - t0 .e16 <- .e11 + 2 * (.e10/.e14) .e18 <- exp(2 * (.e10 * .e15)) .e20 <- .e16 * .e18 - .e11 .e21 <- .e3/.e10 .e22 <- 4 * .e21 .e23 <- .e16 * .e3 .e24 <- .e6/.e10 .e26 <- .e23 * .e15/.e10 .e27 <- 4 * .e26 .e29 <- (2/.e14 + .e22)/.e14 + .e27 .e30 <- 0.5 * .e24 .e31 <- 0.5 * geno_q .e33 <- 2 * (.e3 * .e14) .e34 <- 1 - .e31 .e38 <- .e13 + 2 * (.e10/.e20) .e40 <- .e22 - 2 * (.e29 * .e18 * .e10/.e20) .e41 <- 0.5 * geno_b .e42 <- .e9 * .e10 .e45 <- .e16 * .e6 * .e15/.e10 .e47 <- .e24 - .e12/.e3 .e48 <- .e30 - .e13 .e49 <- 1 - .e41 .e50 <- 2 * .e21 .e51 <- 1/.e10 .e52 <- 2 * .e14 .e58 <- .e40/.e20 + .e51 .e59 <- .e3^2 .e61 <- 2 * ((.e48 * .e10/.e33 + .e30)/.e14) .e62 <- 2 * ((.e21 + 1/.e52)/.e14) .e63 <- 2 * ((1/.e14 + .e50)/.e14) .e64 <- 2 + 2 * ((.e47 * .e10/.e33 + .e24)/.e14) .e65 <- .e22 + 4/.e14 .e67 <- (.e45 + 1 + .e61) * .e18 - 1 .e73 <- (.e64 + 2 * .e45) * .e18 - 2 .e75 <- 0.5 - 0.5 * (.e7/.e9) .e76 <- 1 - (.e34 * .e6 * .e3/.e9 + .e31) .e77 <- .e62 + 2 * .e26 .e78 <- .e63 + .e27 .e91 <- .e23/.e9 .e92 <- .e6/.e42 .e93 <- .e24 - .e73 * .e10/.e20 .e94 <- .e3/.e42 .e95 <- .e21 - .e77 * .e18 * .e10/.e20 .e96 <- .e59/.e42 .e97 <- .e59/.e9 .e98 <- .e30 - .e67 * .e10/.e20 .e99 <- .e50 - .e78 * .e18 * .e10/.e20 .e100 <- 4 * (.e75/.e10) .e101 <- 4 * (.e76/.e10) c(b0 = -(0.5 * ((.e58 * (1 - (.e49 * (.e51 + 2 * (.e99/.e20)) * .e6/.e38 + .e41)) - (((.e78 * .e40 + 2 * (.e29 * .e99 + (.e65/.e14 - 8 * .e97)/.e14 + (4 * .e29 + 4 * (.e63 - 2 * .e91)) * .e3 * .e15)) * .e18/.e20 + 8 * .e96)/.e20 + 2 * .e94) * .e49 * .e6) * .e49/.e38)), b2 = -(0.5 * (geno_b * (.e58 * (0.5 - (1/(2 * .e10) + 2 * (.e95/.e20)) * .e6/.e38) - (((.e77 * .e40 + 2 * (.e29 * .e95 + (.e65/.e52 - 4 * .e97)/.e14 + (2 * .e29 + 4 * (.e62 - .e91)) * .e3 * .e15)) * .e18/.e20 + 4 * .e96)/.e20 + .e94) * .e6) * .e49/.e38)), q0 = -(0.5 * (((.e101 - (.e73 * .e34 * .e40 + 2 * ((((.e47 * .e34 * .e65/.e33 + .e101)/.e14 + (2 * (.e29 * .e34 * .e6) + 4 * (.e76 * .e16 + .e34 * .e64 * .e3)) * .e15/.e10) * .e10 + .e29 * .e93 * .e34) * .e18))/.e20)/.e20 - ((.e47/.e11 + 2 * (.e93/.e20)) * .e58/.e38 + .e92) * .e34) * .e49 * .e5/.e38)), q2 = -(0.5 * (geno_q * ((.e100 - (.e67 * .e40 + 2 * ((((.e29 * .e6 + 4 * (.e75 * .e16 + (1 + .e61) * .e3)) * .e15/.e10 + (.e48 * .e65/.e33 + .e100)/.e14) * .e10 + .e29 * .e98) * .e18))/.e20)/.e20 - ((.e48/.e11 + 2 * (.e98/.e20)) * .e58/.e38 + 0.5 * .e92)) * .e49 * .e5/.e38))) } d_f_j1_b2_bq_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e6 * .e3 .e9 <- .e4^2 + 2 * .e7 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e15 <- tij - t0 .e16 <- .e11 + 2 * (.e10/.e14) .e18 <- exp(2 * (.e10 * .e15)) .e20 <- .e16 * .e18 - .e11 .e21 <- .e3/.e10 .e22 <- .e6/.e10 .e23 <- 2 * .e21 .e24 <- .e16 * .e3 .e27 <- 2 * (.e24 * .e15/.e10) .e29 <- (1/.e14 + .e23)/.e14 + .e27 .e30 <- 0.5 * .e22 .e31 <- 0.5 * geno_q .e33 <- 2 * (.e3 * .e14) .e34 <- 1 - .e31 .e40 <- .e16 * .e6 * .e15/.e10 .e41 <- .e13 + 2 * (.e10/.e20) .e43 <- .e22 - .e12/.e3 .e44 <- .e30 - .e13 .e46 <- .e23 - 2 * (.e29 * .e18 * .e10/.e20) .e47 <- 2 * .e14 .e50 <- .e9 * .e10 .e53 <- 2 * ((.e44 * .e10/.e33 + .e30)/.e14) .e54 <- 2 * ((.e21 + 1/.e47)/.e14) .e55 <- 2 + 2 * ((.e43 * .e10/.e33 + .e22)/.e14) .e57 <- (.e40 + 1 + .e53) * .e18 - 1 .e63 <- .e46/.e20 + 0.5/.e10 .e65 <- (.e55 + 2 * .e40) * .e18 - 2 .e67 <- 0.5 - 0.5 * (.e7/.e9) .e68 <- 1 - (.e34 * .e6 * .e3/.e9 + .e31) .e69 <- .e54 + .e27 .e70 <- .e23 + 2/.e14 .e80 <- .e6/.e50 .e81 <- .e22 - .e65 * .e10/.e20 .e82 <- .e21 - .e69 * .e18 * .e10/.e20 .e83 <- .e3^2 .e84 <- .e30 - .e57 * .e10/.e20 .e85 <- 2 * (.e67/.e10) .e86 <- 2 * (.e68/.e10) c(b2 = -(0.5 * (geno_b^2 * (.e63 * (0.5 - (1/(2 * .e10) + 2 * (.e82/.e20)) * .e6/.e41) - (((.e69 * .e46 + 2 * (.e29 * .e82 + (.e70/.e47 - 2 * (.e83/.e9))/.e14 + (2 * .e29 + 2 * (.e54 - .e24/.e9)) * .e3 * .e15)) * .e18/.e20 + 2 * (.e83/.e50))/.e20 + 0.5 * (.e3/.e50)) * .e6)/.e41)), q0 = -(0.5 * (geno_b * ((.e86 - (.e65 * .e34 * .e46 + 2 * ((((.e43 * .e34 * .e70/.e33 + .e86)/.e14 + (2 * (.e29 * .e34 * .e6) + 2 * (.e68 * .e16 + .e34 * .e55 * .e3)) * .e15/.e10) * .e10 + .e29 * .e81 * .e34) * .e18))/.e20)/.e20 - ((.e43/.e11 + 2 * (.e81/.e20)) * .e63/.e41 + 0.5 * .e80) * .e34) * .e5/.e41)), q2 = -(0.5 * (geno_b * geno_q * ((.e85 - (.e57 * .e46 + 2 * ((((.e29 * .e6 + 2 * (.e67 * .e16 + (1 + .e53) * .e3)) * .e15/.e10 + (.e44 * .e70/.e33 + .e85)/.e14) * .e10 + .e29 * .e84) * .e18))/.e20)/.e20 - ((.e44/.e11 + 2 * (.e84/.e20)) * .e63/.e41 + 0.25 * .e80)) * .e5/.e41))) } d_f_j1_q0_qb_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e6 * .e3 .e9 <- .e4^2 + 2 * .e7 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e15 <- tij - t0 .e16 <- .e11 + 2 * (.e10/.e14) .e18 <- exp(2 * (.e10 * .e15)) .e19 <- .e6/.e10 .e21 <- .e16 * .e18 - .e11 .e22 <- .e11^2 .e24 <- 2 * (.e3 * .e10) .e26 <- .e6/.e24 .e27 <- 2 * (.e12/.e22) .e28 <- 2 * .e19 .e29 <- .e16 * .e6 .e30 <- .e26 - .e27 .e32 <- .e29 * .e15/.e10 .e36 <- 2 * (.e30 * .e10/.e14) + .e28 .e37 <- 2 * .e32 .e40 <- .e36/.e14 + 2 + .e37 .e41 <- 0.5 * .e19 .e42 <- .e3/.e10 .e44 <- .e40 * .e18 - 2 .e45 <- .e12/.e3 .e47 <- 2 * (.e3 * .e14) .e50 <- .e24^2 .e51 <- .e13 + 2 * (.e10/.e21) .e53 <- .e28 - 2 * (.e44 * .e10/.e21) .e54 <- .e19 - .e45 .e55 <- .e41 - .e13 .e56 <- 2 * .e42 .e59 <- .e16 * .e3 * .e15/.e10 .e60 <- .e7/.e9 .e63 <- .e54 * .e10/.e47 + .e19 .e66 <- .e55 * .e10/.e47 + .e41 .e67 <- .e42 + 1/(2 * .e14) .e69 <- 1/.e14 + .e56 .e75 <- .e53/.e21 + .e26 - .e27 .e76 <- .e7/.e50 .e77 <- .e7/.e10 .e79 <- .e5^4/(.e9 * .e10) .e81 <- 1 - 0.5 * geno_q .e83 <- 2 * (.e66/.e14) .e84 <- 2 + 2 * (.e63/.e14) .e86 <- (.e32 + 1 + .e83) * .e18 - 1 .e90 <- (.e84 + .e37) * .e18 - 2 .e91 <- 1 - .e60 .e92 <- 2 - 2 * .e60 .e94 <- 2 * (.e67/.e14) + 2 * .e59 .e96 <- 2 * (.e69/.e14) + 4 * .e59 .e99 <- .e40 * .e3 .e116 <- (2 * .e76 + 2/.e22) * .e3 .e117 <- .e29/.e9 .e118 <- (4 * .e76 + 4/.e22) * .e3 .e119 <- .e19 - .e90 * .e10/.e21 .e120 <- .e42 - .e94 * .e18 * .e10/.e21 .e121 <- .e41 - .e86 * .e10/.e21 .e122 <- 1/.e11 .e123 <- 1/.e3 .e124 <- 2 * ((.e77 + .e10) * .e6/.e50) .e125 <- 2 * ((.e19 - 2 * .e45)/.e22) .e126 <- 2 * ((0.5 * .e77 + 0.5 * .e10) * .e6/.e50) .e127 <- 2 * ((.e41 - .e45)/.e22) .e128 <- 2 * (.e91/.e10) .e129 <- 2 * (.e92/.e10) .e130 <- 2 * .e79 .e131 <- .e56 - .e96 * .e18 * .e10/.e21 .e132 <- 2 * .e10 c(q0 = 0.5 * ((((.e90 * .e53 + 2 * ((((.e54 * .e36/.e11 + 2 * (.e63 * .e30 - (.e124 + .e125) * .e10))/.e14 - .e130)/.e14 + (2 * .e40 + 2 * (.e84 - .e117)) * .e6 * .e15/.e10) * .e18 * .e10 + .e44 * .e119))/.e21 + .e130)/.e21 + (.e54/.e11 + 2 * (.e119/.e21)) * .e75/.e51 + .e124 + .e125) * .e81^2/.e51), q2 = 0.5 * (geno_q * (((.e86 * .e53 + 2 * ((((.e55 * .e36/.e11 + 2 * (.e66 * .e30 - (.e126 + .e127) * .e10))/.e14 - .e79)/.e14 + (.e40 + 2 * (1 + .e83 - 0.5 * .e117)) * .e6 * .e15/.e10) * .e18 * .e10 + .e44 * .e121))/.e21 + .e79)/.e21 + (.e55/.e11 + 2 * (.e121/.e21)) * .e75/.e51 + .e126 + .e127) * .e81/.e51), b0 = -(0.5 * (((.e123 - .e118)/.e10 + (.e129 - (.e96 * .e53 * .e18 + 2 * ((((.e36/.e10 + 2 * (.e30 * .e69 + .e123 - .e118))/.e14 + .e129)/.e14 + (2 * (.e92 * .e16 + 2 * (.e69 * .e6/.e14)) + 4 * .e99) * .e15/.e10) * .e18 * .e10 + .e44 * .e131))/.e21)/.e21 - .e75 * (1/.e10 + 2 * (.e131/.e21))/.e51) * (1 - 0.5 * geno_b) * .e81 * .e5/.e51)), b2 = -(0.5 * (geno_b * ((.e122 - .e116)/.e10 + (.e128 - (.e94 * .e53 * .e18 + 2 * ((((.e36/.e132 + 2 * (.e30 * .e67 + .e122 - .e116))/.e14 + .e128)/.e14 + (2 * .e99 + 2 * (.e91 * .e16 + 2 * (.e67 * .e6/.e14))) * .e15/.e10) * .e18 * .e10 + .e44 * .e120))/.e21)/.e21 - .e75 * (1/.e132 + 2 * (.e120/.e21))/.e51) * .e81 * .e5/.e51))) } d_f_j1_q2_qb_g <- function (a0, a2, b0, b2, q0, q2, r0, tij, t0, geno_a, geno_b, geno_q) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e6 * .e3 .e9 <- .e4^2 + 2 * .e7 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e15 <- tij - t0 .e16 <- .e11 + 2 * (.e10/.e14) .e18 <- exp(2 * (.e10 * .e15)) .e19 <- .e6/.e10 .e21 <- .e16 * .e18 - .e11 .e22 <- .e11^2 .e24 <- 2 * (.e3 * .e10) .e27 <- .e6/.e24 - 2 * (.e12/.e22) .e28 <- 0.5 * .e19 .e31 <- .e27 * .e10/.e14 + .e19 .e34 <- .e16 * .e6 * .e15/.e10 .e35 <- .e3/.e10 .e38 <- .e31/.e14 + .e34 + 1 .e40 <- .e38 * .e18 - 1 .e41 <- .e28 - .e13 .e42 <- 2 * .e35 .e45 <- .e24^2 .e48 <- .e16 * .e3 * .e15/.e10 .e49 <- .e13 + 2 * (.e10/.e21) .e50 <- .e7/.e9 .e51 <- .e19 - 2 * (.e40 * .e10/.e21) .e54 <- .e41 * .e10/(2 * (.e3 * .e14)) + .e28 .e55 <- .e35 + 1/(2 * .e14) .e57 <- 1/.e14 + .e42 .e58 <- (2 * (.e7/.e45) + 2/.e22) * .e3 .e61 <- (.e34 + 1 + 2 * (.e54/.e14)) * .e18 - 1 .e63 <- .e51/.e21 + 0.5 * .e27 .e66 <- 1 - .e50 .e67 <- 2 - 2 * .e50 .e69 <- 2 * (.e55/.e14) + 2 * .e48 .e71 <- 2 * (.e57/.e14) + 4 * .e48 .e72 <- .e38 * .e3 .e79 <- .e66/.e10 .e80 <- .e67/.e10 .e89 <- .e35 - .e69 * .e18 * .e10/.e21 .e90 <- .e28 - .e61 * .e10/.e21 .e91 <- 0.5 * (.e5^4/(.e9 * .e10)) .e92 <- 1/.e11 .e93 <- 1/.e3 .e95 <- 2 * ((0.5 * (.e7/.e10) + 0.5 * .e10) * .e6/.e45) + 2 * ((.e28 - .e12/.e3)/.e22) .e96 <- 2 * .e58 .e97 <- .e42 - .e71 * .e18 * .e10/.e21 .e98 <- 2 * .e10 c(q2 = 0.5 * (geno_q^2 * (((.e61 * .e51 + 2 * ((((.e31 * .e41/.e11 + .e54 * .e27 - .e95 * .e10)/.e14 - .e91)/.e14 + ((.e31 + 2 * .e54)/.e14 + (.e15/.e10 - 0.5/.e9) * .e16 * .e6 + 2) * .e6 * .e15/.e10) * .e18 * .e10 + .e40 * .e90))/.e21 + .e91)/.e21 + .e63 * (.e41/.e11 + 2 * (.e90/.e21))/.e49 + 0.5 * .e95)/.e49), b0 = -(0.5 * (geno_q * ((.e80 - (.e51 * .e71 * .e18 + 2 * ((((.e31/.e10 + .e27 * .e57 + .e93 - .e96)/.e14 + .e80)/.e14 + (.e67 * .e16 + 2 * (.e57 * .e6/.e14) + 4 * .e72) * .e15/.e10) * .e18 * .e10 + .e40 * .e97))/.e21)/.e21 + 0.5 * ((.e93 - .e96)/.e10) - .e63 * (1/.e10 + 2 * (.e97/.e21))/.e49) * (1 - 0.5 * geno_b) * .e5/.e49)), b2 = -(0.5 * (geno_b * geno_q * ((.e79 - (.e51 * .e69 * .e18 + 2 * ((((.e31/.e98 + .e27 * .e55 + .e92 - .e58)/.e14 + .e79)/.e14 + (.e66 * .e16 + 2 * .e72 + 2 * (.e55 * .e6/.e14)) * .e15/.e10) * .e18 * .e10 + .e40 * .e89))/.e21)/.e21 + 0.5 * ((.e92 - .e58)/.e10) - .e63 * (1/.e98 + 2 * (.e89/.e21))/.e49) * .e5/.e49))) } d_f_j2_a0_abqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e1 <- a0 + geno_a * (a2 - a0)/2 .e4 <- geno_q * (q2 - q0)/2 + q0 .e5 <- .e1^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e4 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e4 .e12 <- .e1 + .e10 .e15 <- geno_f * (f2 - f0)/2 .e16 <- .e12/.e11 .e17 <- f0 + .e15 .e18 <- r0 - .e16 .e19 <- tij - t0 .e20 <- .e17 - f1 .e21 <- .e11 + 2 * (.e10/.e18) .e23 <- exp(2 * (.e10 * .e19)) .e24 <- .e1/.e10 .e25 <- .e21 * .e23 .e26 <- .e17 - m0 .e27 <- .e5 * .e20 .e28 <- .e1 * .e20 .e29 <- .e28/.e10 .e31 <- 2 * (.e26 * .e10) .e34 <- 2 * (.e27/.e10) - .e31 .e35 <- .e24 + 1 .e37 <- .e4 * .e18 .e38 <- exp(-(t0 * .e10)) .e39 <- exp(tij * .e10) .e41 <- .e29 + f0 + .e15 .e42 <- .e11 - .e25 .e43 <- .e5/.e9 .e44 <- .e25 - .e11 .e45 <- 0.5 * geno_a .e46 <- 2 * .e24 .e51 <- 2 * (.e34 * .e38 * .e39/.e12) .e52 <- 2 * (.e29 - .e17) .e53 <- .e51 - .e52 .e54 <- .e21 * .e1 .e55 <- 1 - .e45 .e59 <- .e53 * .e4 - .e41 * .e21 * .e23 .e60 <- .e59/.e42 .e61 <- .e35 * .e10 .e62 <- .e7/.e10 .e64 <- .e61/.e37 + .e46 .e66 <- .e54 * .e19/.e10 .e67 <- .e64/.e18 .e68 <- .e67 + 2 * .e66 .e69 <- 2 * .e37 .e70 <- 0.5 * .e24 .e71 <- .e16 + 2 * (.e10/.e44) .e72 <- 4 * .e43 .e73 <- t0 * .e34 .e74 <- 0.5 * .e62 .e77 <- 0.5 * .e73 + f0 + .e15 .e78 <- 8 - .e72 .e79 <- yij - .e60 .e81 <- .e55 * .e1/.e10 .e83 <- 2 * (.e77 - m0) .e84 <- 2 - 2 * .e43 .e86 <- .e78 * .e20/2 .e87 <- 1 - .e43 .e88 <- 2 * .e26 .e89 <- .e86 - .e83 .e90 <- .e21 * .e7 .e91 <- .e4/.e10 .e92 <- .e60 - .e41 .e93 <- .e27/.e9 .e98 <- 2 * (.e89 * .e1/.e10 - .e35 * .e34/.e12) + 2 * (tij * .e34 * .e1/.e10) .e99 <- 2 * .e93 .e103 <- .e9 * .e10 .e104 <- .e87 * .e4 .e105 <- .e84 * .e21 .e107 <- .e90 * .e19/.e10 .e108 <- 0.5 + .e70 .e110 <- .e46 - 2 * (.e68 * .e23 * .e10/.e44) .e111 <- .e99 + .e88 .e113 <- .e105 * .e23/2 .e114 <- 0.5 * geno_f .e115 <- 2 * .e104 .e116 <- .e21 * .e4 .e117 <- .e113 + .e115 .e119 <- .e81 + 1 - .e45 .e121 <- .e62 - .e12/.e4 .e122 <- .e74 - .e16 .e123 <- .e35/.e11 .e124 <- .e123 + .e110/.e44 .e126 <- .e116 * .e19/.e10 .e127 <- .e1/.e9 .e128 <- 0.5 * .e43 .e129 <- .e28/.e9 .e133 <- .e68 * .e92 * .e23 + .e98 * .e38 * .e39 * .e4/.e12 - .e117 * .e20/.e10 .e134 <- 1 - .e114 .e138 <- 2 * ((.e122 * .e10/.e69 + .e74)/.e18) .e139 <- 2 * .e91 .e140 <- 2 * .e10 .e141 <- 2 + 2 * ((.e121 * .e10/.e69 + .e62)/.e18) .e142 <- .e35/.e10 .e143 <- .e37^2 .e144 <- .e55 * .e21 .e149 <- .e107 + 1 + .e138 .e150 <- .e41 - .e60 .e152 <- 0.5 - .e128 .e153 <- 1 - (.e55 * .e5/.e9 + .e45) .e156 <- 2 * (.e5/.e10) - .e140 .e157 <- .e141 + 2 * .e107 .e161 <- .e119 * .e10/.e69 + .e81 .e164 <- 2 * ((.e108 * .e10/.e69 + .e70)/.e18) .e165 <- 2 * ((.e91 + 1/(2 * .e18))/.e18) .e166 <- 2 * ((1/.e18 + .e139)/.e18) .e168 <- .e144 * .e1 .e169 <- 2 * (.e161/.e18) .e171 <- .e133/.e42 + 0.5 * (.e124 * .e79/.e71) .e172 <- .e66 + .e164 .e173 <- .e165 + 2 * .e126 .e174 <- .e166 + 4 * .e126 .e175 <- .e149 * .e23 .e178 <- .e157 * .e23 .e180 <- .e1 * .e7/.e103 .e181 <- .e4^2 .e182 <- .e169 + 2 * (.e168 * .e19/.e10) .e184 <- .e134 * .e1/.e10 .e187 <- 2 * .e129 .e188 <- tij - (1/.e12 + t0) .e189 <- .e67 + .e35 * .e4 * .e10/.e143 .e193 <- .e142 - .e127 .e195 <- .e34/.e9 .e198 <- .e54 * .e7 * .e20/.e103 .e201 <- .e54 * .e20 * .e4/.e103 .e202 <- 0.5 * geno_q .e203 <- 2 - .e43 .e205 <- 2 * ((.e34 * .e188 - .e111) * .e38 * .e39/.e12) + .e187 .e207 <- 2 * ((1 - .e128) * .e20) + m0 .e208 <- .e35/.e12 .e209 <- .e9^2 .e211 <- 0.5 * .e127 .e212 <- 1 - .e202 .e213 <- 2 * (.e203 * .e20) .e214 <- .e92 * .e19 .e216 <- .e175 - 1 .e217 <- .e35 * .e111 .e218 <- .e152 * .e20 .e219 <- .e152/.e10 .e221 <- .e153 * .e20 .e222 <- .e153/.e10 .e223 <- .e184 + 1 .e224 <- .e111/.e10 .e225 <- .e21 * .e5 .e226 <- .e90/.e9 .e227 <- .e116/.e9 .e228 <- .e178 - 2 .e229 <- .e1 * .e4 .e231 <- 0.5 * .e142 - .e211 .e233 <- 0.5 * (tij * .e1/.e10) - .e108/.e12 .e234 <- 0.5 * t0 .e235 <- 0.5 * tij .e236 <- 1 - .e175 .e237 <- 2 - .e178 .e241 <- 2 * tij - (2 * t0 + 2/.e12) .e243 <- t0 * .e111/.e10 .e247 <- tij * .e55 * .e1/.e10 - .e119/.e12 .e253 <- ((.e129 + 2 * (((.e235 - (.e234 + 0.5/.e12)) * .e34 - 0.5 * .e111) * .e38 * .e39/.e12)) * .e7 * .e4/.e10 + 0.5 * .e53 - ((.e149 * .e41 - 0.5 * .e198) * .e23 + .e59 * .e236/.e42))/.e42 .e268 <- ((2 * ((.e233 * .e34 + (.e207 - .e77) * .e1/.e10) * .e38 * .e39/.e12) - 2 * (.e218/.e10)) * .e4 - (.e172 * .e150 + .e152 * .e21 * .e20/.e10) * .e23)/.e42 .e269 <- ((2 * ((.e55 * (.e213 - (.e88 + .e73)) * .e1/.e10 + .e34 * .e247) * .e38 * .e39/.e12) - 2 * (.e221/.e10)) * .e4 - (.e150 * .e182 + .e153 * .e21 * .e20/.e10) * .e23)/.e42 .e270 <- ((2 * ((.e34 * .e241 - 2 * .e111) * .e38 * .e39/.e12) + 4 * .e129) * .e181/.e10 - (.e150 * .e174 - 2 * .e201) * .e23)/.e42 .e271 <- (.e205 * .e7 * .e4/.e10 + .e51 - ((.e41 * .e157 - .e198) * .e23 + .e59 * .e237/.e42 + .e52))/.e42 .e272 <- (.e205 * .e181/.e10 - (.e150 * .e173 - .e201) * .e23)/.e42 .e274 <- (.e156 * .e38 * .e39/.e12 - 2 * (.e70 - 0.5)) * .e4 - .e108 * .e21 * .e23 .e280 <- .e71 * .e42 .e281 <- .e81 - .e182 * .e23 * .e10/.e44 .e289 <- (2 - 4 * (.e1 * .e38 * .e39/.e12)) * .e4 + .e25 .e294 <- (2 * (.e134 * .e156 * .e38 * .e39/.e12) - 2 * (.e184 + .e114 - 1)) * .e4 - (.e223 - .e114) * .e21 * .e23 .e298 <- .e78/2 .e299 <- .e62 - .e228 * .e10/.e44 .e300 <- .e91 - .e173 * .e23 * .e10/.e44 .e301 <- 0.5 * .e89 .e302 <- .e70 - .e172 * .e23 * .e10/.e44 .e303 <- .e74 - .e216 * .e10/.e44 .e304 <- 2 * .e219 .e305 <- 2 * .e222 .e306 <- .e207 - .e17 .e307 <- 2 * .e180 .e308 <- 2 * .e127 .e309 <- .e139 - .e174 * .e23 * .e10/.e44 .e310 <- ((.e189 * .e119/2 + (.e193 * .e55 * .e1 + 1 - .e45)/.e18)/.e4 + .e305)/.e18 .e311 <- ((.e189 * .e108/2 + (.e231 * .e1 + 0.5)/.e18)/.e4 + .e304)/.e18 .e312 <- ((.e189/2 - 2 * (.e229/.e9))/.e10 + .e193/.e18)/.e18 .e313 <- ((.e64 * .e121/2 + .e193 * .e7)/.e37 - (.e35 * (r0 - (.e121/2 + .e16)) * .e10/.e143 + .e307))/.e18 .e314 <- ((.e64 * .e122/2 + .e231 * .e7)/.e37 - (.e35 * (0.5 * .e18 - .e122/2) * .e10/.e143 + .e180))/.e18 .e315 <- ((.e67 + (.e61/.e143 - 4 * .e127) * .e4)/.e10 + (2 * .e142 - .e308)/.e18)/.e18 .e318 <- .e68 * .e7 .e319 <- .e68 * .e4 .e322 <- (.e119/.e11 + 2 * (.e281/.e44)) * .e79/.e71 + .e269 .e323 <- .e253 + (.e122/.e11 + 2 * (.e303/.e44)) * .e79/.e71 .e326 <- (.e121/.e11 + 2 * (.e299/.e44)) * .e79/.e71 + .e271 .e329 <- (.e108/.e11 + 2 * (.e302/.e44)) * .e79/.e71 + .e268 .e331 <- .e117 * .e7/.e9 .e332 <- .e270 + (1/.e10 + 2 * (.e309/.e44)) * .e79/.e71 .e333 <- .e272 + (1/.e140 + 2 * (.e300/.e44)) * .e79/.e71 .e335 <- .e144 + (.e169 - .e168/.e9) * .e1 .e336 <- (1 + .e138 - 0.5 * .e226) * .e1 .e338 <- (.e164 - 0.5 * (.e54/.e9)) * .e1 + 0.5 * .e21 .e339 <- (.e165 - .e227) * .e1 .e340 <- (.e166 - 2 * .e227) * .e1 .e343 <- .e225 * .e7/.e209 .e345 <- .e225 * .e4/.e209 .e346 <- (.e141 - .e226) * .e1 .e347 <- .e12 * .e10 .e348 <- .e129 + 2 * .e214 .e349 <- .e229/.e103 .e351 <- 0.5 * .e195 .e353 <- 2 * ((((.e298 - .e72) * .e20 - .e83)/.e9 - .e243) * .e1 - ((.e208 + .e127) * .e34 + .e217)/.e12) + 2 * (tij * (.e224 + .e195) * .e1) .e354 <- 2 * .e208 .e355 <- .e213 - .e88 .e356 <- 2 * (.e4 * .e10) .e358 <- t0 * .e98 * .e1 c(a0 = (((((.e310 + 2 * (.e335 * .e19/.e10)) * .e92 + .e133 * .e182/.e42 + .e68 * (.e269 + (2 * (.e92 * .e55 * .e1 * .e19) - .e221)/.e10)) * .e23 + (.e55 * (2 * (tij * ((((2 + 2 * .e203) * .e20 - .e88)/.e10 - .e195) * .e5 - .e31)) - .e358)/.e10 + .e98 * .e247 + 2 * ((.e86 - ((((.e298 + 4 * .e87) * .e20 - .e83)/.e9 + t0 * .e355/.e10) * .e5 + .e83)) * .e55/.e10 - ((.e222 - .e119 * .e35/.e12) * .e34 + .e35 * .e55 * .e355 * .e1/.e10)/.e12)) * .e38 * .e39 * .e4/.e12 - (0.5 * ((.e55 * (2 * (.e84 * .e19/.e10) - 4 * (.e87/.e9)) * .e21 * .e1 + 2 * (.e161 * .e84/.e18)) * .e23) - (.e113 + 6 * .e104) * .e55 * .e1/.e9) * .e20/.e10)/.e42 + 0.5 * (((.e153/.e356 + (.e305 - (.e182 * .e110 + 2 * ((.e310 + (2 * (.e68 * .e55 * .e1) + 2 * .e335) * .e19/.e10) * .e10 + .e68 * .e281)) * .e23/.e44)/.e44) * .e79 - .e322 * .e124)/.e71)) * .e79 - .e171 * .e322) * .e55/.e71, a2 = geno_a * (((((.e311 + 2 * (.e338 * .e19/.e10)) * .e92 + ((.e92 * .e1 * .e19 - .e218)/.e10 + .e268) * .e68 + .e133 * .e172/.e42) * .e23 + (.e233 * .e98 + (2 * (tij * ((.e306/.e10 - .e351) * .e5 + 0.5 * .e34)) - 0.5 * .e358)/.e10 + 2 * ((.e301 - ((.e301 + 2 * (.e87 * .e20))/.e9 + t0 * .e306/.e10) * .e5)/.e10 - ((.e219 - .e35 * .e108/.e12) * .e34 + .e35 * .e306 * .e1/.e10)/.e12)) * .e38 * .e39 * .e4/.e12 - (0.5 * ((.e172 * .e84 - 2 * (.e87 * .e21 * .e1/.e9)) * .e23) - (0.5 * .e117 + .e115) * .e1/.e9) * .e20/.e10)/.e42 + 0.5 * (((.e152/.e356 + (.e304 - (.e172 * .e110 + 2 * ((.e311 + (.e68 * .e1 + 2 * .e338) * .e19/.e10) * .e10 + .e68 * .e302)) * .e23/.e44)/.e44) * .e79 - .e329 * .e124)/.e71)) * .e79 - .e171 * .e329) * .e55/.e71, b0 = (((((.e315 + 2 * (.e340 * .e19/.e10)) * .e92 + .e133 * .e174/.e42 + .e68 * (.e270 + (.e187 + 4 * .e214) * .e4/.e10)) * .e23 + ((.e98 * .e241 - (2 * (((2 * .e89 - 8 * .e93)/.e9 - 2 * .e243) * .e1 - ((.e354 + .e308) * .e34 + 2 * .e217)/.e12) + 2 * (tij * (2 * .e224 + 2 * .e195) * .e1))) * .e38 * .e39 * .e181/.e12 - (0.5 * ((.e84 * .e174 + 8 * .e345) * .e23) - (2 * .e117 - 8 * (.e5 * .e4/.e9)) * .e4/.e9) * .e20)/.e10)/.e42 - 0.5 * (((((.e174 * .e110 + 2 * ((.e315 + (2 * .e340 + 4 * .e319) * .e19/.e10) * .e10 + .e68 * .e309)) * .e23/.e44 + 4 * .e349)/.e44 + .e1/.e103) * .e79 + .e332 * .e124)/.e71)) * .e79 - .e171 * .e332) * .e55 * (1 - 0.5 * geno_b) * .e6/.e71, b2 = geno_b * (((((.e312 + 2 * (.e339 * .e19/.e10)) * .e92 + .e133 * .e173/.e42 + .e68 * (.e272 + .e348 * .e4/.e10)) * .e23 + ((.e98 * .e188 - .e353) * .e38 * .e39 * .e181/.e12 - (0.5 * ((.e84 * .e173 + 4 * .e345) * .e23) - (.e113 + (2 * .e87 - .e72) * .e4) * .e4/.e9) * .e20)/.e10)/.e42 - 0.5 * (((((.e173 * .e110 + 2 * ((.e312 + (2 * .e319 + 2 * .e339) * .e19/.e10) * .e10 + .e68 * .e300)) * .e23/.e44 + 2 * .e349)/.e44 + .e1/(2 * .e103)) * .e79 + .e333 * .e124)/.e71)) * .e79 - .e171 * .e333) * .e55 * .e6/.e71, q0 = ((((((.e313 + 2 * (.e346 * .e19/.e10)) * .e92 + .e68 * (.e271 + .e348 * .e7/.e10)) * .e23 - (.e133 * .e237/.e42 + (0.5 * ((.e84 * .e157 + 4 * .e343) * .e23) + 2 * ((2 * (.e8/.e9) - 1) * .e5/.e9 + 1) - .e331) * .e20/.e10)) * .e212 + ((.e98 * .e19 - .e353) * .e212 * .e7 * .e4/.e10 + (1 - (.e212 * .e7 * .e4/.e347 + .e202)) * .e98) * .e38 * .e39/.e12)/.e42 - 0.5 * (((((.e228 * .e110 + 2 * (((.e313 + (2 * .e318 + 2 * .e346) * .e19/.e10) * .e10 + .e68 * .e299) * .e23))/.e44 + .e307)/.e44 + (.e35/.e4 + .e180)/.e11) * .e79 + .e326 * .e124) * .e212/.e71)) * .e79 - .e171 * .e326 * .e212) * .e55/.e71, q2 = geno_q * (((((.e314 + 2 * (.e336 * .e19/.e10)) * .e92 + ((.e214 + 0.5 * .e129) * .e7/.e10 + .e253) * .e68) * .e23 + (((.e235 - .e234) * .e98 - (2 * (((.e301 - .e99)/.e9 - 0.5 * .e243) * .e1 - ((0.5 * .e208 + .e211) * .e34 + 0.5 * .e217)/.e12) + 2 * (tij * (0.5 * .e224 + .e351) * .e1))) * .e7 * .e4/.e10 + (0.5 - 0.5 * (.e8/.e347)) * .e98) * .e38 * .e39/.e12 - (.e133 * .e236/.e42 + (0.5 * ((.e149 * .e84 + 2 * .e343) * .e23) + 2 * (.e5 * .e7 * .e4/.e209 + 0.5 * .e87) - 0.5 * .e331) * .e20/.e10))/.e42 - 0.5 * (((((.e216 * .e110 + 2 * (((.e314 + (.e318 + 2 * .e336) * .e19/.e10) * .e10 + .e68 * .e303) * .e23))/.e44 + .e180)/.e44 + (.e123 + 0.5 * .e180)/.e11) * .e79 + .e323 * .e124)/.e71)) * .e79 - .e171 * .e323) * .e55/.e71, f0 = ((.e68 * (.e294/.e42 + .e114 - .e223) * .e23 + (2 * ((0.5 * (.e134 * .e78) - 2 * (0.5 * (t0 * .e134 * .e156) + 1 - .e114)) * .e1/.e10 - .e35 * .e134 * .e156/.e12) + 2 * (tij * .e134 * .e156 * .e1/.e10)) * .e38 * .e39 * .e4/.e12 - (.e117 * .e134/.e10 + 0.5 * (.e124 * .e294/.e71))) * .e79 - .e171 * .e294) * .e55/.e280, f2 = geno_f * (((.e274/.e42 - .e108) * .e68 * .e23 + (2 * ((0.25 * .e78 - 2 * (0.25 * (t0 * .e156) + 0.5)) * .e1/.e10 - 0.5 * (.e35 * .e156/.e12)) + tij * .e156 * .e1/.e10) * .e38 * .e39 * .e4/.e12 - (0.5 * (.e274 * .e124/.e71) + 0.5 * (.e117/.e10))) * .e79 - .e171 * .e274) * .e55/.e280, f1 = ((((.e68 * (.e289/.e42 + 1) * .e1 + .e105/2) * .e23 + .e115)/.e10 - ((2 * ((0.5 * .e78 - (.e354 + 2 * (t0 * .e1/.e10)) * .e1)/.e10) + 4 * (tij * .e5/.e9)) * .e38 * .e39 * .e4/.e12 + 0.5 * (.e124 * .e289/(.e71 * .e10))) * .e1) * .e79 - .e171 * .e289 * .e1/.e10) * .e55/.e280) } d_f_j2_a2_abqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e1 <- a0 + geno_a * (a2 - a0)/2 .e3 <- geno_q * (q2 - q0)/2 .e4 <- .e3 + q0 .e5 <- .e1^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e4 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e4 .e12 <- .e1 + .e10 .e15 <- geno_f * (f2 - f0)/2 .e16 <- .e12/.e11 .e17 <- f0 + .e15 .e18 <- r0 - .e16 .e19 <- tij - t0 .e20 <- .e17 - f1 .e21 <- .e11 + 2 * (.e10/.e18) .e23 <- exp(2 * (.e10 * .e19)) .e24 <- .e1/.e10 .e25 <- .e21 * .e23 .e26 <- .e5 * .e20 .e27 <- .e17 - m0 .e28 <- .e1 * .e20 .e29 <- .e28/.e10 .e33 <- 2 * (.e26/.e10) - 2 * (.e27 * .e10) .e34 <- .e24 + 1 .e36 <- exp(-(t0 * .e10)) .e37 <- exp(tij * .e10) .e38 <- .e4 * .e18 .e39 <- 2 * .e38 .e40 <- .e11 - .e25 .e42 <- .e29 + f0 + .e15 .e43 <- .e25 - .e11 .e44 <- .e5/.e9 .e49 <- 2 * (.e33 * .e36 * .e37/.e12) .e50 <- 2 * (.e29 - .e17) .e51 <- .e7/.e10 .e52 <- .e21 * .e1 .e53 <- .e49 - .e50 .e57 <- .e53 * .e4 - .e42 * .e21 * .e23 .e58 <- .e34 * .e10 .e59 <- .e57/.e40 .e61 <- .e58/.e39 + .e24 .e63 <- .e52 * .e19/.e10 .e64 <- .e61/.e18 .e65 <- .e64 + .e63 .e66 <- 0.5 * .e24 .e67 <- 0.5 * .e51 .e68 <- .e16 + 2 * (.e10/.e43) .e69 <- 2 * .e44 .e70 <- 2 * .e12 .e71 <- yij - .e59 .e74 <- 0.5 * (t0 * .e33) + f0 + .e15 .e75 <- 4 - .e69 .e76 <- .e21 * .e7 .e77 <- .e4/.e10 .e78 <- .e26/.e9 .e79 <- .e34 * .e33 .e83 <- .e75 * .e20/2 + m0 - .e74 .e85 <- .e76 * .e19/.e10 .e86 <- 0.5 + .e66 .e87 <- 1 - .e44 .e89 <- 2 * .e78 + 2 * .e27 .e90 <- .e59 - .e42 .e91 <- .e9 * .e10 .e92 <- .e21 * .e4 .e93 <- 0.5 * geno_f .e102 <- .e25/2 + .e3 + q0 .e103 <- .e24 - 2 * (.e65 * .e23 * .e10/.e43) .e105 <- 2 * (.e83 * .e1/.e10 - .e79/.e70) + tij * .e33 * .e1/.e10 .e107 <- .e51 - .e12/.e4 .e108 <- .e67 - .e16 .e110 <- .e92 * .e19/.e10 .e111 <- 0.5 * .e44 .e112 <- 4 * .e4 .e113 <- 2 * .e18 .e114 <- .e102 * .e87 .e116 <- .e103/.e43 + .e34/.e112 .e117 <- .e28/.e9 .e120 <- 1 - .e93 .e122 <- 2 * ((.e108 * .e10/.e39 + .e67)/.e18) .e123 <- 2 * .e77 .e124 <- 2 * .e10 .e125 <- 2 + 2 * ((.e107 * .e10/.e39 + .e51)/.e18) .e129 <- .e65 * .e90 * .e23 + .e105 * .e36 * .e37 * .e4/.e12 - .e114 * .e20/.e10 .e131 <- .e85 + 1 + .e122 .e132 <- .e1/.e9 .e134 <- 0.5 - .e111 .e137 <- 2 * (.e5/.e10) - .e124 .e138 <- .e125 + 2 * .e85 .e142 <- .e86 * .e10/.e39 + .e66 .e144 <- 2 * ((.e77 + 1/.e113)/.e18) .e145 <- 2 * ((1/.e18 + .e123)/.e18) .e147 <- .e34/.e10 .e148 <- .e39^2 .e149 <- 2 * (.e142/.e18) .e150 <- .e131 * .e23 .e151 <- .e63 + .e149 .e152 <- .e42 - .e59 .e153 <- 0.5 * geno_q .e154 <- .e144 + 2 * .e110 .e155 <- .e145 + 4 * .e110 .e157 <- .e129/.e40 + 0.5 * (.e116 * .e71/.e68) .e158 <- .e138 * .e23 .e159 <- .e1 * .e7 .e160 <- .e4^2 .e162 <- .e120 * .e1/.e10 .e163 <- 1 - .e153 .e166 <- 2 * .e117 .e167 <- tij - (1/.e12 + t0) .e174 <- .e52 * .e7 * .e20/.e91 .e177 <- .e52 * .e20 * .e4/.e91 .e178 <- .e159/.e91 .e180 <- 2 * ((.e33 * .e167 - .e89) * .e36 * .e37/.e12) + .e166 .e182 <- 2 * ((1 - .e111) * .e20) + m0 .e183 <- .e33/.e9 .e184 <- .e70^2 .e185 <- .e90 * .e19 .e186 <- .e64 + 2 * (.e34 * .e4 * .e10/.e148) .e187 <- .e151 * .e23 .e188 <- .e150 - 1 .e189 <- .e34 * .e89 .e190 <- .e79/.e184 .e191 <- .e147 - .e132 .e192 <- .e134 * .e20 .e194 <- .e162 + 1 .e195 <- .e89/.e10 .e197 <- .e33 * .e1/.e9 .e198 <- .e76/.e9 .e199 <- .e92/.e9 .e200 <- .e158 - 2 .e201 <- .e1 * .e4 .e203 <- 0.5 * .e147 - 0.5 * .e132 .e205 <- 0.5 * (tij * .e1/.e10) - .e86/.e12 .e206 <- 0.5 * t0 .e207 <- 0.5 * tij .e208 <- 1 - .e150 .e209 <- 2 - .e158 .e214 <- 2 * tij - (2 * t0 + 2/.e12) .e216 <- t0 * .e89/.e10 .e222 <- ((.e117 + 2 * (((.e207 - (.e206 + 0.5/.e12)) * .e33 - 0.5 * .e89) * .e36 * .e37/.e12)) * .e7 * .e4/.e10 + 0.5 * .e53 - ((.e131 * .e42 - 0.5 * .e174) * .e23 + .e57 * .e208/.e40))/.e40 .e233 <- ((2 * ((.e205 * .e33 + (.e182 - .e74) * .e1/.e10) * .e36 * .e37/.e12) - 2 * (.e192/.e10)) * .e4 - (.e151 * .e152 + .e134 * .e21 * .e20/.e10) * .e23)/.e40 .e234 <- ((2 * ((.e33 * .e214 - 2 * .e89) * .e36 * .e37/.e12) + 4 * .e117) * .e160/.e10 - (.e152 * .e155 - 2 * .e177) * .e23)/.e40 .e235 <- (.e180 * .e7 * .e4/.e10 + .e49 - ((.e42 * .e138 - .e174) * .e23 + .e57 * .e209/.e40 + .e50))/.e40 .e236 <- (.e180 * .e160/.e10 - (.e152 * .e154 - .e177) * .e23)/.e40 .e238 <- (.e137 * .e36 * .e37/.e12 - 2 * (.e66 - 0.5)) * .e4 - .e86 * .e21 * .e23 .e243 <- .e68 * .e40 .e244 <- .e134/.e10 .e252 <- (2 - 4 * (.e1 * .e36 * .e37/.e12)) * .e4 + .e25 .e257 <- (2 * (.e120 * .e137 * .e36 * .e37/.e12) - 2 * (.e162 + .e93 - 1)) * .e4 - (.e194 - .e93) * .e21 * .e23 .e261 <- .e51 - .e200 * .e10/.e43 .e262 <- .e77 - .e154 * .e23 * .e10/.e43 .e263 <- 0.5 * .e83 .e264 <- 0.5 * .e178 .e265 <- .e66 - .e187 * .e10/.e43 .e266 <- .e67 - .e188 * .e10/.e43 .e267 <- 0.5 * .e75 .e268 <- .e182 - .e17 .e269 <- .e123 - .e155 * .e23 * .e10/.e43 .e270 <- ((.e186 * .e86/2 + (.e203 * .e1 + 0.5)/.e113)/.e4 + .e244)/.e18 .e271 <- ((.e186/2 - .e201/.e9)/.e10 + .e191/.e113)/.e18 .e272 <- ((.e61 * .e107/2 + .e191 * .e7/2)/.e38 - (.e178 + 2 * (.e34 * (r0 - (.e107/2 + .e16)) * .e10/.e148)))/.e18 .e273 <- ((.e61 * .e108/2 + .e203 * .e7/2)/.e38 - (.e264 + 2 * (.e34 * (0.5 * .e18 - .e108/2) * .e10/.e148)))/.e18 .e274 <- ((.e64 + (2 * (.e58/.e148) - 2 * .e132) * .e4)/.e10 + (2 * .e147 - 2 * .e132)/.e113)/.e18 .e276 <- .e65 * .e7 .e277 <- .e65 * .e4 .e278 <- .e222 + (.e108/.e11 + 2 * (.e266/.e43)) * .e71/.e68 .e284 <- (.e107/.e11 + 2 * (.e261/.e43)) * .e71/.e68 + .e235 .e287 <- (.e86/.e11 + 2 * (.e265/.e43)) * .e71/.e68 + .e233 .e288 <- .e234 + (1/.e10 + 2 * (.e269/.e43)) * .e71/.e68 .e289 <- .e236 + (1/.e124 + 2 * (.e262/.e43)) * .e71/.e68 .e290 <- .e34/.e112^2 .e292 <- .e9 * .e4 * .e10 .e293 <- (1 + .e122 - 0.5 * .e198) * .e1 .e294 <- (.e144 - .e199) * .e1 .e295 <- (.e145 - 2 * .e199) * .e1 .e297 <- (.e125 - .e198) * .e1 .e298 <- .e12 * .e10 .e299 <- .e117 + 2 * .e185 .e300 <- .e201/.e91 .e301 <- 0.5 * .e183 .e302 <- 0.5 * .e21 .e303 <- 1 - 3 * .e44 .e304 <- 2 * ((.e189 + .e197)/.e70 + 2 * .e190 - (((.e75/2 - .e69) * .e20 + m0 - .e74)/.e9 - 0.5 * .e216) * .e1) .e305 <- t0 * .e137 .e307 <- tij * (.e195 + .e183) * .e1 c(a2 = geno_a^2 * (((((.e270 + ((.e149 - 0.5 * (.e52/.e9)) * .e1 + .e302) * .e19/.e10) * .e90 + ((.e90 * .e1 * .e19 - .e192)/.e10 + .e233) * .e65 + .e129 * .e151/.e40) * .e23 + (.e205 * .e105 + (tij * ((.e268/.e10 - .e301) * .e5 + 0.5 * .e33) - 0.5 * (t0 * .e105 * .e1))/.e10 + 2 * ((.e263 - (((.e87 * .e20 + .e263)/.e9 + 0.5 * (t0 * .e268/.e10)) * .e5 + (.e34 * .e268 * .e1 + .e134 * .e33)/.e70))/.e10 + 2 * (.e34 * .e86 * .e33/.e184))) * .e36 * .e37 * .e4/.e12 - (0.5 * .e187 - 1.5 * (.e102 * .e1/.e9)) * .e87 * .e20/.e10)/.e40 + 0.5 * ((((.e244 - (.e151 * .e103 + 2 * ((.e270 + (((.e61 + 2 * .e142)/.e18 + (.e19/.e10 - 0.5/.e9) * .e21 * .e1) * .e1 + .e302) * .e19/.e10) * .e10 + .e65 * .e265)) * .e23/.e43)/.e43 + .e134/(4 * (.e4 * .e10))) * .e71 - .e287 * .e116)/.e68)) * .e71 - .e157 * .e287)/.e68, b0 = geno_a * (((((.e274 + .e295 * .e19/.e10) * .e90 + .e129 * .e155/.e40 + .e65 * (.e234 + (.e166 + 4 * .e185) * .e4/.e10)) * .e23 + ((.e105 * .e214 + 2 * ((2 * .e189 + 2 * .e197)/.e70 + 4 * .e190 - ((2 * .e83 - 4 * .e78)/.e9 - .e216) * .e1) - tij * (2 * .e195 + 2 * .e183) * .e1) * .e36 * .e37 * .e160/.e12 - (0.5 * (.e87 * .e155 * .e23) - .e102 * (2 * .e87 - 4 * .e44) * .e4/.e9) * .e20)/.e10)/.e40 - 0.5 * (((((.e103 * .e155 + 2 * ((.e274 + (.e295 + 4 * .e277) * .e19/.e10) * .e10 + .e65 * .e269)) * .e23/.e43 + 2 * .e300)/.e43 + .e1/(2 * .e91)) * .e71 + .e288 * .e116)/.e68)) * .e71 - .e157 * .e288) * (1 - 0.5 * geno_b) * .e6/.e68, b2 = geno_a * geno_b * (((((.e271 + .e294 * .e19/.e10) * .e90 + .e129 * .e154/.e40 + .e65 * (.e236 + .e299 * .e4/.e10)) * .e23 + ((.e105 * .e167 + .e304 - .e307) * .e36 * .e37 * .e160/.e12 - (0.5 * (.e87 * .e154 * .e23) - .e102 * .e303 * .e4/.e9) * .e20)/.e10)/.e40 - 0.5 * (((((.e103 * .e154 + 2 * ((.e271 + (.e294 + 2 * .e277) * .e19/.e10) * .e10 + .e65 * .e262)) * .e23/.e43 + .e300)/.e43 + .e1/(4 * .e91)) * .e71 + .e289 * .e116)/.e68)) * .e71 - .e157 * .e289) * .e6/.e68, q0 = geno_a * ((((((.e272 + .e297 * .e19/.e10) * .e90 + .e65 * (.e235 + .e299 * .e7/.e10)) * .e23 - .e129 * .e209/.e40) * .e163 + ((.e105 * .e19 + .e304 - .e307) * .e163 * .e7 * .e4/.e10 + (1 - (.e163 * .e7 * .e4/.e298 + .e153)) * .e105) * .e36 * .e37/.e12 - ((0.5 * (.e163 * .e138 * .e23) + 1 - .e153) * .e87 - .e102 * .e163 * .e303 * .e7/.e9) * .e20/.e10)/.e40 - 0.5 * (((((.e200 * .e103 + 2 * (((.e272 + (.e297 + 2 * .e276) * .e19/.e10) * .e10 + .e65 * .e261) * .e23))/.e43 + .e178)/.e43 + .e159/(4 * .e292) + 4 * .e290) * .e71 + .e284 * .e116) * .e163/.e68)) * .e71 - .e157 * .e284 * .e163)/.e68, q2 = geno_a * geno_q * (((((.e273 + .e293 * .e19/.e10) * .e90 + ((.e185 + 0.5 * .e117) * .e7/.e10 + .e222) * .e65) * .e23 + (((.e207 - .e206) * .e105 + 2 * (.e190 + (0.5 * .e189 + 0.5 * .e197)/.e70 - ((.e263 - .e78)/.e9 - 0.25 * .e216) * .e1) - tij * (0.5 * .e195 + .e301) * .e1) * .e7 * .e4/.e10 + (0.5 - 0.5 * (.e8/.e298)) * .e105) * .e36 * .e37/.e12 - (.e129 * .e208/.e40 + ((0.5 + 0.5 * .e150) * .e87 - .e102 * (0.5 * .e87 - .e44) * .e7/.e9) * .e20/.e10))/.e40 - 0.5 * (((((.e188 * .e103 + 2 * (((.e273 + (.e276 + .e293) * .e19/.e10) * .e10 + .e65 * .e266) * .e23))/.e43 + .e264)/.e43 + .e159/(8 * .e292) + 2 * .e290) * .e71 + .e278 * .e116)/.e68)) * .e71 - .e157 * .e278)/.e68, f0 = geno_a * ((.e65 * (.e257/.e40 + .e93 - .e194) * .e23 + (2 * (((.e267 - 0.5 * .e305) * .e120 + .e93 - 1) * .e1/.e10 - .e34 * .e120 * .e137/.e70) + tij * .e120 * .e137 * .e1/.e10) * .e36 * .e37 * .e4/.e12 - (.e114 * .e120/.e10 + 0.5 * (.e116 * .e257/.e68))) * .e71 - .e157 * .e257)/.e243, f2 = geno_a * geno_f * (((.e238/.e40 - .e86) * .e65 * .e23 + (0.5 * (tij * .e137 * .e1/.e10) + 2 * ((0.5 * (.e267 - 1) - 0.25 * .e305) * .e1/.e10 - .e34 * .e137/(4 * .e12))) * .e36 * .e37 * .e4/.e12 - (0.5 * (.e238 * .e116/.e68) + 0.5 * (.e114/.e10))) * .e71 - .e157 * .e238)/.e243, f1 = geno_a * (((.e65 * (.e252/.e40 + 1) * .e1 * .e23 + .e114)/.e10 - ((2 * ((.e267 - (.e34/.e12 + t0 * .e1/.e10) * .e1)/.e10) + 2 * (tij * .e5/.e9)) * .e36 * .e37 * .e4/.e12 + 0.5 * (.e116 * .e252/(.e68 * .e10))) * .e1) * .e71 - .e157 * .e252 * .e1/.e10)/.e243) } d_f_j2_b0_bqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e3 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e15 <- geno_f * (f2 - f0)/2 .e16 <- f0 + .e15 .e17 <- .e12/.e11 .e18 <- r0 - .e17 .e19 <- tij - t0 .e20 <- .e16 - f1 .e21 <- 2 * (.e10/.e18) .e22 <- .e11 + .e21 .e24 <- exp(2 * (.e10 * .e19)) .e25 <- .e5 * .e20 .e26 <- .e4 * .e20 .e27 <- .e22 * .e24 .e28 <- .e16 - m0 .e29 <- .e26/.e10 .e33 <- 2 * (.e25/.e10) - 2 * (.e28 * .e10) .e35 <- exp(-(t0 * .e10)) .e36 <- exp(tij * .e10) .e37 <- .e3/.e10 .e38 <- .e11 - .e27 .e39 <- .e27 - .e11 .e41 <- .e29 + f0 + .e15 .e42 <- 4 * .e37 .e43 <- .e22 * .e3 .e44 <- .e7/.e10 .e45 <- 2 * .e10 .e47 <- .e43 * .e19/.e10 .e52 <- 2 * (.e33 * .e35 * .e36/.e12) .e53 <- 2 * (.e29 - .e16) .e54 <- .e52 - .e53 .e58 <- .e54 * .e3 - .e41 * .e22 * .e24 .e59 <- 4 * .e47 .e60 <- .e45^2 .e61 <- .e58/.e38 .e63 <- (2/.e18 + .e42)/.e18 + .e59 .e64 <- 0.5 * .e44 .e65 <- .e26/.e9 .e67 <- 2 * (.e3 * .e18) .e68 <- .e17 + 2 * (.e10/.e39) .e69 <- .e22 * .e4 .e70 <- .e3^2 .e71 <- yij - .e61 .e72 <- .e33/.e12 .e73 <- .e60 * .e10 .e75 <- 2 * .e72 .e76 <- 2 * (.e25/.e9) .e77 <- 2 * .e28 .e79 <- .e69 * .e20 * .e3 .e86 <- 0.5 * geno_f .e90 <- 4 * (tij * .e33) - 2 * (.e75 + 4 * (0.5 * (t0 * .e33) + 4 * (.e25/.e60) + f0 + .e15 - m0)) .e91 <- .e9 * .e10 .e94 <- .e22 * .e7 * .e19/.e10 .e95 <- 0.5 * geno_q .e96 <- .e76 + .e77 .e97 <- .e61 - .e41 .e98 <- 4 * .e65 .e103 <- .e42 - 2 * (.e63 * .e24 * .e10/.e39) .e106 <- .e90 * .e35 * .e36/.e12 .e108 <- .e44 - .e12/.e3 .e109 <- .e64 - .e17 .e110 <- 1/.e10 .e112 <- .e97 * .e63 + 8 * (.e79/.e73) .e113 <- 1 - .e95 .e115 <- .e103/.e39 + .e110 .e116 <- .e106 + .e98 .e117 <- 1 - .e86 .e120 <- 2 * ((.e108 * .e10/.e67 + .e44)/.e18) .e121 <- 2 * ((.e109 * .e10/.e67 + .e64)/.e18) .e122 <- 2 * .e37 .e124 <- .e112 * .e24 + .e116 * .e70/.e10 .e125 <- 2 * .e18 .e126 <- 2 + .e120 .e127 <- .e5/.e10 .e129 <- .e94 + 1 + .e121 .e130 <- .e37 + 1/.e125 .e132 <- 1/.e18 + .e122 .e134 <- .e126 + 2 * .e94 .e137 <- 2 * (.e130/.e18) .e138 <- 2 * (.e132/.e18) .e139 <- .e124/.e38 .e142 <- 0.5 * (.e115 * .e71/.e68) .e143 <- .e139 + .e142 .e144 <- .e129 * .e24 .e145 <- .e117 * .e4 .e146 <- .e134 * .e24 .e149 <- .e137 + 2 * .e47 .e150 <- .e138 + .e59 .e151 <- .e42 + 4/.e18 .e152 <- tij - (1/.e12 + t0) .e153 <- .e145/.e10 .e155 <- 0.5 * (.e4/.e10) .e157 <- 1 - 0.5 * geno_b .e161 <- .e113 * .e7 .e164 <- .e69 * .e7 * .e20/.e91 .e165 <- .e79/.e91 .e166 <- .e41 - .e61 .e167 <- .e127 - .e10 .e169 <- 2 * ((.e33 * .e152 - .e96) * .e35 * .e36/.e12) + 2 * .e65 .e171 <- 2 * .e127 - .e45 .e175 <- .e12 * .e10 .e177 <- 0.5 - 0.5 * (.e8/.e9) .e178 <- 1 - (.e161 * .e3/.e9 + .e95) .e179 <- .e144 - 1 .e180 <- .e73^2 .e181 <- .e117 * .e171 .e182 <- .e153 + 1 .e183 <- .e43/.e9 .e184 <- .e60/.e10 .e186 <- .e146 - 2 .e187 <- .e25/.e45^4 .e188 <- .e70/.e9 .e189 <- 0.5 * .e96 .e193 <- 0.5 * tij - (0.5 * t0 + 0.5/.e12) .e194 <- 0.5 + .e155 .e195 <- 1 - .e144 .e196 <- 2 - .e146 .e197 <- 2 * .e96 .e201 <- 2 * tij - (2 * t0 + 2/.e12) .e203 <- t0 * .e96/.e10 .e204 <- tij * .e96 .e209 <- ((.e65 + 2 * ((.e193 * .e33 - .e189) * .e35 * .e36/.e12)) * .e7 * .e3/.e10 + 0.5 * .e54 - ((.e129 * .e41 - 0.5 * .e164) * .e24 + .e58 * .e195/.e38))/.e38 .e217 <- ((2 * ((.e33 * .e201 - .e197) * .e35 * .e36/.e12) + .e98) * .e70/.e10 - (.e166 * .e150 - 2 * .e165) * .e24)/.e38 .e218 <- (.e169 * .e7 * .e3/.e10 + .e52 - ((.e41 * .e134 - .e164) * .e24 + .e58 * .e196/.e38 + .e53))/.e38 .e219 <- (.e169 * .e70/.e10 - (.e166 * .e149 - .e165) * .e24)/.e38 .e222 <- .e68 * .e38 .e235 <- (1 + .e121) * .e3 .e237 <- (2 - 4 * (.e4 * .e35 * .e36/.e12)) * .e3 + .e27 .e239 <- (2 * (.e167 * .e35 * .e36/.e12) - 2 * (.e155 - 0.5)) * .e3 - .e194 * .e22 * .e24 .e244 <- (2 * (.e181 * .e35 * .e36/.e12) - 2 * (.e153 + .e86 - 1)) * .e3 - (.e182 - .e86) * .e22 * .e24 .e248 <- .e44 - .e186 * .e10/.e39 .e249 <- .e37 - .e149 * .e24 * .e10/.e39 .e250 <- .e64 - .e179 * .e10/.e39 .e251 <- .e122 - .e150 * .e24 * .e10/.e39 .e252 <- 4 * (.e177/.e10) .e253 <- 4 * (.e178/.e10) .e256 <- .e112 * .e7 * .e19/.e10 .e258 <- .e112 * .e19/.e10 .e262 <- ((.e90 * .e152 - 4 * .e204)/.e10 + 2 * (2 * ((.e72 + .e76 + .e77)/.e175) + 4 * (0.5 * .e203 + 32 * .e187))) * .e35 * .e36/.e12 - (.e106 + 12 * .e65)/.e9 .e263 <- .e209 + (.e109/.e11 + 2 * (.e250/.e39)) * .e71/.e68 .e264 <- (.e108 * .e113 * .e151/.e67 + .e253)/.e18 .e267 <- (.e108/.e11 + 2 * (.e248/.e39)) * .e71/.e68 + .e218 .e268 <- (.e109 * .e151/.e67 + .e252)/.e18 .e269 <- .e217 + (.e110 + 2 * (.e251/.e39)) * .e71/.e68 .e270 <- .e219 + (1/.e45 + 2 * (.e249/.e39)) * .e71/.e68 .e271 <- (.e184 + 8 * .e10) * .e22 .e272 <- (.e151/.e125 - 4 * .e188)/.e18 .e273 <- (.e151/.e18 - 8 * .e188)/.e18 .e275 <- .e177 * .e22 + .e235 .e277 <- .e178 * .e22 + .e113 * .e126 * .e3 .e279 <- .e60 * .e18 * .e10 .e282 <- .e4 * .e7 * .e20/.e91 .e284 <- .e26 * .e3/.e91 .e285 <- .e5/.e60 .e286 <- .e3/.e91 .e287 <- .e70/.e91 .e288 <- .e3^3 .e289 <- .e137 - .e183 .e290 <- .e138 - 2 * .e183 .e291 <- 2 * .e116 c(b0 = (((((.e124 * .e150/.e38 + (.e217 + 2 * .e284) * .e63 + .e97 * (.e273 + 4 * (.e290 * .e3 * .e19))/.e10 + (4 * .e258 + 8 * ((2 * (.e132/.e279) - (16 * .e10 + 2 * .e184) * .e22 * .e3/.e180) * .e4 * .e20)) * .e3) * .e24 + (((.e201 * .e90 - 8 * .e204)/.e10 + 2 * (2 * ((.e75 + .e197)/.e175) + 4 * (64 * .e187 + .e203))) * .e35 * .e36/.e12 - (16 * .e65 + .e291)/.e9) * .e288/.e10)/.e38 - 0.5 * (((((.e150 * .e103 + 2 * (.e63 * .e251 + .e273 + (4 * .e63 + 4 * .e290) * .e3 * .e19)) * .e24/.e39 + 8 * .e287)/.e39 + 2 * .e286) * .e71 + .e269 * .e115)/.e68)) * .e7 + .e139 + .e142) * .e71 - .e143 * .e269 * .e7) * .e157^2/.e68, b2 = geno_b * (((((.e124 * .e149/.e38 + (.e219 + .e284) * .e63 + .e97 * (.e272 + 4 * (.e289 * .e3 * .e19))/.e10 + (2 * .e258 + 8 * ((2 * (.e130/.e279) - .e271 * .e3/.e180) * .e4 * .e20)) * .e3) * .e24 + .e262 * .e288/.e10)/.e38 - 0.5 * (((((.e149 * .e103 + 2 * (.e63 * .e249 + .e272 + (2 * .e63 + 4 * .e289) * .e3 * .e19)) * .e24/.e39 + 4 * .e287)/.e39 + .e286) * .e71 + .e270 * .e115)/.e68)) * .e7 + 0.5 * .e143) * .e71 - .e143 * .e270 * .e7) * .e157/.e68, q0 = (((((.e262 * .e7 * .e3 + .e291) * .e3/.e10 - .e124 * .e196/.e38) * .e113 + (((.e218 + .e282) * .e63 + 2 * .e256 + 8 * ((((.e120 + 4) * .e3 + .e21)/.e73 - .e271 * .e7 * .e3/.e180) * .e4 * .e20)) * .e113 + (.e264 + 4 * (.e277 * .e19/.e10)) * .e97) * .e24)/.e38 + 0.5 * ((((.e253 - (.e186 * .e113 * .e103 + 2 * (((.e264 + (2 * (.e63 * .e113 * .e7) + 4 * .e277) * .e19/.e10) * .e10 + .e63 * .e248 * .e113) * .e24))/.e39)/.e39 - .e161/.e91) * .e71 - .e267 * .e115 * .e113)/.e68)) * .e71 - .e143 * .e267 * .e113) * .e157 * .e6/.e68, q2 = geno_q * (((((((.e193 * .e90 - 2 * .e204)/.e10 + 2 * (2 * ((0.5 * .e72 + .e189)/.e175) + 4 * (0.25 * .e203 + 16 * .e187))) * .e35 * .e36/.e12 - (0.5 * .e116 + .e98)/.e9) * .e7 * .e3 + .e106 + .e98) * .e3/.e10 + (.e256 + (.e209 + 0.5 * .e282) * .e63 + (.e268 + 4 * (.e275 * .e19/.e10)) * .e97 + 8 * (((.e235 + 0.5 * .e22)/.e73 - (0.5 * .e184 + 4 * .e10) * .e22 * .e7 * .e3/.e180) * .e4 * .e20)) * .e24 - .e124 * .e195/.e38)/.e38 + 0.5 * ((((.e252 - (.e179 * .e103 + 2 * ((((.e63 * .e7 + 4 * .e275) * .e19/.e10 + .e268) * .e10 + .e63 * .e250) * .e24))/.e39)/.e39 - 0.5 * (.e7/.e91)) * .e71 - .e263 * .e115)/.e68)) * .e71 - .e143 * .e263) * .e157 * .e6/.e68, f0 = ((((.e244/.e38 + .e86 - .e182) * .e63 + 8 * (.e117 * .e22 * .e4 * .e3/.e73)) * .e24 + ((4 * (tij * .e117 * .e171) - 2 * (2 * (.e181/.e12) + 4 * ((0.5 * (t0 * .e171) + 4 * .e285) * .e117 + 1 - .e86))) * .e35 * .e36/.e12 + 4 * (.e145/.e9)) * .e70/.e10 - 0.5 * (.e244 * .e115/.e68)) * .e71 - .e143 * .e244) * .e157 * .e6/.e222, f2 = geno_f * ((((.e239/.e38 - .e194) * .e63 + 4 * (.e69 * .e3/.e73)) * .e24 + ((4 * (tij * .e167) - 2 * (2 * (.e167/.e12) + 4 * (0.5 + 0.5 * (t0 * .e167) + 2 * .e285))) * .e35 * .e36/.e12 + 2 * (.e4/.e9)) * .e70/.e10 - 0.5 * (.e239 * .e115/.e68)) * .e71 - .e143 * .e239) * .e157 * .e6/.e222, f1 = ((((.e237/.e38 + 1) * .e63 - 8 * (.e43/.e60)) * .e24 + ((2 * (4 * (4/.e60 + t0/.e10) + 4/.e175) - 8 * (tij/.e10)) * .e4 * .e35 * .e36/.e12 - 4/.e9) * .e70 - 0.5 * (.e237 * .e115/.e68)) * .e71 - .e143 * .e237) * .e157 * .e4 * .e6/(.e222 * .e10)) } d_f_j2_b2_bqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e3 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e15 <- geno_f * (f2 - f0)/2 .e16 <- .e12/.e11 .e17 <- f0 + .e15 .e18 <- r0 - .e16 .e19 <- tij - t0 .e20 <- .e17 - f1 .e21 <- 2 * (.e10/.e18) .e22 <- .e11 + .e21 .e24 <- exp(2 * (.e10 * .e19)) .e25 <- .e5 * .e20 .e26 <- .e22 * .e24 .e27 <- .e4 * .e20 .e28 <- .e17 - m0 .e29 <- .e27/.e10 .e33 <- 2 * (.e25/.e10) - 2 * (.e28 * .e10) .e35 <- exp(-(t0 * .e10)) .e36 <- exp(tij * .e10) .e37 <- .e3/.e10 .e38 <- .e26 - .e11 .e39 <- .e11 - .e26 .e41 <- .e29 + f0 + .e15 .e42 <- .e7/.e10 .e43 <- 2 * .e37 .e44 <- 2 * .e10 .e49 <- 2 * (.e33 * .e35 * .e36/.e12) .e50 <- 2 * (.e29 - .e17) .e51 <- .e22 * .e3 .e52 <- .e49 - .e50 .e55 <- 2 * (.e51 * .e19/.e10) .e59 <- .e52 * .e3 - .e41 * .e22 * .e24 .e60 <- .e44^2 .e61 <- .e59/.e39 .e63 <- (1/.e18 + .e43)/.e18 + .e55 .e64 <- 0.5 * .e42 .e66 <- 2 * (.e3 * .e18) .e67 <- .e16 + 2 * (.e10/.e38) .e68 <- .e27/.e9 .e69 <- .e22 * .e4 .e70 <- 0.5 * geno_f .e73 <- .e22 * .e7 * .e19/.e10 .e74 <- 0.5 * geno_q .e75 <- yij - .e61 .e76 <- .e33/.e12 .e77 <- .e60 * .e10 .e78 <- 2 * .e68 .e79 <- .e3^2 .e83 <- .e42 - .e12/.e3 .e84 <- .e64 - .e16 .e86 <- 2 * (.e25/.e9) .e87 <- 2 * .e28 .e89 <- 2 * (tij * .e33) - 2 * (.e76 + 2 * (0.5 * (t0 * .e33) + 4 * (.e25/.e60) + f0 + .e15 - m0)) .e90 <- 1 - .e74 .e94 <- .e61 - .e41 .e95 <- .e9 * .e10 .e97 <- .e69 * .e20 * .e3 .e99 <- .e86 + .e87 .e100 <- .e43 - 2 * (.e63 * .e24 * .e10/.e38) .e103 <- .e89 * .e35 * .e36/.e12 .e104 <- 1 - .e70 .e107 <- 2 * ((.e83 * .e10/.e66 + .e42)/.e18) .e108 <- 2 * ((.e84 * .e10/.e66 + .e64)/.e18) .e110 <- .e94 * .e63 + 4 * (.e97/.e77) .e112 <- .e100/.e38 + 0.5/.e10 .e113 <- 2 * .e18 .e114 <- 2 + .e107 .e115 <- .e103 + .e78 .e116 <- .e5/.e10 .e118 <- .e73 + 1 + .e108 .e119 <- .e37 + 1/.e113 .e121 <- .e114 + 2 * .e73 .e123 <- .e110 * .e24 + .e115 * .e79/.e10 .e125 <- 2 * (.e119/.e18) .e126 <- .e118 * .e24 .e127 <- .e104 * .e4 .e128 <- .e121 * .e24 .e131 <- .e125 + .e55 .e132 <- tij - (1/.e12 + t0) .e134 <- .e123/.e39 + 0.5 * (.e112 * .e75/.e67) .e135 <- .e127/.e10 .e137 <- 0.5 * (.e4/.e10) .e141 <- .e90 * .e7 .e144 <- .e69 * .e7 * .e20/.e95 .e145 <- .e116 - .e10 .e147 <- 2 * ((.e33 * .e132 - .e99) * .e35 * .e36/.e12) + .e78 .e149 <- 2 * .e116 - .e44 .e150 <- .e43 + 2/.e18 .e155 <- 0.5 - 0.5 * (.e8/.e9) .e156 <- 1 - (.e141 * .e3/.e9 + .e74) .e157 <- .e126 - 1 .e158 <- .e104 * .e149 .e159 <- .e135 + 1 .e160 <- .e128 - 2 .e161 <- .e12 * .e10 .e162 <- 0.5 * .e99 .e166 <- 0.5 * tij - (0.5 * t0 + 0.5/.e12) .e167 <- 0.5 + .e137 .e168 <- 1 - .e126 .e169 <- 2 - .e128 .e174 <- ((.e68 + 2 * ((.e166 * .e33 - .e162) * .e35 * .e36/.e12)) * .e7 * .e3/.e10 + 0.5 * .e52 - ((.e118 * .e41 - 0.5 * .e144) * .e24 + .e59 * .e168/.e39))/.e39 .e181 <- (.e147 * .e7 * .e3/.e10 + .e49 - ((.e41 * .e121 - .e144) * .e24 + .e59 * .e169/.e39 + .e50))/.e39 .e182 <- (.e147 * .e79/.e10 - ((.e41 - .e61) * .e131 - .e97/.e95) * .e24)/.e39 .e183 <- .e77^2 .e186 <- .e67 * .e39 .e199 <- (1 + .e108) * .e3 .e201 <- (2 - 4 * (.e4 * .e35 * .e36/.e12)) * .e3 + .e26 .e203 <- (2 * (.e145 * .e35 * .e36/.e12) - 2 * (.e137 - 0.5)) * .e3 - .e167 * .e22 * .e24 .e208 <- (2 * (.e158 * .e35 * .e36/.e12) - 2 * (.e135 + .e70 - 1)) * .e3 - (.e159 - .e70) * .e22 * .e24 .e209 <- .e60/.e10 .e211 <- .e25/.e44^4 .e212 <- .e42 - .e160 * .e10/.e38 .e213 <- .e37 - .e131 * .e24 * .e10/.e38 .e214 <- .e64 - .e157 * .e10/.e38 .e215 <- 2 * (.e155/.e10) .e216 <- 2 * (.e156/.e10) .e218 <- t0 * .e99/.e10 .e219 <- tij * .e99 .e222 <- .e110 * .e7 * .e19/.e10 .e226 <- ((.e89 * .e132 - 2 * .e219)/.e10 + 2 * ((.e76 + .e86 + .e87)/.e161 + 2 * (0.5 * .e218 + 32 * .e211))) * .e35 * .e36/.e12 - (.e103 + 6 * .e68)/.e9 .e227 <- .e174 + (.e84/.e11 + 2 * (.e214/.e38)) * .e75/.e67 .e228 <- (.e83 * .e90 * .e150/.e66 + .e216)/.e18 .e231 <- (.e83/.e11 + 2 * (.e212/.e38)) * .e75/.e67 + .e181 .e232 <- (.e84 * .e150/.e66 + .e215)/.e18 .e233 <- .e182 + (1/.e44 + 2 * (.e213/.e38)) * .e75/.e67 .e234 <- (.e150/.e113 - 2 * (.e79/.e9))/.e18 .e235 <- (.e209 + 8 * .e10) * .e22 .e237 <- .e155 * .e22 + .e199 .e239 <- .e156 * .e22 + .e90 * .e114 * .e3 .e243 <- .e4 * .e7 * .e20/.e95 .e244 <- .e5/.e60 .e245 <- .e125 - .e51/.e9 c(b2 = geno_b^2 * (((((.e123 * .e131/.e39 + (.e182 + .e27 * .e3/.e95) * .e63 + .e94 * (.e234 + 2 * (.e245 * .e3 * .e19))/.e10 + (2 * (.e110 * .e19/.e10) + 4 * ((2 * (.e119/(.e60 * .e18 * .e10)) - .e235 * .e3/.e183) * .e4 * .e20)) * .e3) * .e24 + .e226 * .e3^3/.e10)/.e39 - 0.5 * (((((.e131 * .e100 + 2 * (.e63 * .e213 + .e234 + (2 * .e63 + 2 * .e245) * .e3 * .e19)) * .e24/.e38 + 2 * (.e79/.e95))/.e38 + 0.5 * (.e3/.e95)) * .e75 + .e233 * .e112)/.e67)) * .e7 + 0.5 * .e134) * .e75 - .e134 * .e233 * .e7)/.e67, q0 = geno_b * (((((.e226 * .e7 * .e3 + 2 * .e115) * .e3/.e10 - .e123 * .e169/.e39) * .e90 + (((.e181 + .e243) * .e63 + 2 * .e222 + 4 * ((((.e107 + 4) * .e3 + .e21)/.e77 - .e235 * .e7 * .e3/.e183) * .e4 * .e20)) * .e90 + (.e228 + 2 * (.e239 * .e19/.e10)) * .e94) * .e24)/.e39 + 0.5 * ((((.e216 - (.e160 * .e90 * .e100 + 2 * (((.e228 + (2 * (.e63 * .e90 * .e7) + 2 * .e239) * .e19/.e10) * .e10 + .e63 * .e212 * .e90) * .e24))/.e38)/.e38 - 0.5 * (.e141/.e95)) * .e75 - .e231 * .e112 * .e90)/.e67)) * .e75 - .e134 * .e231 * .e90) * .e6/.e67, q2 = geno_b * geno_q * (((((((.e166 * .e89 - .e219)/.e10 + 2 * ((0.5 * .e76 + .e162)/.e161 + 2 * (0.25 * .e218 + 16 * .e211))) * .e35 * .e36/.e12 - (0.5 * .e115 + .e78)/.e9) * .e7 * .e3 + .e103 + .e78) * .e3/.e10 + (.e222 + (.e174 + 0.5 * .e243) * .e63 + (.e232 + 2 * (.e237 * .e19/.e10)) * .e94 + 4 * (((.e199 + 0.5 * .e22)/.e77 - (0.5 * .e209 + 4 * .e10) * .e22 * .e7 * .e3/.e183) * .e4 * .e20)) * .e24 - .e123 * .e168/.e39)/.e39 + 0.5 * ((((.e215 - (.e157 * .e100 + 2 * ((((.e63 * .e7 + 2 * .e237) * .e19/.e10 + .e232) * .e10 + .e63 * .e214) * .e24))/.e38)/.e38 - 0.25 * (.e7/.e95)) * .e75 - .e227 * .e112)/.e67)) * .e75 - .e134 * .e227) * .e6/.e67, f0 = geno_b * ((((.e208/.e39 + .e70 - .e159) * .e63 + 4 * (.e104 * .e22 * .e4 * .e3/.e77)) * .e24 + ((2 * (tij * .e104 * .e149) - 2 * (.e158/.e12 + 2 * ((0.5 * (t0 * .e149) + 4 * .e244) * .e104 + 1 - .e70))) * .e35 * .e36/.e12 + 2 * (.e127/.e9)) * .e79/.e10 - 0.5 * (.e208 * .e112/.e67)) * .e75 - .e134 * .e208) * .e6/.e186, f2 = geno_b * geno_f * ((((.e203/.e39 - .e167) * .e63 + 2 * (.e69 * .e3/.e77)) * .e24 + ((2 * (tij * .e145) - 2 * (.e145/.e12 + 2 * (0.5 + 0.5 * (t0 * .e145) + 2 * .e244))) * .e35 * .e36/.e12 + .e4/.e9) * .e79/.e10 - 0.5 * (.e203 * .e112/.e67)) * .e75 - .e134 * .e203) * .e6/.e186, f1 = geno_b * ((((.e201/.e39 + 1) * .e63 - 4 * (.e51/.e60)) * .e24 + ((2 * (2 * (4/.e60 + t0/.e10) + 2/.e161) - 4 * (tij/.e10)) * .e4 * .e35 * .e36/.e12 - 2/.e9) * .e79 - 0.5 * (.e201 * .e112/.e67)) * .e75 - .e134 * .e201) * .e4 * .e6/(.e186 * .e10)) } d_f_j2_q0_qff1b_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e6 * .e3 .e9 <- .e7 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e16 <- geno_f * (f2 - f0)/2 .e17 <- r0 - .e13 .e18 <- f0 + .e16 .e19 <- tij - t0 .e20 <- .e11 + 2 * (.e10/.e17) .e21 <- .e18 - f1 .e23 <- exp(2 * (.e10 * .e19)) .e24 <- .e6/.e10 .e25 <- .e7 * .e21 .e26 <- .e20 * .e23 .e27 <- .e11^2 .e29 <- 2 * (.e3 * .e10) .e30 <- .e18 - m0 .e31 <- .e4 * .e21 .e33 <- .e6/.e29 .e34 <- 2 * (.e12/.e27) .e35 <- .e31/.e10 .e39 <- 2 * (.e25/.e10) - 2 * (.e30 * .e10) .e40 <- .e33 - .e34 .e41 <- 2 * .e24 .e42 <- .e20 * .e6 .e44 <- .e42 * .e19/.e10 .e46 <- exp(-(t0 * .e10)) .e47 <- exp(tij * .e10) .e48 <- .e26 - .e11 .e52 <- 2 * (.e40 * .e10/.e17) + .e41 .e53 <- 2 * .e44 .e55 <- .e35 + f0 + .e16 .e56 <- .e11 - .e26 .e58 <- .e52/.e17 + 2 .e59 <- .e58 + .e53 .e60 <- 2 * .e10 .e65 <- 2 * (.e39 * .e46 * .e47/.e12) .e66 <- 2 * (.e35 - .e18) .e67 <- .e60^2 .e68 <- .e65 - .e66 .e72 <- .e68 * .e3 - .e55 * .e20 * .e23 .e73 <- 0.5 * .e24 .e74 <- .e59 * .e23 .e75 <- .e8/.e9 .e76 <- .e3/.e10 .e78 <- 2 * (.e3 * .e17) .e79 <- .e12/.e3 .e80 <- .e72/.e56 .e81 <- .e13 + 2 * (.e10/.e48) .e82 <- .e20 * .e4 .e83 <- .e9 * .e10 .e84 <- yij - .e80 .e85 <- .e67 * .e10 .e86 <- 1 - .e75 .e89 <- 2 * (.e25/.e9) + 2 * .e30 .e90 <- .e24 - .e79 .e91 <- .e73 - .e13 .e92 <- .e74 - 2 .e93 <- .e82 * .e6 .e94 <- 2 - .e74 .e95 <- .e93 * .e21 .e101 <- 0.5 * (t0 * .e39) + 4 * (.e25/.e67) + f0 + .e16 - m0 .e102 <- .e29^2 .e103 <- .e40 * .e39 .e104 <- 2 * .e76 .e109 <- .e90 * .e10/.e78 + .e24 .e112 <- .e91 * .e10/.e78 + .e73 .e115 <- .e20 * .e3 * .e19/.e10 .e116 <- 0.5 * geno_f .e118 <- .e41 - 2 * (.e92 * .e10/.e48) .e125 <- 2 * (2 * (.e103 * .e3/.e12) + 2 * (.e101 * .e6/.e10)) .e126 <- 2 * (tij * .e39 * .e6/.e10) .e127 <- .e76 + 1/(2 * .e17) .e129 <- 1/.e17 + .e104 .e130 <- .e126 - .e125 .e136 <- 2 * (.e112/.e17) .e137 <- 2 + 2 * (.e109/.e17) .e139 <- 4 * (.e95/.e85) - .e59 * .e55 .e142 <- .e118/.e48 + .e33 - .e34 .e143 <- .e86 * .e4 .e144 <- .e31/.e9 .e145 <- 1 - .e116 .e150 <- .e44 + 1 + .e136 .e156 <- .e130 * .e46 * .e47 * .e3/.e12 + .e139 * .e23 - (.e72 * .e94/.e56 + 2 * (.e143 * .e21/.e10 - .e18)) .e157 <- .e137 + .e53 .e158 <- .e7/.e10 .e159 <- .e8/.e102 .e160 <- .e8/.e10 .e161 <- .e5^4 .e164 <- 2 - 2 * .e75 .e166 <- 2 * (.e127/.e17) + 2 * .e115 .e168 <- 2 * (.e129/.e17) + 4 * .e115 .e169 <- .e150 * .e23 .e170 <- .e157 * .e23 .e171 <- .e161/.e83 .e174 <- tij - (1/.e12 + t0) .e178 <- .e156/.e56 + 0.5 * (.e142 * .e84/.e81) .e180 <- 1 - 0.5 * geno_q .e181 <- .e59 * .e3 .e185 <- .e95/.e83 .e188 <- .e82 * .e21 * .e3/.e83 .e189 <- .e42/.e9 .e190 <- .e3^2 .e192 <- 2 * ((.e39 * .e174 - .e89) * .e46 * .e47/.e12) + 2 * .e144 .e196 <- .e145 * .e4/.e10 .e198 <- .e158 - .e10 .e199 <- .e160 + .e10 .e200 <- 0.5 * (.e4/.e10) .e202 <- 0.5 * .e160 + 0.5 * .e10 .e203 <- 1/.e11 .e204 <- 1/.e3 .e205 <- 2 * ((.e24 - 2 * .e79)/.e27) .e206 <- 2 * ((.e73 - .e79)/.e27) .e208 <- 2 * .e158 - .e60 .e209 <- 2 * .e159 .e210 <- 2/.e27 .e211 <- 4 * .e159 .e212 <- 4/.e27 .e213 <- .e80 - .e55 .e214 <- .e169 - 1 .e215 <- .e85^2 .e218 <- .e40 * .e89 .e219 <- .e127 * .e6 .e226 <- (.e209 + .e210) * .e3 .e227 <- .e67/.e10 .e229 <- .e170 - 2 .e230 <- (.e211 + .e212) * .e3 .e231 <- .e25/.e60^4 .e235 <- 0.5 * tij - (0.5 * t0 + 0.5/.e12) .e236 <- 1 - .e169 .e237 <- 1 + .e136 .e238 <- 2 - .e170 .e239 <- 2 * (.e199 * .e6/.e102) .e240 <- 2 * (.e202 * .e6/.e102) .e241 <- 2 * (.e86/.e10) .e242 <- 2 * (.e129 * .e6/.e17) .e243 <- 2 * (.e164/.e10) .e244 <- 2 * .e171 .e248 <- 2 * tij - (2 * t0 + 2/.e12) .e250 <- t0 * .e89/.e10 .e251 <- ((.e90 * .e52/.e11 + 2 * (.e109 * .e40 - (.e239 + .e205) * .e10))/.e17 - .e244)/.e17 .e252 <- ((.e91 * .e52/.e11 + 2 * (.e112 * .e40 - (.e240 + .e206) * .e10))/.e17 - .e171)/.e17 .e253 <- ((.e52/.e60 + 2 * (.e40 * .e127 + .e203 - .e226))/.e17 + .e241)/.e17 .e254 <- ((.e52/.e10 + 2 * (.e40 * .e129 + .e204 - .e230))/.e17 + .e243)/.e17 .e255 <- (.e150 * .e55 - 0.5 * .e185) * .e23 .e258 <- (.e55 * .e157 - .e185) * .e23 .e268 <- .e81 * .e56 .e272 <- (.e144 + 2 * ((.e235 * .e39 - 0.5 * .e89) * .e46 * .e47/.e12)) * .e6 * .e3/.e10 + 0.5 * .e68 .e275 <- .e86 * .e20 + 2 * (.e219/.e17) .e277 <- .e196 + 1 - .e116 .e279 <- .e94/.e56 + 0.5 * (.e142/.e81) .e281 <- .e164 * .e20 + .e242 .e283 <- (2 * ((.e39 * .e248 - 2 * .e89) * .e46 * .e47/.e12) + 4 * .e144) * .e190/.e10 .e287 <- .e192 * .e6 * .e3/.e10 + .e65 .e289 <- .e192 * .e190/.e10 .e296 <- .e24 - .e229 * .e10/.e48 .e297 <- .e76 - .e166 * .e23 * .e10/.e48 .e299 <- .e73 - .e214 * .e10/.e48 .e300 <- 0.5 + .e200 .e301 <- .e237 - 0.5 * .e189 .e302 <- 2 * .e188 .e303 <- .e104 - .e168 * .e23 * .e10/.e48 .e304 <- .e137 - .e189 .e306 <- ((.e213 * .e166 + .e188) * .e23 + .e289)/.e56 + (1/.e60 + 2 * (.e297/.e48)) * .e84/.e81 .e308 <- ((.e213 * .e168 + .e302) * .e23 + .e283)/.e56 + (1/.e10 + 2 * (.e303/.e48)) * .e84/.e81 .e309 <- (.e251 + (2 * .e59 + 2 * .e304) * .e6 * .e19/.e10) * .e23 .e310 <- (.e252 + (.e59 + 2 * .e301) * .e6 * .e19/.e10) * .e23 .e311 <- .e253 + (2 * .e181 + 2 * .e275) * .e19/.e10 .e312 <- .e254 + (2 * .e281 + 4 * .e181) * .e19/.e10 .e315 <- (.e272 - (.e255 + .e72 * .e236/.e56))/.e56 + (.e91/.e11 + 2 * (.e299/.e48)) * .e84/.e81 .e320 <- (.e90/.e11 + 2 * (.e296/.e48)) * .e84/.e81 + (.e287 - (.e258 + .e72 * .e238/.e56 + .e66))/.e56 .e323 <- .e181/.e83 .e324 <- .e59/.e83 .e326 <- (.e227 + 8 * .e10) * .e20 * .e6 .e331 <- .e218 * .e6/.e10 .e332 <- .e218 * .e3 .e333 <- .e40/(.e12 * .e10) .e334 <- .e40/.e12 .e335 <- .e101/.e9 .e338 <- .e143/.e10 .e345 <- (2 - 3 * .e75) * .e4 .e347 <- (2 - 4 * (.e4 * .e46 * .e47/.e12)) * .e3 + .e26 .e349 <- (2 * (.e198 * .e46 * .e47/.e12) - 2 * (.e200 - 0.5)) * .e3 - .e300 * .e20 * .e23 .e351 <- (2 * (.e145 * .e208 * .e46 * .e47/.e12) - 2 * (.e196 + .e116 - 1)) * .e3 - .e277 * .e20 * .e23 .e354 <- .e89 * .e6 * .e3/.e10 .e355 <- .e89/.e10 .e356 <- .e39/.e9 .e359 <- .e139 * .e3 * .e19/.e10 .e361 <- .e139 * .e19/.e10 .e362 <- .e7/.e67 .e363 <- 0.5 * .e250 .e364 <- 2 * .e86 .e365 <- 32 * .e231 .e366 <- 4/.e67 c(q0 = ((((((.e324 + 4 * (.e137/.e85 - .e326/.e215)) * .e4 * .e21 + 2 * .e361) * .e6 - (.e251 + 2 * (.e304 * .e6 * .e19/.e10)) * .e55) * .e23 + (((.e130 * .e174 - 2 * (tij * (.e355 + .e356) * .e6)) * .e6/.e10 - 2 * (2 * ((.e103 - (((.e333 + 2 * (.e199/.e102)) * .e6 + .e205) * .e39 + .e331) * .e3)/.e12) - 2 * ((.e335 + .e363 + .e365) * .e161/.e10))) * .e3 + .e126 - .e125) * .e46 * .e47/.e12 + 2 * (.e345 * .e6 * .e21/.e83) - ((.e287 - (.e258 + .e66)) * .e94 + .e156 * .e238 - (.e309 + .e94 * .e238/.e56) * .e72)/.e56)/.e56 - 0.5 * (((((.e229 * .e118 + 2 * (.e309 * .e10 + .e92 * .e296))/.e48 + .e244)/.e48 + .e239 + .e205) * .e84 + .e320 * .e142)/.e81)) * .e84 - .e320 * .e178) * .e180^2/.e81, q2 = geno_q * ((((((.e235 * .e130 - 2 * (tij * (0.5 * .e355 + 0.5 * .e356) * .e6)) * .e6/.e10 - 2 * (2 * ((0.5 * .e103 - (((0.5 * .e333 + 2 * (.e202/.e102)) * .e6 + .e206) * .e39 + 0.5 * .e331) * .e3)/.e12) - 2 * ((0.25 * .e250 + 0.5 * .e335 + 16 * .e231) * .e161/.e10))) * .e3 + 0.5 * .e130) * .e46 * .e47/.e12 + (((0.5 * .e324 + 4 * (.e237/.e85 - (0.5 * .e227 + 4 * .e10) * .e20 * .e6/.e215)) * .e4 * .e21 + .e361) * .e6 - (.e252 + 2 * (.e301 * .e6 * .e19/.e10)) * .e55) * .e23 + 2 * ((0.5 + 0.5 * .e86 - .e75) * .e4 * .e6 * .e21/.e83) - ((.e272 - .e255) * .e94 + .e156 * .e236 - (.e310 + .e236 * .e94/.e56) * .e72)/.e56)/.e56 - 0.5 * (((((.e214 * .e118 + 2 * (.e310 * .e10 + .e92 * .e299))/.e48 + .e171)/.e48 + .e240 + .e206) * .e84 + .e315 * .e142)/.e81)) * .e84 - .e315 * .e178) * .e180/.e81, f0 = (((2 * (tij * .e145 * .e208 * .e6/.e10) - 2 * (2 * (((0.5 * (t0 * .e208) + 4 * .e362) * .e145 + 1 - .e116) * .e6/.e10) + 2 * (.e40 * .e145 * .e208 * .e3/.e12))) * .e46 * .e47 * .e3/.e12 + (4 * (.e145 * .e20 * .e4 * .e6/.e85) - .e277 * .e59) * .e23 - (.e279 * .e351 + 2 * ((.e338 - 1) * .e145))) * .e84 - .e178 * .e351) * .e180/.e268, f2 = geno_f * (((2 * (.e93/.e85) - .e59 * .e300) * .e23 + (2 * (tij * .e198 * .e6/.e10) - 2 * (2 * (.e198 * .e40 * .e3/.e12) + 2 * ((0.5 + 0.5 * (t0 * .e198) + 2 * .e362) * .e6/.e10))) * .e46 * .e47 * .e3/.e12 + 1 - (.e279 * .e349 + .e338)) * .e84 - .e178 * .e349) * .e180/.e268, f1 = (((2 * ((2 * ((.e366 + t0/.e10) * .e6) + 4 * (.e40 * .e3/.e12))/.e10) - 4 * (tij * .e6/.e9)) * .e4 * .e46 * .e47 * .e3/.e12 + (.e364 - (.e279 * .e347 + (.e20 * (.e366 - 2 * (.e19/.e10)) * .e6 - .e58) * .e23))/.e10) * .e84 - .e178 * .e347/.e10) * .e180 * .e4/.e268, b0 = (((((.e130 * .e248 * .e3 + 2 * (tij * (.e164 * .e39 - 2 * .e354)) - 2 * (2 * (((.e204 - (2 * .e334 + .e211 + .e212) * .e3) * .e39 - 2 * .e332) * .e3/.e12) + 2 * (.e101 * .e164 - (64 * .e231 + .e250) * .e6 * .e3))) * .e46 * .e47/.e12 + 2 * ((2 + .e364 - 4 * .e75) * .e4 * .e21/.e9)) * .e3/.e10 + ((2 * .e323 + 4 * ((.e242 + 2 * .e20)/.e85 - (16 * .e10 + 2 * .e227) * .e20 * .e6 * .e3/.e215)) * .e4 * .e21 + 4 * .e359 - (.e254 + 2 * (.e281 * .e19/.e10)) * .e55) * .e23 - ((.e283 - (.e55 * .e168 - .e302) * .e23) * .e94 - ((.e312 - .e94 * .e168/.e56) * .e72 + .e156 * .e168) * .e23)/.e56)/.e56 + 0.5 * ((((.e204 - .e230)/.e10 + (.e243 - (.e168 * .e118 * .e23 + 2 * (.e312 * .e23 * .e10 + .e92 * .e303))/.e48)/.e48) * .e84 - .e308 * .e142)/.e81)) * .e84 - .e308 * .e178) * (1 - 0.5 * geno_b) * .e180 * .e5/.e81, b2 = geno_b * (((((.e323 + 4 * (((2 * .e219 + .e60)/.e17 + .e11)/.e85 - .e326 * .e3/.e215)) * .e4 * .e21 + 2 * .e359 - (.e253 + 2 * (.e275 * .e19/.e10)) * .e55) * .e23 + ((.e130 * .e3 * .e174 + 2 * (tij * (.e86 * .e39 - .e354)) - 2 * (2 * (((.e203 - (.e334 + .e209 + .e210) * .e3) * .e39 - .e332) * .e3/.e12) + 2 * (.e101 * .e86 - (.e363 + .e365) * .e6 * .e3))) * .e46 * .e47/.e12 + 2 * (.e345 * .e21/.e9)) * .e3/.e10 - ((.e289 - (.e55 * .e166 - .e188) * .e23) * .e94 - ((.e311 - .e94 * .e166/.e56) * .e72 + .e156 * .e166) * .e23)/.e56)/.e56 + 0.5 * ((((.e203 - .e226)/.e10 + (.e241 - (.e166 * .e118 * .e23 + 2 * (.e311 * .e23 * .e10 + .e92 * .e297))/.e48)/.e48) * .e84 - .e306 * .e142)/.e81)) * .e84 - .e306 * .e178) * .e180 * .e5/.e81) } d_f_j2_q2_qff1b_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e6 * .e3 .e9 <- .e7 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e17 <- geno_f * (f2 - f0)/2 .e18 <- f0 + .e17 .e19 <- tij - t0 .e20 <- .e11 + 2 * (.e10/.e14) .e22 <- exp(2 * (.e10 * .e19)) .e23 <- .e18 - f1 .e24 <- .e20 * .e22 .e25 <- .e7 * .e23 .e26 <- .e6/.e10 .e27 <- .e11^2 .e29 <- 2 * (.e3 * .e10) .e30 <- .e4 * .e23 .e31 <- .e18 - m0 .e34 <- .e6/.e29 - 2 * (.e12/.e27) .e35 <- .e30/.e10 .e39 <- 2 * (.e25/.e10) - 2 * (.e31 * .e10) .e41 <- .e24 - .e11 .e42 <- exp(-(t0 * .e10)) .e43 <- exp(tij * .e10) .e44 <- .e20 * .e6 .e47 <- .e34 * .e10/.e14 + .e26 .e49 <- .e44 * .e19/.e10 .e51 <- .e35 + f0 + .e17 .e52 <- .e11 - .e24 .e55 <- .e47/.e14 + .e49 + 1 .e56 <- 2 * .e10 .e57 <- 0.5 * .e26 .e63 <- 2 * (.e39 * .e42 * .e43/.e12) - 2 * (.e35 - .e18) .e64 <- .e56^2 .e68 <- .e63 * .e3 - .e51 * .e20 * .e22 .e69 <- .e3/.e10 .e70 <- .e55 * .e22 .e71 <- .e68/.e52 .e72 <- .e13 + 2 * (.e10/.e41) .e73 <- .e57 - .e13 .e74 <- yij - .e71 .e75 <- .e8/.e9 .e76 <- 2 * .e69 .e77 <- .e70 - 1 .e80 <- .e73 * .e10/(2 * (.e3 * .e14)) + .e57 .e83 <- .e20 * .e3 * .e19/.e10 .e85 <- 0.5 * geno_f .e86 <- 1 - .e70 .e88 <- 2 * (.e25/.e9) + 2 * .e31 .e90 <- 2 * (.e24/.e64) .e92 <- .e3/.e9 + .e90 .e93 <- .e69 + 1/(2 * .e14) .e95 <- 1/.e14 + .e76 .e98 <- .e92 * .e6 .e99 <- .e29^2 .e101 <- .e26 - 2 * (.e77 * .e10/.e41) .e106 <- 0.5 * (t0 * .e39) + 4 * (.e25/.e64) + f0 + .e17 - m0 .e108 <- .e9 * .e10 .e109 <- .e98 - 1 .e110 <- 2 * (.e80/.e14) .e116 <- .e101/.e41 + 0.5 * .e34 .e117 <- .e30/.e9 .e122 <- tij * .e39 * .e6/.e10 - 2 * (.e34 * .e39 * .e3/.e12 + .e106 * .e6/.e10) .e124 <- .e49 + 1 + .e110 .e125 <- 1 - .e85 .e127 <- .e42 * .e43 * .e3 .e128 <- .e109 * .e4 .e131 <- .e7/.e10 .e133 <- 2 * (.e93/.e14) .e134 <- 2 * (.e95/.e14) .e135 <- 2 * (.e8/.e99) .e136 <- 2/.e27 .e145 <- .e128 * .e23/.e10 + .e127 * .e122/.e12 + f0 + .e17 - (.e55 * .e51 * .e22 + .e68 * .e86/.e52) .e146 <- .e20 * .e4 .e147 <- 1 - .e75 .e148 <- 2 - 2 * .e75 .e149 <- .e133 + 2 * .e83 .e150 <- .e134 + 4 * .e83 .e151 <- .e135 + .e136 .e152 <- .e124 * .e22 .e153 <- .e151 * .e3 .e154 <- .e3^2 .e156 <- .e145/.e52 + 0.5 * (.e116 * .e74/.e72) .e159 <- .e146 * .e23 * .e3/.e108 .e160 <- .e5^4 .e165 <- .e125 * .e4/.e10 .e167 <- .e131 - .e10 .e168 <- .e19/.e10 .e169 <- 0.5 * (.e4/.e10) .e170 <- 1/.e11 .e171 <- 1/.e3 .e173 <- 2 * ((0.5 * (.e8/.e10) + 0.5 * .e10) * .e6/.e99) + 2 * ((.e57 - .e12/.e3)/.e27) .e175 <- 2 * .e131 - .e56 .e176 <- .e55 * .e3 .e177 <- .e71 - .e51 .e178 <- .e152 - 1 .e179 <- .e147/.e10 .e180 <- .e148/.e10 .e182 <- 0.5 * (.e160/.e108) .e186 <- 0.5 * tij - (0.5 * t0 + 0.5/.e12) .e187 <- 1 - .e152 .e190 <- 2 * .e153 .e191 <- 2 * .e117 .e195 <- 2 * tij - (2 * t0 + 2/.e12) .e196 <- tij - (1/.e12 + t0) .e197 <- ((.e47 * .e73/.e11 + .e80 * .e34 - .e173 * .e10)/.e14 - .e182)/.e14 .e198 <- ((.e47/.e56 + .e34 * .e93 + .e170 - .e153)/.e14 + .e179)/.e14 .e199 <- ((.e47/.e10 + .e34 * .e95 + .e171 - .e190)/.e14 + .e180)/.e14 .e200 <- (.e124 * .e51 - 0.5 * (.e146 * .e6 * .e23/.e108)) * .e22 .e213 <- .e72 * .e52 .e217 <- (.e117 + 2 * ((.e186 * .e39 - 0.5 * .e88) * .e42 * .e43/.e12)) * .e6 * .e3/.e10 + 0.5 * .e63 .e218 <- .e51 * .e19 .e219 <- .e34 * .e88 .e223 <- .e86/.e52 + 0.5 * (.e116/.e72) .e224 <- .e147 * .e20 .e226 <- .e165 + 1 - .e85 .e230 <- .e148 * .e20 + 2 * (.e95 * .e6/.e14) .e232 <- (2 * ((.e39 * .e195 - 2 * .e88) * .e42 * .e43/.e12) + 4 * .e117) * .e154/.e10 .e234 <- (2 * ((.e39 * .e196 - .e88) * .e42 * .e43/.e12) + .e191) * .e154/.e10 .e242 <- .e25/.e56^4 .e243 <- .e69 - .e149 * .e22 * .e10/.e41 .e244 <- .e57 - .e178 * .e10/.e41 .e245 <- 0.5 + .e169 .e246 <- 2 * (.e93 * .e6/.e14) .e247 <- 2 * .e159 .e248 <- .e76 - .e150 * .e22 * .e10/.e41 .e250 <- t0 * .e88/.e10 .e251 <- (.e197 + ((.e47 + 2 * .e80)/.e14 + (.e168 - 0.5/.e9) * .e20 * .e6 + 2) * .e6 * .e19/.e10) * .e22 .e253 <- ((.e177 * .e149 + .e159) * .e22 + .e234)/.e52 + (1/.e56 + 2 * (.e243/.e41)) * .e74/.e72 .e255 <- ((.e177 * .e150 + .e247) * .e22 + .e232)/.e52 + (1/.e10 + 2 * (.e248/.e41)) * .e74/.e72 .e256 <- .e198 + (.e224 + 2 * .e176 + .e246) * .e19/.e10 .e257 <- .e199 + (.e230 + 4 * .e176) * .e19/.e10 .e260 <- (.e217 - (.e200 + .e68 * .e187/.e52))/.e52 + (.e73/.e11 + 2 * (.e244/.e41)) * .e74/.e72 .e267 <- .e219 * .e3 .e268 <- .e34/.e12 .e278 <- (2 - 4 * (.e4 * .e42 * .e43/.e12)) * .e3 + .e24 .e280 <- (2 * (.e167 * .e42 * .e43/.e12) - 2 * (.e169 - 0.5)) * .e3 - .e245 * .e20 * .e22 .e282 <- (2 * (.e125 * .e175 * .e42 * .e43/.e12) - 2 * (.e165 + .e85 - 1)) * .e3 - .e226 * .e20 * .e22 .e285 <- .e88 * .e6 * .e3/.e10 .e286 <- .e7/.e64 .e287 <- .e154/.e9^2 .e288 <- 4/.e64 c(q2 = geno_q^2 * (((((.e186 * .e6 * .e3/.e10 + 0.5) * .e122 - (2 * ((.e34 * (0.5 - 0.5 * (.e8/(.e12 * .e10))) * .e39 - (.e173 * .e39 + 0.5 * (.e219 * .e6/.e10)) * .e3)/.e12 - (0.25 * .e250 + 0.5 * (.e106/.e9) + 16 * .e242) * .e160/.e10) + tij * (0.5 * (.e88/.e10) + 0.5 * (.e39/.e9)) * .e160/.e10) * .e3) * .e42 * .e43/.e12 + ((0.5 - (.e75 + 0.5 * .e109))/.e9 + 2 * (((.e168 - .e288) * .e20 * .e6 + 1 + .e110) * .e22/.e64)) * .e4 * .e6 * .e23/.e10 - (((.e197 + (1 + .e110 - 0.5 * (.e44/.e9)) * .e6 * .e19/.e10) * .e51 + .e55 * (.e218 - 0.5 * .e117) * .e6/.e10) * .e22 + (.e145 * .e187 + (.e217 - .e200) * .e86 - (.e251 + .e86 * .e187/.e52) * .e68)/.e52))/.e52 - 0.5 * (((((.e178 * .e101 + 2 * (.e251 * .e10 + .e77 * .e244))/.e41 + .e182)/.e41 + 0.5 * .e173) * .e74 + .e260 * .e116)/.e72)) * .e74 - .e156 * .e260)/.e72, f0 = geno_q * ((.e109 * .e125 * .e4/.e10 + 1 + .e127 * (tij * .e125 * .e175 * .e6/.e10 - 2 * (((0.5 * (t0 * .e175) + 4 * .e286) * .e125 + 1 - .e85) * .e6/.e10 + .e34 * .e125 * .e175 * .e3/.e12))/.e12 - (.e55 * .e226 * .e22 + .e223 * .e282 + .e85)) * .e74 - .e156 * .e282)/.e213, f2 = geno_f * geno_q * ((0.5 * (.e128/.e10 + 1) + .e127 * (tij * .e167 * .e6/.e10 - 2 * (.e167 * .e34 * .e3/.e12 + (0.5 + 0.5 * (t0 * .e167) + 2 * .e286) * .e6/.e10))/.e12 - (.e55 * .e245 * .e22 + .e223 * .e280)) * .e74 - .e156 * .e280)/.e213, f1 = geno_q * (((2 * (((.e288 + t0/.e10) * .e6 + 2 * (.e34 * .e3/.e12))/.e10) - 2 * (tij * .e6/.e9)) * .e4 * .e42 * .e43 * .e3/.e12 - (.e223 * .e278 + .e98 - (.e70 + 1))/.e10) * .e74 - .e156 * .e278/.e10) * .e4/.e213, b0 = geno_q * ((((((2 * ((.e20 * (4 * .e168 - 16/.e64) * .e3 + .e134) * .e22/.e64) - 4 * .e287) * .e6 + 2 * .e92 - 2 * (.e109 * .e3/.e9)) * .e4 * .e23 + (.e195 * .e3 * .e122 + tij * (.e148 * .e39 - 2 * .e285) - 2 * ((((.e171 - (2 * .e268 + 2 * .e151) * .e3) * .e39 - 2 * .e267)/.e12 - (64 * .e242 + .e250) * .e6) * .e3 + .e106 * .e148)) * .e42 * .e43 * .e3/.e12)/.e10 - (((.e199 + .e230 * .e19/.e10) * .e51 + .e55 * (4 * .e218 - .e191) * .e3/.e10) * .e22 + ((.e232 - (.e51 * .e150 - .e247) * .e22) * .e86 - ((.e257 - .e86 * .e150/.e52) * .e68 + .e145 * .e150) * .e22)/.e52))/.e52 + 0.5 * ((((.e180 - (.e101 * .e150 * .e22 + 2 * (.e257 * .e22 * .e10 + .e77 * .e248))/.e41)/.e41 + 0.5 * ((.e171 - .e190)/.e10)) * .e74 - .e255 * .e116)/.e72)) * .e74 - .e255 * .e156) * (1 - 0.5 * geno_b) * .e5/.e72, b2 = geno_b * geno_q * ((((((2 - .e98) * .e3/.e9 + (2 * (((2 * .e168 - 8/.e64) * .e20 * .e3 + .e133) * .e22/.e64) - 2 * .e287) * .e6 + .e90) * .e4 * .e23 + (.e3 * .e196 * .e122 + tij * (.e147 * .e39 - .e285) - 2 * ((((.e170 - (.e268 + .e135 + .e136) * .e3) * .e39 - .e267)/.e12 - (0.5 * .e250 + 32 * .e242) * .e6) * .e3 + .e106 * .e147)) * .e42 * .e43 * .e3/.e12)/.e10 - (((.e198 + (.e224 + .e246) * .e19/.e10) * .e51 + .e55 * (2 * .e218 - .e117) * .e3/.e10) * .e22 + ((.e234 - (.e51 * .e149 - .e159) * .e22) * .e86 - ((.e256 - .e86 * .e149/.e52) * .e68 + .e145 * .e149) * .e22)/.e52))/.e52 + 0.5 * ((((.e179 - (.e101 * .e149 * .e22 + 2 * (.e256 * .e22 * .e10 + .e77 * .e243))/.e41)/.e41 + 0.5 * ((.e170 - .e153)/.e10)) * .e74 - .e253 * .e116)/.e72)) * .e74 - .e253 * .e156) * .e5/.e72) } d_f_j2_f0_ff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e7 <- sqrt(.e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3)) .e8 <- 2 * .e3 .e9 <- .e4 + .e7 .e10 <- .e9/.e8 .e11 <- .e8 + 2 * (.e7/(r0 - .e10)) .e13 <- exp(2 * (.e7 * (tij - t0))) .e14 <- .e4/.e7 .e15 <- 0.5 * geno_f .e16 <- .e11 * .e13 .e18 <- 1 - .e15 .e19 <- exp(-(t0 * .e7)) .e20 <- exp(tij * .e7) .e23 <- 2 * (.e5/.e7) - 2 * .e7 .e26 <- .e23 * .e19 * .e20/.e9 .e27 <- (.e10 + 2 * (.e7/(.e16 - .e8))) * (.e8 - .e16)^2 .e31 <- (2 * .e26 - 2 * (.e14 - 1)) * .e3 - (.e14 + 1) * .e11 * .e13 .e33 <- .e18 * .e4/.e7 .e34 <- 0.5 * .e14 c(f0 = -(((2 * (.e18 * .e23 * .e19 * .e20/.e9) - 2 * (.e33 + .e15 - 1)) * .e3 - (.e33 + 1 - .e15) * .e11 * .e13) * .e31 * .e18/.e27), f2 = -(geno_f * ((.e26 - 2 * (.e34 - 0.5)) * .e3 - (0.5 + .e34) * .e11 * .e13) * .e31 * .e18/.e27), f1 = .e31 * ((4 * (.e4 * .e19 * .e20/.e9) - 2) * .e3 - .e16) * .e18 * .e4/(.e27 * .e7)) } d_f_j2_f2_ff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e7 <- sqrt(.e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3)) .e8 <- 2 * .e3 .e9 <- .e4 + .e7 .e10 <- .e9/.e8 .e11 <- .e8 + 2 * (.e7/(r0 - .e10)) .e13 <- exp(2 * (.e7 * (tij - t0))) .e14 <- .e4/.e7 .e15 <- .e11 * .e13 .e17 <- exp(-(t0 * .e7)) .e18 <- exp(tij * .e7) .e21 <- (2 * (.e5/.e7) - 2 * .e7) * .e17 * .e18/.e9 .e23 <- (.e21 + 1 - .e14) * .e3 - 0.5 * ((.e14 + 1) * .e11 * .e13) .e24 <- (.e10 + 2 * (.e7/(.e15 - .e8))) * (.e8 - .e15)^2 .e25 <- 0.5 * .e14 c(f2 = -(geno_f^2 * ((.e21 - 2 * (.e25 - 0.5)) * .e3 - (0.5 + .e25) * .e11 * .e13) * .e23/.e24), f1 = geno_f * .e23 * ((4 * (.e4 * .e17 * .e18/.e9) - 2) * .e3 - .e15) * .e4/(.e24 * .e7)) } d_f_j2_f1_f1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, m0, r0, tij, yij, t0, geno_a, geno_b, geno_q, geno_f) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- .e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3) .e7 <- sqrt(.e6) .e8 <- 2 * .e3 .e9 <- .e4 + .e7 .e10 <- .e9/.e8 .e11 <- (.e8 + 2 * (.e7/(r0 - .e10))) * exp(2 * (.e7 * (tij - t0))) .e16 <- 4 * (.e4 * exp(-(t0 * .e7)) * exp(tij * .e7)/.e9) ((2 - .e16) * .e3 + .e11) * ((.e16 - 2) * .e3 - .e11) * .e5/((.e10 + 2 * (.e7/(.e11 - .e8))) * (.e8 - .e11)^2 * .e6^1) } deriv_mu_int_a0_abqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_a * (a2 - a0)/2 .e4 <- a0 + .e3 .e7 <- geno_q * (q2 - q0)/2 + q0 .e8 <- .e4^2 .e9 <- b0 + geno_b * (b2 - b0)/2 .e10 <- .e9^2 .e11 <- .e10 * .e7 .e12 <- .e8 + 2 * .e11 .e13 <- sqrt(.e12) .e14 <- 2 * .e7 .e15 <- .e4 + .e13 .e16 <- .e15/.e14 .e17 <- r0 - .e16 .e20 <- geno_f * (f2 - f0)/2 .e21 <- f0 + .e20 .e22 <- 2 * (.e13/.e17) .e23 <- .e4/.e13 .e24 <- .e14 + .e22 .e25 <- .e21 - f1 .e26 <- tij - t0 .e27 <- .e7 * .e17 .e28 <- .e23 + 1 .e29 <- .e21 - m0 .e30 <- .e8 * .e25 .e32 <- exp(2 * (.e13 * .e26)) .e35 <- 0.5 * geno_a .e37 <- 2 * (.e30/.e13) - 2 * (.e29 * .e13) .e38 <- 2 * .e13 .e40 <- .e28 * .e13/.e27 .e41 <- 2 * .e23 .e42 <- .e40 + .e41 .e43 <- 1 - .e35 .e45 <- .e14 - .e24 * .e32 .e46 <- t0 * .e13 .e47 <- .e42/.e17 .e48 <- .e8/.e12 .e49 <- .e38^2 .e50 <- .e10/.e13 .e51 <- .e24 * .e4 .e53 <- exp(-.e46) .e54 <- 2 * .e27 .e56 <- .e51 * .e26/.e13 .e57 <- t0 * .e24 .e59 <- .e57 * .e4/.e13 .e60 <- .e47 - 2 * .e59 .e61 <- 2 * .e56 .e62 <- .e47 + .e61 .e63 <- 4 * .e48 .e64 <- t0 * .e37 .e65 <- 8 - .e63 .e66 <- .e43 * .e4 .e67 <- 0.5 * .e64 .e71 <- 2 * (.e67 + f0 + .e20 - m0) .e73 <- .e66/.e13 .e74 <- 0.5 * .e23 .e75 <- exp(-(2 * .e46)) .e77 <- .e65 * .e25/2 .e79 <- .e27/.e38 + 0.5 .e81 <- .e7/.e45 - 0.5 .e83 <- .e77 - .e71 .e84 <- exp(-(tij * .e13)) .e85 <- 0.5 * .e50 .e86 <- .e43 * .e8 .e89 <- .e83 * .e4/.e13 - .e28 * .e37/.e15 .e90 <- .e7/.e13 .e91 <- .e62 * .e32 .e93 <- .e86/.e12 + .e35 .e94 <- .e45^2 .e95 <- .e24 * .e49 .e97 <- (-.e22)^2 .e98 <- 2 * .e29 .e99 <- 1 - .e93 .e100 <- .e97 * .e17 .e102 <- .e73 + 1 - .e35 .e103 <- 0.5 + .e74 .e104 <- .e30/.e12 .e105 <- 2 * .e104 .e106 <- t0 * .e79 .e107 <- tij * .e81 .e109 <- .e50 - .e15/.e7 .e110 <- .e85 - .e16 .e111 <- .e42 * .e7 .e112 <- .e12 * .e13 .e114 <- .e24 * .e15^2 * .e75 .e115 <- .e106 * .e4 .e117 <- .e107 * .e4/.e13 .e124 <- .e111/.e100 + .e115/.e13 .e128 <- 2 * (.e60 * .e13) + 4 * (.e51/.e13) .e130 <- 4 * .e89 - 2 * (.e60 * .e37/.e24) .e131 <- .e117 - .e91 * .e7/.e94 .e132 <- .e4 * .e10 .e133 <- .e105 + .e98 .e134 <- .e4 * .e7 .e135 <- .e25^2 .e136 <- 0.5 * .e48 .e137 <- .e53^2 .e139 <- .e124 * .e53 + .e84 * .e131 .e140 <- 2 * .e90 .e142 <- (-(4 * (.e12/.e17)))^2 .e145 <- .e102 * .e13/.e54 + .e73 .e148 <- .e103 * .e13/.e54 + .e74 .e149 <- .e90 + 1/(2 * .e17) .e151 <- 1/.e17 + .e140 .e152 <- .e24 * .e10 .e153 <- .e24 * .e7 .e154 <- 32 * .e37 .e155 <- .e142 * .e17 .e156 <- (2 * (.e45 * .e13))^2 .e158 <- .e79 * .e53 + .e81 * .e84 .e161 <- .e109 * .e13/.e54 + .e50 .e164 <- .e110 * .e13/.e54 + .e85 .e165 <- 0.5 * geno_q .e168 <- .e99 * .e4 .e169 <- .e128 * .e37 .e170 <- .e45 * .e4 .e172 <- 2 * (.e164/.e17) .e173 <- 2 + 2 * (.e161/.e17) .e177 <- (32 * .e89 - 64 * (.e169 * .e13/.e95)) * .e4 + .e154 .e178 <- .e132/.e112 .e179 <- .e170/.e13 .e182 <- 2 * (.e8/.e13) - .e38 .e184 <- t0 * .e49/.e13 .e188 <- .e168 * .e135/.e49 .e191 <- 2 * (.e42 * .e13) + 4 * .e4 .e193 <- 2 * .e179 - 2 * (.e91 * .e13) .e195 <- .e152 * .e26/.e13 .e197 <- .e153 * .e26/.e13 .e198 <- .e132/.e12 .e199 <- .e134/.e112 .e200 <- .e134/.e12 .e201 <- 0.5 - .e136 .e202 <- 0.5 * geno_f .e203 <- 1 - .e165 .e205 <- .e43 * .e24 .e207 <- 2 * (.e149/.e17) .e208 <- 2 * (.e151/.e17) .e209 <- 64 * .e188 .e210 <- .e139 * .e37 .e216 <- (2 * (.e37 * .e53 * .e7/.e15))^2 .e217 <- .e24 * .e75 .e218 <- 1 - .e202 .e220 <- 2 * (.e43 * .e37 * .e130 * .e137 * .e7/.e114) + .e209 .e221 <- .e158 * .e177 .e223 <- .e17/.e38 + 1/.e45 .e225 <- .e221 - 32 * (.e210 * .e4) .e226 <- .e99/.e49 .e227 <- .e152/.e12 .e228 <- .e153/.e12 .e229 <- 1 - .e48 .e230 <- 1 + .e172 .e234 <- .e191/.e155 + .e193/.e156 .e236 <- .e95 * .e15 * .e75 .e237 <- 2 * (.e145/.e17) .e238 <- 2 * (.e148/.e17) .e239 <- 2 * .e12 .e240 <- (.e4 * .e25/.e38)^2 .e242 <- .e109/2 + .e16 .e243 <- .e110/2 .e245 <- .e205 * .e4 .e249 <- 2 * ((1 - .e136) * .e25) + m0 - .e21 .e250 <- 2 * ((2 - .e48) * .e25) .e251 <- .e99/.e13 .e252 <- .e250 - .e98 .e254 <- 8 - 2 * .e184 .e255 <- .e62 * .e10 .e256 <- .e62 * .e7 .e257 <- .e145 * .e28 .e258 <- .e148 * .e28 .e259 <- (.e195 + 1 + .e172) * .e32 .e261 <- .e28 * (.e50 - (r0 - .e242) * .e13/.e27) .e263 <- .e28 * .e149 - .e200 .e264 <- .e28 * (.e85 - (0.5 * .e17 - .e243) * .e13/.e27) .e266 <- .e28 * .e151 - 2 * .e200 .e271 <- .e86/.e12^2 .e273 <- .e216/.e217 + 32 * (.e240 * .e7) .e275 <- .e37 * .e4/.e12 .e276 <- .e37/.e15 .e277 <- .e56 + .e238 .e278 <- (.e173 + 2 * .e195) * .e32 .e279 <- 0.5 * .e198 .e280 <- .e237 + 2 * (.e245 * .e26/.e13) .e281 <- .e207 + 2 * .e197 .e282 <- 2 * (.e201/.e13) .e283 <- 2 * .e251 .e284 <- .e208 + 4 * .e197 .e285 <- 2 * .e178 .e286 <- 2 * .e199 .e287 <- 4 * .e199 .e289 <- t0 * .e133/.e13 .e290 <- .e100^2 .e291 <- .e155^2 .e292 <- .e91 + .e42 * .e45/.e38 .e294 <- .e114^2 .e295 <- .e277 * .e32 .e296 <- .e217^2 .e297 <- .e229 * .e43 .e298 <- .e280 * .e32 .e299 <- .e281 * .e32 .e300 <- .e284 * .e32 .e301 <- .e45 * .e10 .e302 <- .e45 * .e7 .e303 <- .e24 * (4 - .e184) .e304 <- .e24 * .e254 .e305 <- .e65/2 .e306 <- .e27/.e12 .e308 <- 0.5 * .e83 .e309 <- 1 - .e259 .e310 <- .e230 - 0.5 * .e227 .e311 <- 2 - .e278 .e312 <- .e207 - .e228 .e313 <- .e208 - 2 * .e228 .e314 <- .e173 - .e227 .e316 <- 32 * (.e89 * .e4) + .e154 .e317 <- 8 * .e226 .e319 <- t0 * .e124 * .e53 .e321 <- tij * .e84 * .e131 .e322 <- ((.e42 * .e109/2 + .e261 - .e198)/.e27 - .e285)/.e17 .e323 <- ((.e42 * .e110/2 + .e264 - .e279)/.e27 - .e178)/.e17 .e325 <- (.e257 + .e42 * .e102/2 + 1 - .e93)/.e27 + .e283 .e326 <- (.e263/.e7 + .e42/.e38)/.e17 .e327 <- (.e266/.e7 + .e42/.e13)/.e17 .e329 <- (.e42 * .e103/2 + .e258 + 0.5 - .e136)/.e27 + .e282 .e330 <- t0 * .e130 .e331 <- t0 * .e4 .e332 <- .e325/.e17 .e333 <- (.e326 - .e286)/.e17 .e334 <- (.e327 - .e287)/.e17 .e335 <- .e329/.e17 .e336 <- .e60 * .e133 .e338 <- .e62 * .e43 * .e4 .e339 <- .e62 * .e4 .e343 <- ((.e276 + .e105 + .e98) * .e28 + .e275)/.e15 + (((.e63 - .e305) * .e25 + .e71)/.e12 + .e289) * .e4 .e347 <- .e201 * .e24 + 2 * (.e148 * .e4/.e17) .e349 <- .e297 * .e24 + 2 * (.e145 * .e4/.e17) .e352 <- .e43 * .e252 * .e4/.e13 .e353 <- .e43 * .e45 .e354 <- .e310 * .e4 .e355 <- .e312 * .e4 .e357 <- .e249 * .e4/.e13 .e358 <- .e313 * .e4 .e359 <- .e133 * .e130 .e360 <- .e302/.e12 .e361 <- .e38^3 .e362 <- .e314 * .e4 .e363 <- .e15 * .e13 .e364 <- 0.5 * .e133 .e366 <- 2 * .e271 - .e317 .e367 <- 2 * .e133 .e368 <- 4 * .e226 .e369 <- t0 * .e43 .e370 <- t0 * .e15 .e371 <- .e331/.e13 .e372 <- .e322 + (2 * .e255 + 2 * .e362) * .e26/.e13 .e373 <- .e323 + (.e255 + 2 * .e354) * .e26/.e13 .e374 <- .e335 + (.e339 + 2 * .e347) * .e26/.e13 .e375 <- .e139 * .e133 .e377 <- (.e257 + 1 - .e93)/.e27 + .e283 .e379 <- (.e258 + 0.5 - .e136)/.e27 + .e282 .e383 <- (.e261 - .e198)/.e27 - .e285 .e385 <- .e263/.e27 - .e286 .e387 <- (.e264 - .e279)/.e27 - .e178 .e389 <- .e266/.e27 - .e287 .e394 <- .e168 * .e25 .e395 <- .e353 * .e4 .e398 <- .e205 * .e254 * .e4 + 2 * (.e145 * .e49/.e17) .e400 <- .e203 * .e10 * .e7 .e402 <- .e230 * .e49 + .e303 * .e10 .e407 <- (16 - 4 * .e184) * .e24 * .e7 + 2 * (.e151 * .e49/.e17) .e412 <- (2 * .e338 + 2 * .e349) * .e26/.e13 .e414 <- (2 * .e256 + 2 * .e355) * .e26/.e13 .e415 <- .e299/.e94 .e416 <- .e366 * .e4 .e417 <- .e300/.e94 .e419 <- (2 * .e358 + 4 * .e256) * .e26/.e13 .e420 <- .e301/.e12 .e422 <- .e303 * .e4 + 2 * (.e148 * .e49/.e17) .e424 <- .e304 * .e10 + .e49 * .e173 .e426 <- .e304 * .e7 + 2 * (.e149 * .e49/.e17) .e428 <- .e306 + 1/.e38 .e429 <- 0.5 - .e11/.e239 .e431 <- 1/.e13 + 2 * .e306 .e432 <- 2 * .e64 .e433 <- 32 - 64 * (.e128 * .e4 * .e13/.e95) .e434 <- .e319 + .e321 .e435 <- .e369 * .e4 .e436 <- .e332 + .e412 .e437 <- .e333 + .e414 .e438 <- .e334 + .e419 .e439 <- .e139 * .e43 .e441 <- .e375 * .e7/.e13 .e444 <- .e60 * .e43 .e446 <- .e336 * .e10/.e13 .e448 <- .e336 * .e7/.e13 .e449 <- .e60 * .e4 .e451 <- .e60 * .e10/.e13 .e453 <- .e60 * .e7/.e13 .e454 <- .e255/.e13 .e455 <- .e256/.e13 .e460 <- .e225 * .e53 * .e25 * .e7/.e236 + .e234 * .e273 .e464 <- (.e28 * (0.5 * .e276 + .e364) + 0.5 * .e275)/.e15 + ((.e105 - .e308)/.e12 + 0.5 * .e289) * .e4 .e466 <- (.e28 * (2 * .e276 + .e367) + 2 * .e275)/.e15 + ((8 * .e104 - 2 * .e83)/.e12 + 2 * .e289) * .e4 .e468 <- .e42 * .e10/.e13 .e469 <- .e111/.e13 .e475 <- .e102/.e15 + .e435/.e13 .e477 <- .e102/2 + .e66 * .e7 * .e17/.e12 .e481 <- (.e271 - .e368) * .e4 * .e10 * .e135/.e49 .e483 <- .e295 * .e7/.e94 .e486 <- (.e77 - ((((.e305 + 4 * .e229) * .e25 - .e71)/.e12 + t0 * .e252/.e13) * .e8 + .e71)) * .e43/.e13 - ((.e352 - .e102 * .e37/.e15) * .e28 + .e99 * .e37/.e13)/.e15 .e492 <- .e28/.e14 .e495 <- .e428/.e38 .e496 <- .e79 * .e43 .e498 <- .e79 * .e10/.e12 .e499 <- .e79/.e12 .e500 <- .e81 * .e43 .e501 <- .e81/.e12 .e504 <- .e223 * .e220 * .e7/.e38 .e507 <- (0.25 * .e65 - 2 * (0.25 * (t0 * .e182) + 0.5)) * .e4/.e13 - 0.5 * (.e28 * .e182/.e15) .e508 <- (0.5 - .e309 * .e7/.e45)/.e45 .e510 <- .e429 * .e17 - .e243 .e511 <- .e201 * .e43 .e514 <- (0.5 * (.e218 * .e65) - 2 * (0.5 * (t0 * .e218 * .e182) + 1 - .e202)) * .e4/.e13 - .e28 * .e218 * .e182/.e15 .e516 <- (.e308 - ((.e308 + 2 * (.e229 * .e25))/.e12 + t0 * .e249/.e13) * .e8)/.e13 - ((.e357 - .e103 * .e37/.e15) * .e28 + .e201 * .e37/.e13)/.e15 .e518 <- (0.5 * .e99 - (.e297/.e12 + .e368) * .e8) * .e135/.e49 .e520 <- .e103/.e15 + 0.5 * .e371 .e522 <- .e103/2 + .e134 * .e17/.e239 .e524 <- (1 - ((.e43 * (1 + 2 * .e229)/.e12 + .e317) * .e8 + .e35)) * .e135/.e49 .e527 <- .e99 * .e218 * .e4 * .e25 .e529 <- .e394 * .e26/.e49 .e531 <- .e395/.e12 + .e298 .e534 <- .e43/.e112 .e535 <- .e218 * .e182 .e542 <- .e431/.e38 .e543 <- (2 - 2 * .e370) * .e24 .e544 <- .e128 * (.e133 + .e432) .e546 <- .e298 * .e7/.e94 .e550 <- .e299 + .e360 .e551 <- .e220 * .e4 .e552 <- .e220/.e12 .e555 <- .e416 * .e10 * .e135/.e49 .e556 <- .e300 + 2 * .e360 .e558 <- .e359 * .e10/.e13 .e560 <- .e359 * .e7/.e13 .e562 <- .e133 * .e10/.e13 .e564 <- .e133 * .e7/.e13 .e568 <- .e37 * .e182 * .e137 * .e7/.e114 .e569 <- .e37 * .e130 .e571 <- .e301/.e13 .e572 <- .e302/.e13 .e573 <- .e114 * .e13 .e578 <- .e8 * .e10 * .e135 * .e7/(.e361 * .e13) .e579 <- .e30/.e49 .e581 <- .e8 * .e135/.e361 .e583 <- .e10 * .e17 .e585 <- .e7^2 .e586 <- .e17 * .e13 .e587 <- 0.5 - 0.5 * (.e11/.e363) .e589 <- 0.5 * .e65 - (2 * (.e28/.e15) + 2 * .e371) * .e4 .e591 <- 0.5 * .e319 + 0.5 * .e321 .e592 <- 1 - (.e203 * .e311 * .e7/.e45 + .e165) .e593 <- 1 - (.e400/.e363 + .e165) .e595 <- 1/.e15 + t0 .e597 <- 2 - (.e420 + .e278) .e598 <- 2 * (.e7 * .e13) .e599 <- 2 * (t0 * (.e205 + (.e237 - .e245/.e12) * .e4)/.e13) .e600 <- 2 * (t0 * ((.e238 - 0.5 * (.e51/.e12)) * .e4 + 0.5 * .e24)/.e13) .e601 <- 2 * (t0 * .e310 * .e4/.e13) .e602 <- 2 * (t0 * .e312 * .e4/.e13) .e603 <- 2 * (t0 * .e313 * .e4/.e13) .e604 <- 2 * (t0 * .e314 * .e4/.e13) .e607 <- 2 * t0 + 2/.e15 .e609 <- 4 * .e343 - 2 * .e330 .e611 <- 4 * .e271 - 16 * .e226 .e612 <- 8 * .e188 .e613 <- r0 - (.e242 + .e11 * .e17/.e12) .e616 <- t0 * .e225 * .e10/.e13 .e617 <- .e106 * .e10 .e619 <- .e57 * .e10/.e13 .e621 <- .e57 * .e7/.e13 .e623 <- t0 * .e8/.e13 .e624 <- .e107 * .e10 .e625 <- .e107/.e13 c(a0 = (((.e99/.e598 + 8 * .e524) * .e7 - .e251) * .e26 - 0.5 * (((.e332 + .e292 * .e280/.e45 + .e412) * .e32 + (.e377 * .e45 - .e42 * .e531)/.e38)/.e45)) * .e43 + (((.e298/.e94 - (.e102/.e14 + .e66 * .e17/.e12)/.e38) * .e220 + .e223 * .e43 * (2 * (((.e43 * (.e250 - (.e98 + .e432)) * .e130 * .e4/.e13 + .e37 * (4 * .e486 - 2 * ((((.e325 - 2 * (.e60 * .e145/.e24))/.e17 - .e599) * .e37 + .e444 * .e252 * .e4/.e13)/.e24)))/.e114 - ((2 * .e102 - 2 * (.e435 * .e15/.e13)) * .e24 + 2 * (.e145 * .e15/.e17)) * .e37 * .e130 * .e15 * .e75/.e294) * .e137 * .e7) + 64 * .e524 - .e551/.e12)) * .e7/.e38 - ((((.e546 - .e107 * .e43 * .e4/.e13) * .e84 - (.e477/2 + .e106 * .e43 * .e4) * .e53/.e13) * .e177 + .e158 * (32 * (.e486 * .e4 + .e89 * .e43) + 32 * .e352 - (.e398 * .e316 + 64 * (((.e43 * .e128 * .e252 * .e4/.e13 + (2 * ((.e332 - .e599) * .e13 + .e444 * .e4/.e13) + 4 * (.e349/.e13)) * .e37) * .e4 + .e43 * (1 - 2 * .e623) * .e128 * .e37) * .e13 + (.e73 - 2 * (.e398 * .e13/.e95)) * .e128 * .e37 * .e4))/.e95) - (.e225 * .e475 + 32 * (((((.e377/.e100 - .e42 * (8 * (.e145 * .e13/.e17) - .e97 * .e102/.e14)/.e290) * .e7 + t0 * (.e496 - (.e477/.e38 + .e496 * .e4/.e12) * .e4)/.e13) * .e53 + .e84 * (tij * ((.e546 - .e500 * .e4/.e12) * .e4 + .e500)/.e13 - (.e436 + 2 * (.e62 * .e280 * .e32/.e45)) * .e32 * .e7/.e94) - (.e139 * .e398/.e95 + .e66 * .e434/.e13)) * .e37 + .e439 * .e252 * .e4/.e13) * .e4 + .e439 * .e37))) * .e53 * .e25 * .e7/.e236 + ((2 * (.e377 * .e13 + .e42 * .e43 * .e4/.e13) + 4 * .e43)/.e155 + (2 * ((.e353 - .e531 * .e4)/.e13) - (2 * ((.e436 * .e13 + .e338/.e13) * .e32) + 8 * ((.e395/.e13 - .e298 * .e13) * .e193 * .e45 * .e13/.e156)))/.e156 - .e191 * (32 * ((.e102 * .e12/.e54 + 2 * .e66) * .e12/.e17) - .e142 * .e102/.e14)/.e291) * .e273 + .e234 * ((.e209 + 8 * ((.e352 - .e475 * .e37) * .e37 * .e137 * .e7/.e114)) * .e7 - (.e237 - 2 * (.e369 * .e24 * .e4/.e13)) * .e216 * .e75/.e296)) * .e43) * .e7, a2 = geno_a * ((((.e295/.e94 - (.e103/.e14 + .e4 * .e17/.e239)/.e38) * .e220 + .e223 * (2 * (((.e249 * .e130 * .e4/.e13 + .e37 * (4 * .e516 - (2 * ((((.e329 - 2 * (.e60 * .e148/.e24))/.e17 - .e600) * .e37 + .e60 * .e249 * .e4/.e13)/.e24) + .e330 * .e4/.e13)))/.e114 - ((2 * .e103 - .e331 * .e15/.e13) * .e24 + 2 * (.e148 * .e15/.e17)) * .e37 * .e130 * .e15 * .e75/.e294) * .e43 * .e137 * .e7) + 64 * .e518 - .e551/.e239)) * .e7/.e38 - ((((.e483 - 0.5 * .e117) * .e84 - (.e522/2 + 0.5 * .e115) * .e53/.e13) * .e177 + .e158 * (32 * (.e516 * .e4 + 0.5 * .e89) + 32 * .e357 - (.e422 * .e316 + 64 * ((((2 * ((.e335 - .e600) * .e13 + 0.5 * (.e449/.e13)) + 4 * (.e347/.e13)) * .e37 + .e128 * .e249 * .e4/.e13) * .e4 + (0.5 - .e623) * .e128 * .e37) * .e13 + (.e74 - 2 * (.e422 * .e13/.e95)) * .e128 * .e37 * .e4))/.e95) - (.e225 * .e520 + 32 * (((((.e379/.e100 - .e42 * (8 * (.e148 * .e13/.e17) - .e97 * .e103/.e14)/.e290) * .e7 + t0 * (0.5 * .e79 - (.e522/.e38 + 0.5 * (.e79 * .e4/.e12)) * .e4)/.e13) * .e53 + .e84 * (tij * ((.e483 - 0.5 * (.e81 * .e4/.e12)) * .e4 + 0.5 * .e81)/.e13 - (.e374 + 2 * (.e62 * .e277 * .e32/.e45)) * .e32 * .e7/.e94) - (.e139 * .e422/.e95 + .e591 * .e4/.e13)) * .e37 + .e139 * .e249 * .e4/.e13) * .e4 + 0.5 * .e210))) * .e53 * .e25 * .e7/.e236 + .e234 * ((64 * ((0.5 - .e8/.e239) * .e4 * .e135/.e49) + 8 * ((.e357 - .e520 * .e37) * .e37 * .e137 * .e7/.e114)) * .e7 - (.e238 - .e59) * .e216 * .e75/.e296) + ((2 * ((0.5 * .e45 - (.e295 + 0.5 * (.e170/.e12)) * .e4)/.e13) - (2 * ((.e374 * .e13 + 0.5 * (.e339/.e13)) * .e32) + 8 * ((0.5 * .e179 - .e295 * .e13) * .e193 * .e45 * .e13/.e156)))/.e156 + (2 + 2 * (.e379 * .e13 + 0.5 * (.e42 * .e4/.e13)))/.e155 - .e191 * (32 * ((.e12 * .e103/.e54 + a0 + .e3) * .e12/.e17) - .e142 * .e103/.e14)/.e291) * .e273) * .e43) * .e7 + ((.e511/.e598 + 8 * .e518) * .e7 - .e511/.e13) * .e26 - 0.5 * (((.e374 + .e292 * .e277/.e45) * .e32 + (.e379 * .e45 - (.e295 + .e170/.e239) * .e42)/.e38) * .e43/.e45)), b0 = ((((.e417 - .e542) * .e220 + .e223 * (2 * (((((4 * .e466 - 4 * .e330) * .e7/.e13 - 2 * ((((.e327 - (2 * (.e60 * .e151/.e24) + .e287))/.e17 - .e603) * .e37 - 2 * .e448)/.e24)) * .e37 - 2 * .e560)/.e114 - (.e24 * (4 - 4 * .e370) * .e7/.e13 + 2 * (.e151 * .e15/.e17)) * .e37 * .e130 * .e15 * .e75/.e294) * .e43 * .e137) + 64 * (.e611 * .e4 * .e135/.e49) - 2 * .e552) * .e7) * .e7/.e38 + (.e534 + 8 * (.e611 * .e135 * .e7/.e49)) * .e4 * .e26 - (((((.e417 - 2 * .e625) * .e84 - (.e431/2 + 2 * .e106) * .e53/.e13) * .e177 - .e225 * .e607/.e13) * .e7 + .e158 * ((32 * (.e466 * .e7/.e13) - 64 * ((((2 * ((.e334 - .e603) * .e13 + 2 * .e453) + 4 * (.e358/.e13)) * .e37 - .e128 * (.e367 + 4 * .e64) * .e7/.e13) * .e13 + .e169 * (.e140 - 2 * (.e407 * .e13/.e95)))/.e95)) * .e4 - (.e407 * .e316/.e95 + 64 * .e564)) - 32 * (((((.e389/.e100 - (.e42 * (8 * (.e151 * .e13/.e17) - .e97/.e13)/.e290 + t0 * (.e542 + 2 * .e499) * .e4/.e13)) * .e53 + .e84 * (tij * (.e417 - 2 * .e501) * .e4/.e13 - (.e438 + 2 * (.e62 * .e284 * .e32/.e45)) * .e32/.e94) - (2 * .e319 + 2 * .e321)/.e13) * .e7 - .e139 * .e407/.e95) * .e37 - 2 * .e441) * .e4)) * .e53 * .e25 * .e7/.e236 + .e273 * (2 * ((.e389 * .e13 + 2 * .e469)/.e155) - ((2 * ((.e438 * .e13 + 2 * .e455) * .e32) + 2 * (.e556 * .e4/.e13) + 8 * (.e193 * (2 * .e572 - .e300 * .e13) * .e45 * .e13/.e156))/.e156 + .e191 * (32 * ((.e12/.e586 + 4 * .e7) * .e12/.e17) - .e142/.e13)/.e291)) - .e234 * ((.e208 - 4 * .e621) * .e216 * .e75/.e296 + (256 * .e581 + 8 * ((.e37 * .e607 + .e367) * .e37 * .e137 * .e7/.e114)) * .e585/.e13)) * .e43) * .e7 - 0.5 * (((.e334 + .e292 * .e284/.e45 + .e419) * .e32 + (.e389 * .e45 - .e42 * .e556)/.e38) * .e43/.e45)) * (1 - 0.5 * geno_b) * .e9, b2 = geno_b * ((((.e415 - .e495) * .e220 + .e223 * (2 * ((((.e609 * .e7/.e13 - 2 * ((((.e326 - (2 * (.e60 * .e149/.e24) + .e286))/.e17 - .e602) * .e37 - .e448)/.e24)) * .e37 - .e560)/.e114 - (.e543 * .e7/.e13 + 2 * (.e149 * .e15/.e17)) * .e37 * .e130 * .e15 * .e75/.e294) * .e43 * .e137) + 64 * (.e416 * .e135/.e49) - .e552) * .e7) * .e7/.e38 + (0.5 * .e534 + 8 * (.e366 * .e135 * .e7/.e49)) * .e4 * .e26 - (((((.e415 - .e625) * .e84 - (.e428/2 + .e106) * .e53/.e13) * .e177 - .e225 * .e595/.e13) * .e7 + .e158 * ((32 * (.e343 * .e7/.e13) - 64 * ((((2 * ((.e333 - .e602) * .e13 + .e453) + 4 * (.e355/.e13)) * .e37 - .e544 * .e7/.e13) * .e13 + (.e90 - 2 * (.e426 * .e13/.e95)) * .e128 * .e37)/.e95)) * .e4 - (.e426 * .e316/.e95 + 32 * .e564)) - 32 * (((((.e385/.e100 - (.e42 * (8 * (.e149 * .e13/.e17) - .e97/.e38)/.e290 + t0 * (.e495 + .e499) * .e4/.e13)) * .e53 + .e84 * (tij * (.e415 - .e501) * .e4/.e13 - (.e437 + 2 * (.e62 * .e281 * .e32/.e45)) * .e32/.e94) - .e434/.e13) * .e7 - .e139 * .e426/.e95) * .e37 - .e441) * .e4)) * .e53 * .e25 * .e7/.e236 + .e273 * (2 * ((.e385 * .e13 + .e469)/.e155) - ((2 * ((.e437 * .e13 + .e455) * .e32) + 2 * (.e550 * .e4/.e13) + 8 * ((.e572 - .e299 * .e13) * .e193 * .e45 * .e13/.e156))/.e156 + .e191 * (32 * ((.e12/(2 * .e586) + .e14) * .e12/.e17) - .e142/.e38)/.e291)) - ((128 * .e581 + 8 * ((.e595 * .e37 + .e105 + .e98) * .e37 * .e137 * .e7/.e114)) * .e585/.e13 + (.e207 - 2 * .e621) * .e216 * .e75/.e296) * .e234) * .e43) * .e7 - 0.5 * (((.e333 + .e292 * .e281/.e45 + .e414) * .e32 + (.e385 * .e45 - .e42 * .e550)/.e38) * .e43/.e45)) * .e9, q0 = (((.e492 + .e178) * .e43 + (8 * .e555 - (.e28/.e7 + .e178) * .e43/.e14) * .e7 + .e612) * .e26 + .e504 - (.e460 + 0.5 * ((.e372 * .e32 + (.e383 * .e45 + .e42 * .e597)/.e38 - .e292 * .e311/.e45)/.e45)) * .e43) * .e203 + (((.e223 * (2 * (((((.e609 * .e10/.e13 - 2 * (((.e322 - (.e60 * .e173/.e24 + .e604)) * .e37 - .e446)/.e24)) * .e37 - .e558) * .e7 + .e569)/.e114 - (.e543 * .e10/.e13 + .e173 * .e15) * .e37 * .e130 * .e15 * .e75 * .e7/.e294) * .e43 * .e137) + 64 * .e555) - ((.e109/.e14 + .e583/.e12)/.e38 + .e311/.e94) * .e220) * .e203 * .e7 + .e223 * (1 - (.e400/.e12 + .e165)) * .e220)/.e38 - ((((.e158 * ((32 * (.e343 * .e10/.e13) - 64 * ((((2 * ((.e322 - .e604) * .e13 + .e451) + 4 * (.e362/.e13)) * .e37 - .e544 * .e10/.e13) * .e13 + (.e50 - 2 * (.e424 * .e13/.e95)) * .e128 * .e37)/.e95)) * .e4 - (.e424 * .e316/.e95 + 32 * .e562)) - .e616) * .e203 + (((.e613/2 - .e617) * .e53 - .e624 * .e84) * .e203/.e13 + .e592 * .e84/.e45) * .e177 - 32 * ((((((.e383 * .e7 + .e40 + .e41)/.e100 + t0 * (.e613/.e38 - .e498) * .e4/.e13 - .e42 * (8 * (.e161 * .e13/.e17) - .e97 * .e109/.e14) * .e7/.e290) * .e53 - (.e139 * .e424/.e95 + .e10 * .e434/.e13)) * .e203 + .e84 * (tij * (.e592/.e45 - .e81 * .e203 * .e10/.e12) * .e4/.e13 - ((.e372 - 2 * (.e62 * .e311/.e45)) * .e7 + .e47 + .e61) * .e203 * .e32/.e94)) * .e37 - .e139 * .e203 * .e133 * .e10/.e13) * .e4)) * .e7 + .e225 * .e593) * .e53 * .e25/.e236 + (.e203 * (32 * (.e240 - 4 * .e578) - .e216 * (.e173 - 2 * .e619) * .e75/.e296) + 8 * ((.e593 * .e37 - .e203 * (.e133 + .e64) * .e10 * .e7/.e13) * .e37 * .e137 * .e7/.e114)) * .e234 + ((2 * (.e597 * .e4/.e13) - (2 * ((.e372 * .e13 + .e454) * .e32) + 8 * ((.e311 * .e13 + .e571) * .e193 * .e45 * .e13/.e156)))/.e156 + 2 * ((.e383 * .e13 + .e468)/.e155) - .e191 * (32 * ((.e12 * .e109/.e54 + 2 * .e10) * .e12/.e17) - .e142 * .e109/.e14)/.e291) * .e273 * .e203) * .e43) * .e7, q2 = geno_q * ((((.e223 * (2 * ((((((4 * .e464 - .e330) * .e10/.e13 - 2 * (((.e323 - (.e60 * .e230/.e24 + .e601)) * .e37 - 0.5 * .e446)/.e24)) * .e37 - 0.5 * .e558) * .e7 + 0.5 * .e569)/.e114 - ((1 - .e370) * .e24 * .e10/.e13 + .e230 * .e15) * .e37 * .e130 * .e15 * .e75 * .e7/.e294) * .e43 * .e137) + 64 * .e481) - ((.e110/.e14 + .e583/.e239)/.e38 + .e309/.e94) * .e220) * .e7 + .e223 * .e429 * .e220)/.e38 - (((((.e510/2 - 0.5 * .e617) * .e53/.e13 + (.e508 - 0.5 * (.e624/.e13)) * .e84) * .e177 + .e158 * ((32 * (.e464 * .e10/.e13) - 64 * ((((2 * ((.e323 - .e601) * .e13 + 0.5 * .e451) + 4 * (.e354/.e13)) * .e37 - (.e364 + .e64) * .e128 * .e10/.e13) * .e13 + (.e85 - 2 * (.e402 * .e13/.e95)) * .e128 * .e37)/.e95)) * .e4 - (.e402 * .e316/.e95 + 16 * .e562)) - (0.5 * .e616 + 32 * (((((.e387 * .e7 + 0.5 * .e42)/.e100 + t0 * (.e510/.e38 - 0.5 * .e498) * .e4/.e13 - .e42 * (8 * (.e164 * .e13/.e17) - .e97 * .e110/.e14) * .e7/.e290) * .e53 + .e84 * (tij * (.e508 - 0.5 * (.e81 * .e10/.e12)) * .e4/.e13 - ((.e373 - 2 * (.e62 * .e309/.e45)) * .e7 + 0.5 * .e62) * .e32/.e94) - (.e139 * .e402/.e95 + .e591 * .e10/.e13)) * .e37 - 0.5 * (.e375 * .e10/.e13)) * .e4))) * .e7 + .e225 * .e587) * .e53 * .e25/.e236 + .e234 * (32 * (0.5 * .e240 - 2 * .e578) + 8 * ((.e587 * .e37 - (.e364 + .e67) * .e10 * .e7/.e13) * .e37 * .e137 * .e7/.e114) - (.e230 - .e619) * .e216 * .e75/.e296) + ((2 * ((1 - (.e259 + 0.5 * .e420)) * .e4/.e13) - (2 * ((.e373 * .e13 + 0.5 * .e454) * .e32) + 8 * ((.e309 * .e13 + 0.5 * .e571) * .e193 * .e45 * .e13/.e156)))/.e156 + 2 * ((.e387 * .e13 + 0.5 * .e468)/.e155) - .e191 * (32 * ((.e12 * .e110/.e54 + .e10) * .e12/.e17) - .e142 * .e110/.e14)/.e291) * .e273) * .e43) * .e7 + ((8 * .e481 - (.e492 + 0.5 * .e178) * .e43/.e14) * .e7 + 0.5 * (.e28 * .e43/.e14 + .e612) + 0.5 * (.e66 * .e10/.e112)) * .e26 + 0.5 * (.e504 - .e460 * .e43) - 0.5 * ((.e373 * .e32 + (.e387 * .e45 + .e42 * (1 - (.e259 + .e301/.e239)))/.e38 - .e292 * .e309/.e45) * .e43/.e45)), f0 = ((.e223 * (128 * (.e527/.e49) + 2 * ((.e535 * .e130 + .e37 * (4 * .e514 - 2 * (.e60 * .e218 * .e182/.e24))) * .e43 * .e137 * .e7/.e114))/.e38 - (((.e158 * (.e535 * .e433 + 32 * (.e514 * .e4)) - 32 * (.e139 * .e218 * .e182 * .e4)) * .e25 + .e225 * .e218) * .e53/.e236 + .e234 * .e218 * (64 * .e579 + 8 * .e568)) * .e43) * .e7 + 16 * (.e527 * .e26/.e49)) * .e7, f2 = geno_f * ((.e223 * (2 * ((.e37 * (4 * .e507 - .e60 * .e182/.e24) + 0.5 * (.e182 * .e130)) * .e43 * .e137 * .e7/.e114) + 64 * (.e394/.e49))/.e38 - (((.e158 * (0.5 * (.e182 * .e433) + 32 * (.e507 * .e4)) - 16 * (.e139 * .e182 * .e4)) * .e25 + 0.5 * .e225) * .e53/.e236 + .e234 * (32 * .e579 + 4 * .e568)) * .e43) * .e7 + 8 * .e529) * .e7, f1 = ((.e223 * (2 * ((.e37 * (4 * (.e449/.e24) - 4 * .e589) - 2 * (.e130 * .e4)) * .e43 * .e137 * .e7/.e573) - 128 * (.e99 * .e25/.e49)) * .e4/.e38 - ((((64 * (.e139 * .e4) - .e158 * (2 * .e433 + 32 * .e589)) * .e4 * .e25/.e13 + 32 * .e210) * .e4 - .e221) * .e53/.e236 - .e234 * (16 * (.e37 * .e137 * .e7/.e573) + 64 * (.e25/.e49)) * .e8) * .e43) * .e7 - 16 * .e529) * .e7) } deriv_mu_int_a2_abqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_a * (a2 - a0)/2 .e4 <- a0 + .e3 .e7 <- geno_q * (q2 - q0)/2 + q0 .e8 <- .e4^2 .e9 <- b0 + geno_b * (b2 - b0)/2 .e10 <- .e9^2 .e11 <- .e10 * .e7 .e12 <- .e8 + 2 * .e11 .e13 <- sqrt(.e12) .e14 <- 2 * .e7 .e15 <- .e4 + .e13 .e16 <- .e15/.e14 .e17 <- r0 - .e16 .e20 <- geno_f * (f2 - f0)/2 .e21 <- f0 + .e20 .e22 <- .e4/.e13 .e23 <- 2 * (.e13/.e17) .e24 <- .e14 + .e23 .e25 <- .e21 - f1 .e26 <- .e7 * .e17 .e27 <- tij - t0 .e28 <- .e22 + 1 .e29 <- .e8 * .e25 .e30 <- .e21 - m0 .e34 <- 2 * (.e29/.e13) - 2 * (.e30 * .e13) .e36 <- exp(2 * (.e13 * .e27)) .e37 <- 2 * .e26 .e38 <- 2 * .e13 .e39 <- .e28 * .e13 .e41 <- .e14 - .e24 * .e36 .e42 <- t0 * .e13 .e43 <- .e39/.e37 .e44 <- .e43 + .e22 .e45 <- .e38^2 .e46 <- .e10/.e13 .e47 <- .e24 * .e4 .e49 <- exp(-.e42) .e50 <- .e8/.e12 .e51 <- 2 * .e22 .e53 <- .e39/.e26 + .e51 .e54 <- t0 * .e24 .e56 <- .e47 * .e27/.e13 .e58 <- .e54 * .e4/.e13 .e61 <- 0.5 * (.e53/.e17) - .e58 .e62 <- 2 * .e50 .e63 <- 2 * .e15 .e64 <- .e44/.e17 .e65 <- 4 - .e62 .e66 <- t0 * .e34 .e67 <- .e64 + .e56 .e68 <- 0.5 * .e66 .e70 <- exp(-(2 * .e42)) .e71 <- .e28 * .e34 .e75 <- .e65 * .e25/2 + m0 - (.e68 + f0 + .e20) .e76 <- 0.5 * .e22 .e79 <- .e26/.e38 + 0.5 .e81 <- .e7/.e41 - 0.5 .e82 <- 0.5 * .e46 .e83 <- exp(-(tij * .e13)) .e86 <- .e75 * .e4/.e13 - .e71/.e63 .e87 <- 2 * .e12 .e88 <- .e67 * .e36 .e89 <- .e24 * .e45 .e90 <- .e41^2 .e92 <- (-.e23)^2 .e93 <- .e29/.e12 .e94 <- .e7/.e13 .e95 <- .e92 * .e17 .e96 <- .e28/.e13 .e98 <- .e4/.e12 .e99 <- .e46 - .e15/.e7 .e100 <- .e82 - .e16 .e101 <- 0.5 + .e76 .e102 <- 2 * .e93 .e103 <- 2 * .e30 .e104 <- .e102 + .e103 .e105 <- t0 * .e79 .e106 <- tij * .e81 .e108 <- .e24 * .e15^2 * .e70 .e110 <- 0.5 - .e8/.e87 .e115 <- 4 * .e86 - 2 * (.e61 * .e34/.e24) .e116 <- .e44 * .e7 .e117 <- .e12 * .e13 .e118 <- 0.5 * (.e106 * .e4/.e13) .e119 <- .e105 * .e4 .e123 <- .e116/.e95 + 0.5 * (.e119/.e13) .e126 <- .e25^2 .e127 <- .e118 - .e88 * .e7/.e90 .e129 <- 2 * (.e61 * .e13) + 2 * (.e47/.e13) .e130 <- .e37^2 .e131 <- .e49^2 .e132 <- 2 * .e17 .e133 <- .e24 * .e10 .e134 <- .e24 * .e7 .e136 <- .e123 * .e49 + .e127 * .e83 .e137 <- 0.5 * .e50 .e139 <- (-(4 * (.e12/.e17)))^2 .e140 <- 16 * .e34 .e141 <- 2 * .e94 .e144 <- .e99 * .e13/.e37 + .e46 .e147 <- .e100 * .e13/.e37 + .e82 .e150 <- .e101 * .e13/.e37 + .e76 .e151 <- .e94 + 1/.e132 .e153 <- 1/.e17 + .e141 .e154 <- .e139 * .e17 .e158 <- .e79 * .e49 + .e81 * .e83 .e159 <- (2 * (.e41 * .e13))^2 .e160 <- .e4/.e117 .e162 <- 2 * (.e147/.e17) .e163 <- 2 + 2 * (.e144/.e17) .e164 <- .e110 * .e4 .e165 <- .e129 * .e34 .e168 <- 2 * (.e8/.e13) - .e38 .e171 <- .e41 * .e4 .e173 <- (32 * .e86 - 64 * (.e165 * .e13/.e89)) * .e4 + .e140 .e174 <- 0.5 * geno_q .e175 <- .e96 - .e98 .e177 <- .e164 * .e126/.e45 .e178 <- .e34 * .e115 .e179 <- .e171/.e13 .e181 <- .e133 * .e27/.e13 .e183 <- .e134 * .e27/.e13 .e184 <- 0.5 - .e137 .e186 <- 0.5 * .e96 - 0.5 * .e98 .e191 <- .e179 - 2 * (.e88 * .e13) .e193 <- 2 * (.e44 * .e13) + 2 * .e4 .e194 <- 2 * (.e151/.e17) .e195 <- 2 * (.e153/.e17) .e196 <- 64 * .e177 .e198 <- t0 * .e45/.e13 .e202 <- 0.5 * geno_f .e203 <- 1 - .e174 .e205 <- 2 * (.e178 * .e131 * .e7/.e108) + .e196 .e206 <- .e136 * .e34 .e207 <- .e158 * .e173 .e208 <- .e28/.e130 .e209 <- (2 * (.e34 * .e49 * .e7/.e15))^2 .e211 <- .e89 * .e15 * .e70 .e212 <- .e133/.e12 .e213 <- .e134/.e12 .e214 <- .e24 * .e70 .e216 <- .e17/.e38 + 1/.e41 .e217 <- 1 - .e202 .e218 <- 1 + .e162 .e220 <- .e207 - 32 * (.e206 * .e4) .e222 <- 2 * (.e150/.e17) .e224 <- .e191/.e159 + .e193/.e154 .e226 <- .e99/2 + .e16 .e227 <- .e110/.e45 .e228 <- .e100/2 .e231 <- .e63^2 .e232 <- .e8/.e87^2 .e235 <- 2 * ((1 - .e137) * .e25) + m0 - .e21 .e236 <- (.e4 * .e25/.e38)^2 .e237 <- .e184/.e13 .e238 <- .e67 * .e10 .e239 <- .e67 * .e7 .e240 <- (.e181 + 1 + .e162) * .e36 .e242 <- .e28 * (0.5 * .e17 - .e228) * .e13 .e243 <- .e28 * .e104 .e244 <- .e71/.e231 .e246 <- .e28 * (r0 - .e226) * .e13 .e247 <- .e186 * .e4 .e249 <- .e34 * .e4/.e12 .e250 <- .e56 + .e222 .e251 <- (.e163 + 2 * .e181) * .e36 .e253 <- 2 * .e96 - 2 * .e98 .e254 <- .e194 + 2 * .e183 .e255 <- .e195 + 4 * .e183 .e257 <- t0 * .e104/.e13 .e260 <- .e209/.e214 + 32 * (.e236 * .e7) .e261 <- 1 - .e240 .e262 <- 2 - .e251 .e263 <- .e175/.e37 .e264 <- (.e247 + 0.5)/.e37 .e267 <- .e186/.e37 .e268 <- .e24 * (4 - .e198) .e269 <- .e24 * (8 - 2 * .e198) .e270 <- .e4 * .e7 .e271 <- .e26/.e12 .e273 <- 0.5 * .e75 .e274 <- 0.5 * .e65 .e275 <- .e218 - 0.5 * .e212 .e276 <- 2 * (.e242/.e130) .e277 <- 2 * (.e246/.e130) .e278 <- 2 * .e208 .e279 <- .e194 - .e213 .e280 <- .e195 - 2 * .e213 .e281 <- .e163 - .e212 .e282 <- .e95^2 .e283 <- .e154^2 .e284 <- .e88 + .e44 * .e41/.e38 .e285 <- (.e263 - .e160) * .e10 .e287 <- (.e208 - .e160) * .e7 .e288 <- (.e267 - 0.5 * .e160) * .e10 .e289 <- .e108^2 .e290 <- .e250 * .e36 .e291 <- .e214^2 .e292 <- .e28 * .e101 .e293 <- (.e278 - 2 * .e160) * .e7 .e294 <- .e254 * .e36 .e295 <- .e255 * .e36 .e297 <- .e4 * .e10/.e117 .e298 <- .e140 + 32 * (.e86 * .e4) .e299 <- 4 * .e7 .e301 <- t0 * .e123 * .e49 .e302 <- t0 * .e115 .e303 <- t0 * .e4 .e305 <- tij * .e127 * .e83 .e308 <- .e220 * .e49 * .e25/.e211 .e311 <- (((.e62 - .e65/2) * .e25 + .e68 + f0 + .e20 - m0)/.e12 + 0.5 * .e257) * .e4 + (.e243 + .e249)/.e63 + 2 * .e244 .e313 <- .e216 * .e205/.e38 .e314 <- .e184 * .e24 .e315 <- .e61 * .e104 .e316 <- .e275 * .e4 .e317 <- .e279 * .e4 .e318 <- .e280 * .e4 .e319 <- .e104 * .e115 .e320 <- .e41 * .e10 .e321 <- .e41 * .e7 .e322 <- .e38^3 .e323 <- .e281 * .e4 .e324 <- .e270/.e117 .e325 <- 2 * .e232 .e326 <- 4 * .e227 .e328 <- 4 * .e232 - 8 * .e227 .e329 <- t0 * .e168 .e330 <- t0 * .e15 .e331 <- .e303/.e13 .e334 <- (((.e44 + 2 * .e150)/.e17 + .e56) * .e4 + .e314) * .e27/.e13 + ((.e44/.e37 + .e39/.e130) * .e101 + .e264 + .e237)/.e17 .e335 <- .e136 * .e104 .e336 <- ((.e44/.e38 + .e175/2)/.e17 + .e287)/.e17 .e339 <- (.e238 + .e316) * .e27/.e13 + (.e44 * .e100/.e37 + .e288 - .e276)/.e17 .e340 <- ((.e44/.e13 + .e253/2)/.e17 + .e293)/.e17 .e342 <- (.e285 + .e44 * .e99/.e37 - .e277)/.e17 + (.e323 + 2 * .e238) * .e27/.e13 .e343 <- .e175/.e132 .e345 <- .e264 + .e292 * .e13/.e130 + .e237 .e349 <- (.e317 + 2 * .e239) * .e27/.e13 .e351 <- (.e318 + 4 * .e239) * .e27/.e13 .e354 <- .e313 - .e308 .e355 <- .e164 * .e25 .e357 <- .e218 * .e45 + .e268 * .e10 .e362 <- (16 - 4 * .e198) * .e24 * .e7 + 2 * (.e153 * .e45/.e17) .e363 <- .e253/.e132 .e364 <- .e294/.e90 .e368 <- .e295/.e90 .e369 <- .e205/.e12 .e371 <- .e268 * .e4 + 2 * (.e150 * .e45/.e17) .e373 <- .e269 * .e10 + .e45 * .e163 .e375 <- .e269 * .e7 + 2 * (.e151 * .e45/.e17) .e376 <- .e271 + 1/.e38 .e378 <- 1/.e15 + t0 .e380 <- 1/.e13 + 2 * .e271 .e381 <- 16 - 64 * (.e129 * .e4 * .e13/.e89) .e385 <- ((.e53/2 + .e43) * .e101 + .e247 + 0.5)/.e26 + 2 * .e237 .e387 <- .e335 * .e7/.e13 .e388 <- .e336 + .e349 .e389 <- .e340 + .e351 .e391 <- ((.e175 * .e7 + .e28/.e132)/.e7 + .e53/.e38)/.e17 - 2 * .e324 .e393 <- (.e53/.e13 + (.e28/.e17 + .e253 * .e7)/.e7)/.e17 - 4 * .e324 .e394 <- .e238/.e13 .e395 <- .e239/.e13 .e396 <- .e285 - .e277 .e397 <- .e220 * .e378 .e400 <- .e224 * .e260 .e401 <- .e44 * .e4 .e403 <- .e44 * .e10/.e13 .e404 <- .e116/.e13 .e405 <- (.e43 + .e51)/.e12 .e406 <- .e287 + .e343 .e410 <- ((.e93 - .e273)/.e12 + 0.25 * .e257) * .e4 + .e244 + (0.5 * .e243 + 0.5 * .e249)/.e63 .e411 <- .e354 * .e7 .e412 <- .e288 - .e276 .e415 <- ((.e274 - 0.5 * .e329) * .e217 + .e202 - 1) * .e4/.e13 - .e28 * .e217 * .e168/.e63 .e417 <- .e290 * .e7/.e90 .e420 <- ((4 * .e93 - 2 * .e75)/.e12 + .e257) * .e4 + (2 * .e243 + 2 * .e249)/.e63 + 4 * .e244 .e425 <- .e28/.e299 .e426 <- .e28/.e299^2 .e428 <- .e12 * .e7 * .e13 .e430 <- .e376/.e38 .e432 <- .e79 * .e10/.e12 .e433 <- .e79/.e12 .e434 <- .e81/.e12 .e435 <- (0.5 - .e261 * .e7/.e41)/.e41 .e438 <- .e110 * .e217 * .e4 * .e25 .e440 <- .e355 * .e27/.e45 .e442 <- (0.5 - .e11/.e87) * .e17 - .e228 .e444 <- .e315 * .e10/.e13 .e446 <- .e315 * .e7/.e13 .e447 <- .e61 * .e4 .e449 <- .e61 * .e10/.e13 .e451 <- .e61 * .e7/.e13 .e453 <- (.e273 - ((((1 - .e50) * .e25 + .e273)/.e12 + 0.5 * (t0 * .e235/.e13)) * .e8 + (.e28 * .e235 * .e4 + .e184 * .e34)/.e63))/.e13 + 2 * (.e292 * .e34/.e231) .e455 <- (0.5 * .e110 - (1/.e87 + .e326 - .e325) * .e8) * .e126/.e45 .e458 <- (0.5 * (.e274 - 1) - 0.25 * .e329) * .e4/.e13 - .e28 * .e168/(4 * .e15) .e460 <- .e101/.e15 + 0.5 * .e331 .e462 <- .e101/2 + .e270 * .e17/.e87 .e467 <- .e380/.e38 .e468 <- (2 - 2 * .e330) * .e24 .e471 <- .e293 + .e363 .e472 <- .e129 * (.e104 + 2 * .e66) .e474 <- .e235 * .e4/.e13 .e476 <- .e319 * .e10/.e13 .e478 <- .e319 * .e7/.e13 .e480 <- .e104 * .e10/.e13 .e482 <- .e104 * .e7/.e13 .e486 <- .e34 * .e168 * .e131 * .e7/.e108 .e487 <- .e320/.e12 .e488 <- .e320/.e13 .e489 <- .e321/.e12 .e490 <- .e321/.e13 .e491 <- .e108 * .e13 .e496 <- .e328 * .e126 .e497 <- .e15 * .e13 .e501 <- .e8 * .e10 * .e126 * .e7/(.e322 * .e13) .e502 <- .e29/.e45 .e504 <- .e8 * .e126/.e322 .e505 <- .e10 * .e17 .e506 <- .e7^2 .e507 <- .e17 * .e13 .e508 <- 0.5 * (((.e53 * .e99/2 + .e175 * .e10 - .e246/.e26)/.e26 - 2 * .e297)/.e17) .e509 <- 0.5 * (((.e53 * .e100/2 + .e186 * .e10 - .e242/.e26)/.e26 - .e297)/.e17) .e510 <- 0.5 * .e104 .e511 <- .e274 - (.e28/.e15 + .e331) * .e4 .e513 <- 0.5 * .e301 + 0.5 * .e305 .e514 <- 1 - (.e203 * .e262 * .e7/.e41 + .e174) .e516 <- .e325 - .e326 .e517 <- 2 * .e104 .e520 <- 2 * t0 + 2/.e15 .e522 <- 4 * .e311 - 2 * .e302 .e523 <- 64 * (.e328 * .e4 * .e126/.e45) .e525 <- 8 * .e232 - 16 * .e227 .e526 <- r0 - (.e226 + .e11 * .e17/.e12) .e527 <- .e301 + .e305 .e529 <- t0 * ((.e222 - 0.5 * (.e47/.e12)) * .e4 + 0.5 * .e24)/.e13 .e530 <- .e105 * .e10 .e533 <- t0 * .e275 * .e4/.e13 .e536 <- t0 * .e279 * .e4/.e13 .e539 <- t0 * .e280 * .e4/.e13 .e541 <- .e54 * .e10/.e13 .e543 <- .e54 * .e7/.e13 .e546 <- t0 * .e281 * .e4/.e13 .e547 <- .e106 * .e10 .e548 <- .e106/.e13 c(a2 = geno_a^2 * (((((.e290/.e90 - (.e101/.e14 + .e4 * .e17/.e87)/.e38) * .e205 + .e216 * (2 * (((.e235 * .e115 * .e4/.e13 + .e34 * (4 * .e453 - (2 * ((((0.5 * .e385 - 2 * (.e150 * .e61/.e24))/.e17 - .e529) * .e34 + .e61 * .e235 * .e4/.e13)/.e24) + .e302 * .e4/.e13)))/.e108 - ((2 * .e101 - .e303 * .e15/.e13) * .e24 + 2 * (.e150 * .e15/.e17)) * .e34 * .e115 * .e15 * .e70/.e289) * .e131 * .e7) + 64 * .e455 - .e205 * .e4/.e87))/.e38 - (((.e417 - .e118) * .e83 - (.e462/2 + 0.5 * .e119) * .e49/.e13) * .e173 + .e158 * (16 * .e474 + 32 * (.e453 * .e4 + 0.5 * .e86) - (.e371 * .e298 + 64 * ((((2 * ((.e314 + 2 * (.e150 * .e4/.e17))/.e13) + 2 * ((0.5 * (.e385/.e17) - .e529) * .e13 + 0.5 * (.e447/.e13))) * .e34 + .e129 * .e235 * .e4/.e13) * .e4 + (0.5 - t0 * .e8/.e13) * .e129 * .e34) * .e13 + (.e76 - 2 * (.e371 * .e13/.e89)) * .e129 * .e34 * .e4))/.e89) - (.e220 * .e460 + 32 * (((((.e345/.e95 - .e44 * (8 * (.e150 * .e13/.e17) - .e92 * .e101/.e14)/.e282) * .e7 + 0.5 * (t0 * (0.5 * .e79 - (.e462/.e38 + 0.5 * (.e79 * .e4/.e12)) * .e4)/.e13)) * .e49 + (0.5 * (tij * ((.e417 - 0.5 * (.e81 * .e4/.e12)) * .e4 + 0.5 * .e81)/.e13) - (.e334 + 2 * (.e67 * .e250 * .e36/.e41)) * .e36 * .e7/.e90) * .e83 - (.e136 * .e371/.e89 + .e513 * .e4/.e13)) * .e34 + .e136 * .e235 * .e4/.e13) * .e4 + 0.5 * .e206))) * .e49 * .e25/.e211) * .e7 - ((((0.5 * .e41 - (.e290 + 0.5 * (.e171/.e12)) * .e4)/.e13 - (2 * ((.e334 * .e13 + 0.5 * (.e67 * .e4/.e13)) * .e36) + 8 * (.e191 * (0.5 * .e179 - .e290 * .e13) * .e41 * .e13/.e159)))/.e159 + (1 + 2 * (.e345 * .e13 + 0.5 * (.e401/.e13)))/.e154 - .e193 * (32 * ((.e12 * .e101/.e37 + a0 + .e3) * .e12/.e17) - .e139 * .e101/.e14)/.e283) * .e260 + .e224 * ((.e196 + 8 * ((.e474 - .e460 * .e34) * .e34 * .e131 * .e7/.e108)) * .e7 - (.e222 - .e58) * .e209 * .e70/.e291))) * .e7 + ((.e184/(4 * (.e7 * .e13)) + 8 * .e455) * .e7 - 0.5 * .e237) * .e27 - 0.5 * (((.e334 + .e284 * .e250/.e41) * .e36 + ((.e345 - .e401/.e87) * .e41 - .e44 * .e250 * .e36)/.e38)/.e41)), b0 = geno_a * (((((.e368 - .e467) * .e205 + .e216 * (2 * (((((4 * .e420 - 4 * .e302) * .e7/.e13 - 2 * ((((0.5 * .e393 - 2 * (.e61 * .e153/.e24))/.e17 - .e539) * .e34 - 2 * .e446)/.e24)) * .e34 - 2 * .e478)/.e108 - (.e24 * (4 - 4 * .e330) * .e7/.e13 + 2 * (.e153 * .e15/.e17)) * .e34 * .e115 * .e15 * .e70/.e289) * .e131) + 64 * (.e525 * .e4 * .e126/.e45) - 2 * .e369) * .e7)/.e38 - ((((.e368 - 2 * .e548) * .e83 - (.e380/2 + 2 * .e105) * .e49/.e13) * .e173 - .e220 * .e520/.e13) * .e7 + .e158 * ((32 * (.e420 * .e7/.e13) - 64 * ((((2 * ((0.5 * (.e393/.e17) - .e539) * .e13 + 2 * .e451) + 2 * (.e318/.e13)) * .e34 - .e129 * (.e517 + 4 * .e66) * .e7/.e13) * .e13 + .e165 * (.e141 - 2 * (.e362 * .e13/.e89)))/.e89)) * .e4 - (.e362 * .e298/.e89 + 32 * .e482)) - 32 * (((((.e471/.e95 - (.e44 * (8 * (.e153 * .e13/.e17) - .e92/.e13)/.e282 + 0.5 * (t0 * (.e467 + 2 * .e433) * .e4/.e13))) * .e49 + (0.5 * (tij * (.e368 - 2 * .e434) * .e4/.e13) - (.e389 + 2 * (.e67 * .e255 * .e36/.e41)) * .e36/.e90) * .e83 - (2 * .e301 + 2 * .e305)/.e13) * .e7 - .e136 * .e362/.e89) * .e34 - 2 * .e387) * .e4)) * .e49 * .e25/.e211) * .e7 + .e224 * ((.e195 - 4 * .e543) * .e209 * .e70/.e291 + (256 * .e504 + 8 * ((.e34 * .e520 + .e517) * .e34 * .e131 * .e7/.e108)) * .e506/.e13) + (0.5/.e117 + 8 * (.e525 * .e126 * .e7/.e45)) * .e4 * .e27 - .e260 * (2 * ((.e471 * .e13 + 2 * .e404)/.e154) - (((.e295 + 2 * .e489) * .e4/.e13 + 2 * ((.e389 * .e13 + 2 * .e395) * .e36) + 8 * (.e191 * (2 * .e490 - .e295 * .e13) * .e41 * .e13/.e159))/.e159 + .e193 * (32 * ((.e12/.e507 + .e299) * .e12/.e17) - .e139/.e13)/.e283))) * .e7 - 0.5 * (((.e284 * .e255/.e41 + .e340 + .e351) * .e36 + (((.e278 - (2 * .e44 + .e51)/.e12) * .e7 + .e363) * .e41 - .e44 * .e255 * .e36)/.e38)/.e41)) * (1 - 0.5 * geno_b) * .e9, b2 = geno_a * geno_b * (((((.e364 - .e430) * .e205 + .e216 * (2 * ((((.e522 * .e7/.e13 - 2 * ((((0.5 * .e391 - 2 * (.e151 * .e61/.e24))/.e17 - .e536) * .e34 - .e446)/.e24)) * .e34 - .e478)/.e108 - (.e468 * .e7/.e13 + 2 * (.e151 * .e15/.e17)) * .e34 * .e115 * .e15 * .e70/.e289) * .e131) + .e523 - .e369) * .e7)/.e38 - ((((.e364 - .e548) * .e83 - (.e376/2 + .e105) * .e49/.e13) * .e173 - .e397/.e13) * .e7 + .e158 * ((32 * (.e311 * .e7/.e13) - 64 * ((((2 * ((0.5 * (.e391/.e17) - .e536) * .e13 + .e451) + 2 * (.e317/.e13)) * .e34 - .e472 * .e7/.e13) * .e13 + (.e94 - 2 * (.e375 * .e13/.e89)) * .e129 * .e34)/.e89)) * .e4 - (.e375 * .e298/.e89 + 16 * .e482)) - 32 * (((((.e406/.e95 - (.e44 * (8 * (.e151 * .e13/.e17) - .e92/.e38)/.e282 + 0.5 * (t0 * (.e430 + .e433) * .e4/.e13))) * .e49 + (0.5 * (tij * (.e364 - .e434) * .e4/.e13) - (.e388 + 2 * (.e67 * .e254 * .e36/.e41)) * .e36/.e90) * .e83 - .e527/.e13) * .e7 - .e136 * .e375/.e89) * .e34 - .e387) * .e4)) * .e49 * .e25/.e211) * .e7 + .e224 * ((128 * .e504 + 8 * ((.e378 * .e34 + .e102 + .e103) * .e34 * .e131 * .e7/.e108)) * .e506/.e13 + (.e194 - 2 * .e543) * .e209 * .e70/.e291) + (0.25/.e117 + 8 * (.e496 * .e7/.e45)) * .e4 * .e27 - .e260 * (2 * ((.e406 * .e13 + .e404)/.e154) - (((.e294 + .e489) * .e4/.e13 + 2 * ((.e388 * .e13 + .e395) * .e36) + 8 * (.e191 * (.e490 - .e294 * .e13) * .e41 * .e13/.e159))/.e159 + .e193 * (32 * ((.e12/(2 * .e507) + .e14) * .e12/.e17) - .e139/.e38)/.e283))) * .e7 - 0.5 * (((.e336 + .e284 * .e254/.e41 + .e349) * .e36 + (((.e208 - .e405) * .e7 + .e343) * .e41 - .e44 * .e254 * .e36)/.e38)/.e41)) * .e9, q0 = geno_a * ((((((.e523 - .e369) * .e10 + 2 * (((((.e522 * .e10/.e13 - 2 * (((.e508 - (.e61 * .e163/.e24 + .e546)) * .e34 - .e444)/.e24)) * .e34 - .e476) * .e7 + .e178)/.e108 - (.e468 * .e10/.e13 + .e163 * .e15) * .e34 * .e115 * .e15 * .e70 * .e7/.e289) * .e131)) * .e216 - ((.e99/.e14 + .e505/.e12)/.e38 + .e262/.e90) * .e205) * .e203/.e38 - ((.e158 * ((32 * (.e311 * .e10/.e13) - 64 * ((((2 * ((.e508 - .e546) * .e13 + .e449) + 2 * (.e323/.e13)) * .e34 - .e472 * .e10/.e13) * .e13 + (.e46 - 2 * (.e373 * .e13/.e89)) * .e129 * .e34)/.e89)) * .e4 - (.e373 * .e298/.e89 + 16 * .e480)) - .e397 * .e10/.e13) * .e203 + (((.e526/2 - .e530) * .e49 - .e547 * .e83) * .e203/.e13 + .e514 * .e83/.e41) * .e173 - 32 * ((((((.e396 * .e7 + .e43 + .e22)/.e95 + 0.5 * (t0 * (.e526/.e38 - .e432) * .e4/.e13) - .e44 * (8 * (.e144 * .e13/.e17) - .e92 * .e99/.e14) * .e7/.e282) * .e49 - (.e136 * .e373/.e89 + .e10 * .e527/.e13)) * .e203 + (0.5 * (tij * (.e514/.e41 - .e81 * .e203 * .e10/.e12) * .e4/.e13) - ((.e342 - 2 * (.e67 * .e262/.e41)) * .e7 + .e64 + .e56) * .e203 * .e36/.e90) * .e83) * .e34 - .e136 * .e203 * .e104 * .e10/.e13) * .e4)) * .e49 * .e25/.e211) * .e7 + (.e313 - (.e308 + (((2 - (.e487 + .e251)) * .e4/.e13 - (2 * ((.e342 * .e13 + .e394) * .e36) + 8 * ((.e262 * .e13 + .e488) * .e191 * .e41 * .e13/.e159)))/.e159 + 2 * ((.e396 * .e13 + .e403)/.e154) - .e193 * (32 * ((.e12 * .e99/.e37 + 2 * .e10) * .e12/.e17) - .e139 * .e99/.e14)/.e283) * .e260)) * .e203 - .e224 * (.e203 * (32 * (.e236 - 4 * .e501) - .e209 * (.e163 - 2 * .e541) * .e70/.e291) + 8 * (((1 - (.e203 * .e10 * .e7/.e497 + .e174)) * .e34 - .e203 * (.e104 + .e66) * .e10 * .e7/.e13) * .e34 * .e131 * .e7/.e108))) * .e7 + ((((8 * (.e496/.e45) - 1/(4 * .e428)) * .e4 * .e10 - 4 * .e426) * .e7 + .e425 + (0.5 * (.e10/.e117) + 8 * (.e110 * .e126/.e45)) * .e4) * .e27 + .e411 - (.e400 + 0.5 * (((((.e263 - .e405) * .e10 - .e277) * .e41 + .e44 * .e262)/.e38 + .e342 * .e36 - .e284 * .e262/.e41)/.e41))) * .e203), q2 = geno_a * geno_q * ((((((64 * (.e516 * .e4 * .e126/.e45) - .e205/.e87) * .e10 + 2 * ((((((4 * .e410 - .e302) * .e10/.e13 - 2 * (((.e509 - (.e61 * .e218/.e24 + .e533)) * .e34 - 0.5 * .e444)/.e24)) * .e34 - 0.5 * .e476) * .e7 + 0.5 * .e178)/.e108 - ((1 - .e330) * .e24 * .e10/.e13 + .e218 * .e15) * .e34 * .e115 * .e15 * .e70 * .e7/.e289) * .e131)) * .e216 - ((.e100/.e14 + .e505/.e87)/.e38 + .e261/.e90) * .e205)/.e38 - (((.e442/2 - 0.5 * .e530) * .e49/.e13 + (.e435 - 0.5 * (.e547/.e13)) * .e83) * .e173 + .e158 * ((32 * (.e410 * .e10/.e13) - 64 * ((((2 * ((.e509 - .e533) * .e13 + 0.5 * .e449) + 2 * (.e316/.e13)) * .e34 - (.e510 + .e66) * .e129 * .e10/.e13) * .e13 + (.e82 - 2 * (.e357 * .e13/.e89)) * .e129 * .e34)/.e89)) * .e4 - (.e357 * .e298/.e89 + 8 * .e480)) - (.e220 * (0.5 * t0 + 0.5/.e15) * .e10/.e13 + 32 * (((((.e412 * .e7 + 0.5 * .e44)/.e95 + 0.5 * (t0 * (.e442/.e38 - 0.5 * .e432) * .e4/.e13) - .e44 * (8 * (.e147 * .e13/.e17) - .e92 * .e100/.e14) * .e7/.e282) * .e49 + (0.5 * (tij * (.e435 - 0.5 * (.e81 * .e10/.e12)) * .e4/.e13) - ((.e339 - 2 * (.e67 * .e261/.e41)) * .e7 + 0.5 * .e67) * .e36/.e90) * .e83 - (.e136 * .e357/.e89 + .e513 * .e10/.e13)) * .e34 - 0.5 * (.e335 * .e10/.e13)) * .e4))) * .e49 * .e25/.e211) * .e7 + 0.5 * .e354 - ((((1 - (.e240 + 0.5 * .e487)) * .e4/.e13 - (2 * ((.e339 * .e13 + 0.5 * .e394) * .e36) + 8 * ((.e261 * .e13 + 0.5 * .e488) * .e191 * .e41 * .e13/.e159)))/.e159 + 2 * ((.e412 * .e13 + 0.5 * .e403)/.e154) - .e193 * (32 * ((.e12 * .e100/.e37 + .e10) * .e12/.e17) - .e139 * .e100/.e14)/.e283) * .e260 + .e224 * (32 * (0.5 * .e236 - 2 * .e501) + 8 * (((0.5 - 0.5 * (.e11/.e497)) * .e34 - (.e510 + .e68) * .e10 * .e7/.e13) * .e34 * .e131 * .e7/.e108) - (.e218 - .e541) * .e209 * .e70/.e291))) * .e7 + (((8 * (.e516 * .e126/.e45) - 1/(8 * .e428)) * .e4 * .e10 - 2 * .e426) * .e7 + 0.25 * .e297 + 0.5 * (.e425 + 8 * .e177)) * .e27 + 0.5 * (.e411 - .e400) - 0.5 * ((.e339 * .e36 + (((.e267 - (.e44/2 + .e76)/.e12) * .e10 - .e276) * .e41 + .e44 * .e261)/.e38 - .e284 * .e261/.e41)/.e41)), f0 = geno_a * ((.e216 * (128 * (.e438/.e45) + 2 * ((.e217 * .e168 * .e115 + .e34 * (4 * .e415 - 2 * (.e61 * .e217 * .e168/.e24))) * .e131 * .e7/.e108))/.e38 - (((.e158 * (.e217 * .e381 * .e168 + 32 * (.e415 * .e4)) - 32 * (.e136 * .e217 * .e168 * .e4)) * .e25 + .e220 * .e217) * .e49/.e211 + .e224 * .e217 * (64 * .e502 + 8 * .e486))) * .e7 + 16 * (.e438 * .e27/.e45)) * .e7, f2 = geno_a * geno_f * ((.e216 * (2 * ((.e34 * (4 * .e458 - .e61 * .e168/.e24) + 0.5 * (.e168 * .e115)) * .e131 * .e7/.e108) + 64 * (.e355/.e45))/.e38 - (((.e158 * (0.5 * (.e381 * .e168) + 32 * (.e458 * .e4)) - 16 * (.e136 * .e168 * .e4)) * .e25 + 0.5 * .e220) * .e49/.e211 + .e224 * (32 * .e502 + 4 * .e486))) * .e7 + 8 * .e440) * .e7, f1 = geno_a * (((.e224 * (16 * (.e34 * .e131 * .e7/.e491) + 64 * (.e25/.e45)) * .e4 + .e216 * (2 * ((.e34 * (4 * (.e447/.e24) - 4 * .e511) - 2 * (.e115 * .e4)) * .e131 * .e7/.e491) - 128 * (.e110 * .e25/.e45))/.e38) * .e4 - (((64 * (.e136 * .e4) - .e158 * (2 * .e381 + 32 * .e511)) * .e4 * .e25/.e13 + 32 * .e206) * .e4 - .e207) * .e49/.e211) * .e7 - 16 * .e440) * .e7) } deriv_mu_int_b0_bqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e3 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e17 <- geno_f * (f2 - f0)/2 .e18 <- f0 + .e17 .e19 <- 2 * (.e10/.e14) .e20 <- .e11 + .e19 .e21 <- .e18 - f1 .e22 <- tij - t0 .e23 <- .e5 * .e21 .e24 <- 2 * .e10 .e26 <- exp(2 * (.e10 * .e22)) .e27 <- .e18 - m0 .e28 <- .e3/.e10 .e32 <- 2 * (.e23/.e10) - 2 * (.e27 * .e10) .e33 <- 4 * .e28 .e35 <- 2/.e14 + .e33 .e36 <- t0 * .e10 .e37 <- .e20 * .e26 .e38 <- .e11 - .e37 .e39 <- .e24^2 .e40 <- .e35/.e14 .e41 <- .e20 * .e3 .e42 <- .e3 * .e14 .e43 <- .e7/.e10 .e45 <- exp(-.e36) .e48 <- .e41 * .e22/.e10 .e49 <- exp(-(2 * .e36)) .e50 <- 0.5 * geno_q .e51 <- 4 * .e48 .e52 <- t0 * .e20 .e54 <- .e52 * .e3/.e10 .e55 <- .e40 + .e51 .e56 <- 4 * .e54 .e57 <- .e40 - .e56 .e58 <- 1 - .e50 .e59 <- t0 * .e32 .e60 <- .e32/.e12 .e61 <- .e20 * .e39 .e62 <- 0.5 * .e43 .e65 <- .e42/.e24 + 0.5 .e67 <- .e3/.e38 - 0.5 .e68 <- exp(-(tij * .e10)) .e69 <- .e23/.e39 .e70 <- 2 * .e60 .e71 <- 0.5 * .e59 .e76 <- .e70 + 4 * (.e71 + 4 * .e69 + f0 + .e17 - m0) .e77 <- .e55 * .e26 .e78 <- 2 * .e42 .e80 <- .e76 * .e3/.e10 .e82 <- (-.e19)^2 .e83 <- .e38^2 .e84 <- .e24^3 .e85 <- .e82 * .e14 .e87 <- 1/.e14 .e88 <- 2 * (.e23/.e9) .e89 <- 2 * .e27 .e91 <- .e43 - .e12/.e3 .e92 <- .e62 - .e13 .e93 <- .e21^2 .e95 <- .e20 * .e12^2 * .e49 .e96 <- t0 * .e65 .e97 <- tij * .e67 .e98 <- .e88 + .e89 .e99 <- .e97/.e10 .e100 <- 2 * .e99 .e105 <- .e35/.e85 + 2 * (.e96/.e10) .e107 <- 2 * (.e57 * .e10) + 8 * (.e41/.e10) .e108 <- .e100 - .e77/.e83 .e109 <- .e45^2 .e110 <- .e5 * .e93 .e114 <- 2 * (.e57 * .e32/.e20) + 4 * .e80 .e116 <- .e105 * .e45 + .e108 * .e68 .e117 <- .e84 * .e10 .e119 <- (-(4 * (.e9/.e14)))^2 .e120 <- 2 * .e28 .e123 <- .e91 * .e10/.e78 + .e43 .e126 <- .e92 * .e10/.e78 + .e62 .e127 <- .e28 + 1/(2 * .e14) .e128 <- .e3^2 .e129 <- .e87 + .e120 .e133 <- .e65 * .e45 + .e67 * .e68 .e134 <- .e20 * .e7 .e135 <- 2 * (.e123/.e14) .e136 <- 2 * (.e126/.e14) .e137 <- .e119 * .e14 .e138 <- (2 * (.e38 * .e10))^2 .e139 <- .e38 * .e3 .e140 <- .e107 * .e32 .e141 <- .e5/.e10 .e144 <- .e139/.e10 .e146 <- 32 * .e80 + 64 * (.e140 * .e10/.e61) .e147 <- .e58 * .e7 .e148 <- .e61 * .e49 .e150 <- .e134 * .e22/.e10 .e151 <- 2 + .e135 .e154 <- .e147 * .e3 .e158 <- .e35/2 + .e87 .e161 <- .e14/.e24 + 1/.e38 .e162 <- 0.5 - 0.5 * (.e8/.e9) .e164 <- 2 * (.e127/.e14) .e165 <- 2 * (.e129/.e14) .e167 <- 2 * (.e35 * .e10) + 8 * .e3 .e169 <- 4 * .e144 - 2 * (.e77 * .e10) .e174 <- .e128/.e9 .e176 <- 2 * (.e114 * .e32 * .e109/.e95) + 256 * (.e110/.e117) .e179 <- .e133 * .e146 .e182 <- 0.5 * geno_f .e183 <- 1 - (.e154/.e9 + .e50) .e184 <- 32 * (.e116 * .e32 * .e3) .e185 <- .e179 + .e184 .e186 <- (2 * (.e32 * .e45 * .e3/.e12))^2 .e187 <- .e41/.e9 .e188 <- .e20 * .e49 .e189 <- .e12 * .e10 .e190 <- .e14^2 .e191 <- 1 + .e136 .e193 <- t0 * .e39/.e10 .e195 <- .e167/.e137 + .e169/.e138 .e196 <- 1 - .e182 .e197 <- (.e4 * .e21/.e24)^2 .e198 <- .e24^4 .e199 <- .e110 * .e3 .e201 <- .e61 * .e12 * .e49 .e202 <- .e141 - .e10 .e204 <- 2 * .e141 - .e24 .e205 <- (.e150 + 1 + .e136) * .e26 .e210 <- .e186/.e188 + 32 * (.e197 * .e3) .e211 <- .e148 * .e10 .e212 <- (.e151 + 2 * .e150) * .e26 .e213 <- .e23/.e198 .e215 <- 1 + 32 * (.e199/.e84) .e216 <- .e164 + 2 * .e48 .e217 <- .e165 + .e51 .e218 <- 4 * (.e162/.e10) .e219 <- 4 * (.e183/.e10) .e221 <- t0 * .e98/.e10 .e222 <- .e55 * .e7 .e224 <- 1 - .e205 .e225 <- 1 - 0.5 * geno_b .e226 <- 2 - .e212 .e227 <- 2 * .e9 .e228 <- 4 * .e174 .e229 <- 8 * .e174 .e234 <- .e185 * .e4 * .e45 * .e21/.e201 - .e161 * .e176 * .e3/.e24 .e235 <- .e77 + .e38 * .e35/.e24 .e237 <- .e162 * .e20 + .e191 * .e3 .e238 <- .e20 * (8 - 2 * .e193) .e239 <- .e42/.e9 .e240 <- .e3 * .e190 .e241 <- .e164 - .e187 .e242 <- .e165 - 2 * .e187 .e243 <- (.e158 * .e91 * .e58/.e42 + .e219)/.e14 .e244 <- (.e158 * .e92/.e42 + .e218)/.e14 .e245 <- (.e158/.e14 - .e228)/.e14 .e246 <- ((.e33 + 4/.e14)/.e14 - .e229)/.e14 .e247 <- .e216 * .e26 .e248 <- .e217 * .e26 .e249 <- 0.5 * .e98 .e250 <- 2 * .e98 .e251 <- .e85^2 .e252 <- .e137^2 .e254 <- .e234 * .e3 - (.e210 * .e195 + .e215 * .e22/.e10) .e256 <- .e211^2 .e257 <- .e148^2 .e258 <- .e95^2 .e259 <- .e188^2 .e260 <- .e117^2 .e261 <- .e91 * .e58 .e263 <- (.e135 + 4 - .e134/.e9) * .e3 + .e19 .e264 <- .e38 * .e7 .e265 <- .e5/.e39 .e268 <- 2 * ((.e60 + .e88 + .e89)/.e189) .e269 <- .e98 + 2 * .e59 .e270 <- 4 * (0.5 * .e221 + 32 * .e213) .e272 <- t0 * .e105 * .e45 .e273 <- t0 * .e12 .e275 <- tij * .e108 * .e68 .e276 <- .e116 * .e98 .e279 <- (.e222 + 4 * .e237) * .e22/.e10 + .e244 .e280 <- .e57 * .e58 .e281 <- .e57 * .e98 .e285 <- .e92/.e240 + .e218 .e286 <- .e58 * .e226 .e288 <- .e191 * .e39 + .e20 * (4 - .e193) * .e7 .e293 <- (16 - 4 * .e193) * .e20 * .e3 + 2 * (.e129 * .e39/.e14) .e294 <- .e247/.e83 .e295 <- .e248/.e83 .e296 <- .e76/.e9 .e298 <- .e238 * .e7 + .e39 * .e151 .e300 <- .e238 * .e3 + 2 * (.e127 * .e39/.e14) .e301 <- .e39 * .e5 .e302 <- .e35 * .e7 .e304 <- .e239 + 1/.e24 .e305 <- 0.5 - .e8/.e227 .e307 <- 1/.e12 + t0 .e308 <- 1/.e190 .e310 <- 1/.e10 + 2 * .e239 .e312 <- 2 * .e222 + 4 * .e263 .e314 <- 2 * .e55 + 4 * .e241 .e315 <- 2/.e190 .e317 <- 4 * .e55 + 4 * .e242 .e318 <- .e254 * .e3 .e320 <- .e276 * .e3/.e10 .e322 <- .e243 + .e58 * .e312 * .e22/.e10 .e323 <- .e245 + .e314 * .e3 * .e22 .e324 <- .e288 * .e10 .e325 <- .e293 * .e10 .e326 <- .e298 * .e10 .e327 <- .e300 * .e10 .e329 <- .e281 * .e3/.e10 .e330 <- .e57/.e10 .e331 <- .e55/.e10 .e332 <- .e246 + .e317 * .e3 * .e22 .e335 <- .e261/.e240 + .e219 .e337 <- .e304/.e24 .e338 <- .e65/.e9 .e339 <- .e67/.e9 .e340 <- (0.5 - .e224 * .e3/.e38)/.e38 .e342 <- .e305 * .e14 - .e92/2 .e347 <- (1 - (.e286 * .e3/.e38 + .e50))/.e38 .e351 <- .e183 * .e14 - .e261/2 .e354 <- .e58 * .e35 .e355 <- .e215/.e9 .e356 <- .e310/.e24 .e357 <- (2 - 2 * .e273) * .e20 .e359 <- (2 * (.e202/.e12) + 4 * (0.5 + 0.5 * (t0 * .e202) + 2 * .e265)) * .e3/.e10 .e361 <- (2 * ((0.5 * .e60 + .e249)/.e189) + 4 * (0.25 * .e221 + 16 * .e213)) * .e7 * .e3 .e363 <- (2 * (.e196 * .e204/.e12) + 4 * ((0.5 * (t0 * .e204) + 4 * .e265) * .e196 + 1 - .e182)) * .e3/.e10 .e364 <- .e176/.e9 .e367 <- .e296 + .e268 + .e270 .e368 <- .e264/.e9 .e369 <- .e264/.e10 .e370 <- .e139/.e9 .e372 <- .e61 * .e7/.e10 .e374 <- .e61 * .e3/.e10 .e375 <- .e20 * .e14 .e377 <- .e301 * .e93/.e260 .e380 <- .e35 * .e3/.e9 .e381 <- .e35/.e10 .e382 <- (4 * (4/.e39 + t0/.e10) + 4/.e189) * .e3 .e386 <- .e5 * .e7 * .e93 * .e3/.e117 .e387 <- .e23 * .e22 .e388 <- .e199/(.e198 * .e10) .e389 <- .e110/.e84 .e390 <- .e7 * .e14 .e391 <- .e3/.e9 .e392 <- .e14 * .e10 .e393 <- 0.5 * (.e235/.e38) .e394 <- .e249 + .e59 .e395 <- .e268 + .e270 .e396 <- 2 * ((.e70 + .e250)/.e189) .e397 <- .e250 + 4 * .e59 .e399 <- 2 * t0 + 2/.e12 .e400 <- .e228 - .e308 .e401 <- 4 * (64 * .e213 + .e221) .e402 <- 4 * (t0 * .e237/.e10) .e403 <- 4 * (t0 * (.e183 * .e20 + .e58 * .e151 * .e3)/.e10) .e404 <- .e229 - .e315 .e405 <- .e272 + .e275 .e406 <- t0 * .e241 .e407 <- t0 * .e242 .e409 <- .e52 * .e7/.e10 c(b0 = ((((((((.e295 - .e100) * .e68 - (.e310/2 + 2 * .e96) * .e45/.e10) * .e146 + 32 * (((2 * (tij * (.e295 - 2 * .e339) * .e3/.e10) - (.e332/.e10 + 2 * (.e55 * .e217 * .e26/.e38)) * .e26/.e83) * .e68 - (.e116 * .e293/.e61 + ((.e404/.e85 + 2 * (t0 * (.e356 + 2 * .e338) * .e3))/.e10 + .e35 * (8 * (.e129 * .e10/.e14) - .e82/.e10)/.e251) * .e45 + (2 * .e272 + 2 * .e275) * .e3/.e10)) * .e32 - 2 * .e320) - .e185 * .e399/.e10) * .e3/.e148 + .e133 * (64 * ((((2 * (.e246 + (2 * .e330 - 4 * .e407) * .e3) + 8 * (.e242 * .e3/.e10)) * .e32 - .e107 * .e397 * .e3/.e10) * .e10 + .e140 * (.e120 - 2 * (.e325/.e61))) * .e49/.e257) - 32 * (((.e325 + 2 * .e374) * .e76 * .e49/.e256 + (.e396 + .e401) * .e3/.e211) * .e3))) * .e4 * .e45 * .e21/.e12 + ((2 * .e355 + 384 * .e388) * .e22 - ((.e295 - .e356) * .e176 + .e161 * (2 * ((((2 * ((((.e246 - 4 * (.e407 * .e3))/.e10 - 2 * (.e57 * .e129/.e375)) * .e32 - 2 * .e329)/.e20) - 4 * ((.e396 + 2 * .e296 + .e401) * .e128/.e10)) * .e32 - .e114 * .e397 * .e3/.e10)/.e95 - (.e20 * (4 - 4 * .e273) * .e3/.e10 + 2 * (.e129 * .e12/.e14)) * .e114 * .e32 * .e12 * .e49/.e258) * .e109) - (2 * .e364 + 4096 * .e377) * .e3)) * .e3/2)/.e10) * .e3 + ((.e165 - .e56) * .e186 * .e49/.e259 + (256 * .e389 + 8 * ((.e32 * .e399 + .e250) * .e32 * .e109 * .e3/.e95)) * .e128/.e10) * .e195 - .e210 * (2 * (((2 * .e381 - 8 * .e391) * .e3 + .e315)/.e137) - ((2 * (((.e317 * .e22 + 2 * .e331) * .e3 + .e246) * .e26) + 4 * ((.e248 + 2 * .e370) * .e3/.e10) + 8 * ((2 * .e144 - .e248 * .e10) * .e38 * .e169 * .e10/.e138))/.e138 + .e167 * (32 * ((.e9/.e392 + 4 * .e3) * .e9/.e14) - .e119/.e10)/.e252))) * .e3 - 0.5 * (((.e332 * .e26 - ((.e404/.e10 + 2 * .e380) * .e38 + .e217 * .e35 * .e26)/2)/.e10 + .e235 * .e217 * .e26/.e38)/.e38)) * .e7 + .e318 - .e393) * .e225^2, b2 = geno_b * ((((((((.e294 - .e99) * .e68 - (.e304/2 + .e96) * .e45/.e10) * .e146 + 32 * (((2 * (tij * (.e294 - .e339) * .e3/.e10) - (.e323/.e10 + 2 * (.e55 * .e216 * .e26/.e38)) * .e26/.e83) * .e68 - (.e116 * .e300/.e61 + ((.e400/.e85 + 2 * (t0 * (.e337 + .e338) * .e3))/.e10 + .e35 * (8 * (.e127 * .e10/.e14) - .e82/.e24)/.e251) * .e45 + .e3 * .e405/.e10)) * .e32 - .e320) - .e185 * .e307/.e10) * .e3/.e148 + .e133 * (64 * ((((2 * ((.e330 - 4 * .e406) * .e3 + .e245) + 8 * (.e241 * .e3/.e10)) * .e32 - .e107 * .e269 * .e3/.e10) * .e10 + (.e28 - 2 * (.e327/.e61)) * .e107 * .e32) * .e49/.e257) - 32 * (((.e327 + .e374) * .e76 * .e49/.e256 + .e395 * .e3/.e211) * .e3))) * .e4 * .e45 * .e21/.e12 + ((.e355 + 192 * .e388) * .e22 - ((.e294 - .e337) * .e176 + .e161 * (2 * ((((2 * ((((.e245 - 4 * (.e406 * .e3))/.e10 - 2 * (.e57 * .e127/.e375)) * .e32 - .e329)/.e20) - 4 * (.e367 * .e128/.e10)) * .e32 - .e114 * .e269 * .e3/.e10)/.e95 - (.e357 * .e3/.e10 + 2 * (.e127 * .e12/.e14)) * .e114 * .e32 * .e12 * .e49/.e258) * .e109) - (.e364 + 2048 * .e377) * .e3)) * .e3/2)/.e10) * .e3 + ((128 * .e389 + 8 * ((.e307 * .e32 + .e88 + .e89) * .e32 * .e109 * .e3/.e95)) * .e128/.e10 + (.e164 - 2 * .e54) * .e186 * .e49/.e259) * .e195 - .e210 * (2 * (((.e381 - 4 * .e391) * .e3 + .e308)/.e137) - ((2 * (((.e331 + .e314 * .e22) * .e3 + .e245) * .e26) + 4 * ((.e247 + .e370) * .e3/.e10) + 8 * ((.e144 - .e247 * .e10) * .e38 * .e169 * .e10/.e138))/.e138 + .e167 * (32 * ((.e9/(2 * .e392) + .e11) * .e9/.e14) - .e119/.e24)/.e252))) * .e3 - 0.5 * (((.e323 * .e26 - ((.e380 + .e400/.e10) * .e38 + .e216 * .e35 * .e26)/2)/.e10 + .e235 * .e216 * .e26/.e38)/.e38)) * .e7 + 0.5 * (.e318 - .e393)) * .e225, q0 = (((((((.e351/2 - .e96 * .e58 * .e7) * .e45/.e10 + (.e347 - .e97 * .e58 * .e7/.e10) * .e68) * .e146 + 32 * ((((.e335/.e85 + 2 * (t0 * (.e351/.e24 - .e65 * .e58 * .e7/.e9)/.e10) - .e354 * (8 * (.e123 * .e10/.e14) - .e82 * .e91/.e11)/.e251) * .e45 + (2 * (tij * (.e347 - .e67 * .e58 * .e7/.e9)/.e10) - (.e243 + (.e312 * .e22/.e10 - 2 * (.e55 * .e226/.e38)) * .e58) * .e26/.e83) * .e68 - .e147 * .e405/.e10) * .e32 - .e116 * .e58 * .e98 * .e7/.e10) * .e3 + .e116 * (1 - (.e298 * .e58 * .e3/.e61 + .e50)) * .e32) - .e185 * .e58 * .e307 * .e7/.e10)/.e148 + .e133 * (32 * (((.e76 - .e395 * .e7 * .e3)/.e211 - (.e326 + .e372) * .e76 * .e49 * .e3/.e256) * .e58) + 64 * ((((2 * ((.e243 - .e403) * .e10 + .e280 * .e7/.e10) + 8 * (.e263 * .e58/.e10)) * .e32 - .e58 * .e107 * .e269 * .e7/.e10) * .e10 + (.e43 - 2 * (.e326/.e61)) * .e58 * .e107 * .e32) * .e49/.e257))) * .e4 * .e45 * .e21/.e12 - ((.e161 * (2 * ((((2 * (((.e243 - (.e280 * .e151/.e20 + .e403)) * .e32 - .e280 * .e98 * .e7/.e10)/.e20) + 4 * (.e58 * (.e76 - .e367 * .e7 * .e3)/.e10)) * .e32 - .e58 * .e114 * .e269 * .e7/.e10)/.e95 - (.e357 * .e7/.e10 + .e151 * .e12) * .e58 * .e114 * .e32 * .e12 * .e49/.e258) * .e109) - 2048 * (.e58 * .e39 * .e5 * .e7 * .e93/.e260)) - ((.e91/.e11 + .e390/.e9)/.e24 + .e226/.e83) * .e58 * .e176) * .e3 + .e161 * .e183 * .e176)/.e24) * .e3 + .e234 * .e58 - (((.e58 * (4 * (((4 - (.e368 + .e212)) * .e3 - .e37)/.e10) - 8 * ((.e226 * .e10 + .e369) * .e38 * .e169 * .e10/.e138)) - 2 * ((.e322 * .e10 + .e55 * .e58 * .e7/.e10) * .e26))/.e138 + (2 * (.e335 * .e10 + .e354 * .e7/.e10) + 8 * .e58)/.e137 - .e58 * .e167 * (32 * ((.e9 * .e91/.e78 + 2 * .e7) * .e9/.e14) - .e119 * .e91/.e11)/.e252) * .e210 + (.e58 * (32 * (.e197 - 4 * .e386) - .e186 * (.e151 - 2 * .e409) * .e49/.e259) + 8 * (((1 - (.e154/.e189 + .e50)) * .e32 - .e58 * (.e98 + .e59) * .e7 * .e3/.e10) * .e32 * .e109 * .e3/.e95)) * .e195 + (32 * ((1 - (.e50 + 6 * (.e154/.e10))) * .e5 * .e93/.e84) - .e58 * .e215 * .e7/.e9) * .e22/.e10)) * .e3 + .e254 * .e58 - 0.5 * (((((.e91/.e240 - .e302/.e9) * .e58 + .e219) * .e38 + .e286 * .e35)/.e24 + .e322 * .e26 - .e235 * .e58 * .e226/.e38)/.e38)) * .e225 * .e6, q2 = geno_q * (((((((.e342/2 - 0.5 * (.e96 * .e7)) * .e45/.e10 + (.e340 - 0.5 * (.e97 * .e7/.e10)) * .e68) * .e146 + 32 * ((((.e285/.e85 + 2 * (t0 * (.e342/.e24 - 0.5 * (.e65 * .e7/.e9))/.e10) - .e35 * (8 * (.e126 * .e10/.e14) - .e82 * .e92/.e11)/.e251) * .e45 + (2 * (tij * (.e340 - 0.5 * (.e67 * .e7/.e9))/.e10) - (.e279 - 2 * (.e55 * .e224/.e38)) * .e26/.e83) * .e68 - (0.5 * .e272 + 0.5 * .e275) * .e7/.e10) * .e32 - 0.5 * (.e276 * .e7/.e10)) * .e3 + .e116 * (0.5 - .e288 * .e3/.e61) * .e32) - .e185 * (0.5 * t0 + 0.5/.e12) * .e7/.e10)/.e148 + .e133 * (32 * ((0.5 * .e76 - .e361)/.e211 - (.e324 + 0.5 * .e372) * .e76 * .e49 * .e3/.e256) + 64 * ((((2 * ((.e244 - .e402) * .e10 + 0.5 * (.e57 * .e7/.e10)) + 8 * (.e237/.e10)) * .e32 - .e394 * .e107 * .e7/.e10) * .e10 + (.e62 - 2 * (.e324/.e61)) * .e107 * .e32) * .e49/.e257))) * .e4 * .e45 * .e21/.e12 - ((.e161 * (2 * ((((2 * (((.e244 - (.e57 * .e191/.e20 + .e402)) * .e32 - 0.5 * (.e281 * .e7/.e10))/.e20) + 4 * ((.e162 * .e76 - .e361)/.e10)) * .e32 - .e394 * .e114 * .e7/.e10)/.e95 - ((1 - .e273) * .e20 * .e7/.e10 + .e191 * .e12) * .e114 * .e32 * .e12 * .e49/.e258) * .e109) - 1024 * (.e301 * .e7 * .e93/.e260)) - ((.e92/.e11 + .e390/.e227)/.e24 + .e224/.e83) * .e176) * .e3 + .e161 * .e305 * .e176)/.e24) * .e3 + 0.5 * .e234 - (((2 * (.e285 * .e10 + 0.5 * (.e302/.e10)) + 4)/.e137 + (4 * (((1 - (.e205 + 0.5 * .e368)) * .e3 + 0.5 * .e38)/.e10) - (2 * ((.e279 * .e10 + 0.5 * (.e222/.e10)) * .e26) + 8 * ((.e224 * .e10 + 0.5 * .e369) * .e38 * .e169 * .e10/.e138)))/.e138 - .e167 * (32 * ((.e9 * .e92/.e78 + .e7) * .e9/.e14) - .e119 * .e92/.e11)/.e252) * .e210 + .e195 * (32 * (0.5 * .e197 - 2 * .e386) + 8 * (((0.5 - 0.5 * (.e8/.e189)) * .e32 - (.e249 + .e71) * .e7 * .e3/.e10) * .e32 * .e109 * .e3/.e95) - (.e191 - .e409) * .e186 * .e49/.e259) + (32 * ((0.5 - 3 * .e8/.e227) * .e5 * .e93/.e84) - 0.5 * (.e215 * .e7/.e9)) * .e22/.e10)) * .e3 + 0.5 * .e254 - 0.5 * ((.e279 * .e26 + ((.e285 - .e302/.e227) * .e38 + .e224 * .e35)/.e24 - .e235 * .e224/.e38)/.e38)) * .e225 * .e6, f0 = (((.e133 * (32 * .e363 + 64 * (.e196 * .e107 * .e204 * .e10/.e61)) + 32 * (.e116 * .e196 * .e204 * .e3)) * .e21 + .e185 * .e196) * .e4 * .e45/.e201 - ((.e195 * (64 * .e69 + 8 * (.e32 * .e204 * .e109 * .e3/.e95)) + 64 * (.e387/.e117)) * .e196 + .e161 * (2 * ((.e196 * .e114 * .e204 + (2 * (.e57 * .e196 * .e204/.e20) + 4 * .e363) * .e32) * .e109/.e95) + 512 * (.e196 * .e5 * .e21/.e117)) * .e3/.e24)) * .e225 * .e6 * .e128, f2 = geno_f * (((.e133 * (32 * .e359 + 64 * (.e202 * .e107 * .e10/.e61)) + 32 * (.e116 * .e202 * .e3)) * .e21 + 0.5 * .e185) * .e4 * .e45/.e201 - ((.e161 * (2 * ((.e202 * .e114 + (2 * (.e57 * .e202/.e20) + 4 * .e359) * .e32) * .e109/.e95) + 256 * (.e23/.e117)) * .e3/2 + 32 * (.e387/.e84))/.e10 + .e195 * (32 * .e69 + 8 * (.e202 * .e32 * .e109 * .e3/.e95)))) * .e225 * .e6 * .e128, f1 = ((.e195 * (16 * (.e32 * .e109 * .e3/(.e95 * .e10)) + 64 * (.e21/.e39)) + .e161 * (2 * ((.e32 * (4 * (.e57/.e20) + 4 * .e382) + 2 * .e114) * .e109/.e95) + 512 * (.e21/.e84)) * .e3/.e227 + 64 * (.e21 * .e22/.e117)) * .e4 - ((.e133 * (128 * (.e107/.e61) + 32 * (.e382/.e10)) + 64 * (.e116 * .e3/.e10)) * .e5 * .e21 + .e179 + .e184) * .e45/.e201) * .e225 * .e4 * .e6 * .e128) } deriv_mu_int_b2_bqff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- b0 + geno_b * (b2 - b0)/2 .e7 <- .e6^2 .e8 <- .e7 * .e3 .e9 <- .e5 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e17 <- geno_f * (f2 - f0)/2 .e18 <- f0 + .e17 .e19 <- 2 * (.e10/.e14) .e20 <- .e11 + .e19 .e21 <- .e18 - f1 .e22 <- tij - t0 .e23 <- .e5 * .e21 .e24 <- 2 * .e10 .e26 <- exp(2 * (.e10 * .e22)) .e27 <- .e18 - m0 .e30 <- .e3/.e10 .e32 <- 2 * (.e23/.e10) - 2 * (.e27 * .e10) .e33 <- t0 * .e10 .e34 <- .e20 * .e26 .e35 <- .e11 - .e34 .e36 <- .e24^2 .e37 <- .e7/.e10 .e39 <- 1/.e14 + 2 * .e30 .e40 <- .e3 * .e14 .e41 <- .e20 * .e3 .e43 <- exp(-.e33) .e44 <- 0.5 * geno_q .e46 <- exp(-(2 * .e33)) .e47 <- 1 - .e44 .e50 <- 2 * (.e41 * .e22/.e10) .e51 <- 4 * .e30 .e52 <- t0 * .e20 .e53 <- 0.5 * .e37 .e54 <- 2 * (.e52 * .e3/.e10) .e57 <- 0.5 * ((2/.e14 + .e51)/.e14) - .e54 .e59 <- .e39/.e14 + .e50 .e60 <- t0 * .e32 .e61 <- .e32/.e12 .e62 <- 2 * .e40 .e64 <- .e20 * .e36 .e66 <- .e40/.e24 + 0.5 .e68 <- .e3/.e35 - 0.5 .e69 <- exp(-(tij * .e10)) .e70 <- .e23/.e36 .e71 <- 0.5 * .e60 .e72 <- .e61 + 2 * (.e71 + 4 * .e70 + f0 + .e17 - m0) .e73 <- .e59 * .e26 .e75 <- .e37 - .e12/.e3 .e76 <- .e53 - .e13 .e78 <- .e72 * .e3/.e10 .e80 <- (-.e19)^2 .e81 <- 2 * .e14 .e82 <- .e35^2 .e83 <- .e24^3 .e84 <- 1/.e81 .e85 <- .e80 * .e14 .e87 <- 2 * (.e23/.e9) .e88 <- 2 * .e27 .e90 <- .e20 * .e12^2 * .e46 .e91 <- .e21^2 .e92 <- t0 * .e66 .e93 <- tij * .e68 .e94 <- .e93/.e10 .e98 <- .e39/.e85 + .e92/.e10 .e101 <- 2 * (.e57 * .e10) + 4 * (.e41/.e10) .e102 <- .e43^2 .e103 <- .e94 - .e73/.e82 .e104 <- .e87 + .e88 .e107 <- .e75 * .e10/.e62 + .e37 .e110 <- .e76 * .e10/.e62 + .e53 .e111 <- .e30 + .e84 .e115 <- .e98 * .e43 + .e69 * .e103 .e118 <- .e20 * .e7 .e119 <- .e83 * .e10 .e120 <- 2 * (.e107/.e14) .e121 <- 2 * (.e110/.e14) .e123 <- 2 * (.e57 * .e32/.e20) + 4 * .e78 .e124 <- .e5 * .e91 .e126 <- (-(4 * (.e9/.e14)))^2 .e127 <- .e5/.e10 .e129 <- .e66 * .e43 + .e68 * .e69 .e130 <- .e47 * .e7 .e132 <- .e118 * .e22/.e10 .e133 <- 2 + .e120 .e134 <- .e126 * .e14 .e136 <- .e130 * .e3 .e137 <- (2 * (.e35 * .e10))^2 .e139 <- 0.5 - 0.5 * (.e8/.e9) .e140 <- 2 * (.e111/.e14) .e144 <- .e35 * .e3 .e146 <- 32 * .e78 + 64 * (.e101 * .e32 * .e10/.e64) .e149 <- .e144/.e10 .e151 <- .e14/.e24 + 1/.e35 .e152 <- 0.5 * geno_f .e153 <- 1 - (.e136/.e9 + .e44) .e156 <- .e64 * .e46 .e157 <- .e3^2 .e158 <- 1 + .e121 .e161 <- 2 * (.e39 * .e10) + 4 * .e3 .e163 <- 2 * .e149 - 2 * (.e73 * .e10) .e166 <- .e129 * .e146 .e171 <- 1 - .e152 .e173 <- 128 * (.e124/.e119) + 2 * (.e123 * .e32 * .e102/.e90) .e174 <- 32 * (.e115 * .e32 * .e3) .e175 <- .e166 + .e174 .e176 <- .e12 * .e10 .e178 <- .e39/2 + .e84 .e180 <- .e161/.e134 + .e163/.e137 .e181 <- (2 * (.e32 * .e43 * .e3/.e12))^2 .e182 <- .e20 * .e46 .e183 <- .e127 - .e10 .e184 <- .e14^2 .e186 <- 2 * .e127 - .e24 .e188 <- t0 * .e36/.e10 .e189 <- (.e132 + 1 + .e121) * .e26 .e190 <- (.e4 * .e21/.e24)^2 .e191 <- .e139/.e10 .e192 <- .e153/.e10 .e194 <- .e64 * .e12 * .e46 .e195 <- (.e133 + 2 * .e132) * .e26 .e196 <- .e140 + .e50 .e197 <- .e59 * .e7 .e198 <- .e24^4 .e199 <- .e124 * .e3 .e200 <- .e157/.e9 .e201 <- 1 - .e189 .e202 <- 2 - .e195 .e203 <- 2 * .e9 .e205 <- .e75 * .e47 .e207 <- .e139 * .e20 + .e158 * .e3 .e209 <- .e181/.e182 + 32 * (.e190 * .e3) .e210 <- .e156 * .e10 .e211 <- .e20 * (8 - 2 * .e188) .e213 <- .e23/.e198 .e216 <- 0.5 + 16 * (.e199/.e83) .e217 <- .e140 - .e41/.e9 .e218 <- 2 * .e191 .e219 <- 2 * .e192 .e220 <- 2 * (.e3 * .e184) .e221 <- .e51 + 4/.e14 .e223 <- t0 * .e104/.e10 .e228 <- .e175 * .e4 * .e43 * .e21/.e194 - .e151 * .e173 * .e3/.e24 .e229 <- .e196 * .e26 .e230 <- 0.5 * .e104 .e231 <- 2 * .e200 .e232 <- .e73 + .e39 * .e35/.e24 .e233 <- (.e61 + .e87 + .e88)/.e176 .e235 <- (.e120 + 4 - .e118/.e9) * .e3 + .e19 .e236 <- .e35 * .e7 .e237 <- .e5/.e36 .e240 <- .e104 + 2 * .e60 .e241 <- 2 * (0.5 * .e223 + 32 * .e213) .e242 <- .e85^2 .e243 <- .e134^2 .e245 <- .e228 * .e3 - (.e180 * .e209 + .e216 * .e22/.e10) .e248 <- (.e197 + 2 * .e207) * .e22/.e10 + (.e178 * .e76/.e40 + .e218)/.e14 .e249 <- (.e178 * .e75 * .e47/.e40 + .e219)/.e14 .e250 <- (.e178/.e14 - .e231)/.e14 .e251 <- .e210^2 .e252 <- .e156^2 .e253 <- .e90^2 .e254 <- .e182^2 .e255 <- .e119^2 .e258 <- .e57 * .e47 .e260 <- .e76/.e220 + .e218 .e261 <- .e47 * .e39 .e263 <- .e158 * .e36 + .e20 * (4 - .e188) * .e7 .e264 <- .e39 * .e7 .e265 <- .e229/.e82 .e267 <- .e211 * .e7 + .e36 * .e133 .e269 <- .e211 * .e3 + 2 * (.e111 * .e36/.e14) .e272 <- .e40/.e9 + 1/.e24 .e273 <- 0.5 - .e8/.e203 .e274 <- 1/(2 * .e184) .e276 <- 1/.e12 + t0 .e278 <- 2 * .e197 + 2 * .e235 .e280 <- 2 * .e59 + 2 * .e217 .e282 <- t0 * .e98 * .e43 .e283 <- t0 * .e12 .e285 <- tij * .e69 * .e103 .e286 <- .e115 * .e104 .e287 <- .e249 + .e47 * .e278 * .e22/.e10 .e288 <- .e250 + .e280 * .e3 * .e22 .e290 <- (.e183/.e12 + 2 * (0.5 + 0.5 * (t0 * .e183) + 2 * .e237)) * .e3/.e10 .e293 <- ((0.5 * .e61 + .e230)/.e176 + 2 * (0.25 * .e223 + 16 * .e213)) * .e7 * .e3 .e296 <- (.e171 * .e186/.e12 + 2 * ((0.5 * (t0 * .e186) + 4 * .e237) * .e171 + 1 - .e152)) * .e3/.e10 .e297 <- .e263 * .e10 .e299 <- .e233 + .e72/.e9 + .e241 .e300 <- .e233 + .e241 .e301 <- .e267 * .e10 .e302 <- .e269 * .e10 .e305 <- .e205/.e220 + .e219 .e307 <- .e272/.e24 .e308 <- (0.5 - .e201 * .e3/.e35)/.e35 .e310 <- .e273 * .e14 - .e76/2 .e311 <- .e57 * .e104 .e312 <- (1 - (.e47 * .e202 * .e3/.e35 + .e44))/.e35 .e316 <- .e153 * .e14 - .e205/2 .e317 <- (2 - 2 * .e283) * .e20 .e318 <- (2 * (4/.e36 + t0/.e10) + 2/.e176) * .e3 .e319 <- .e236/.e9 .e320 <- .e236/.e10 .e322 <- .e64 * .e7/.e10 .e323 <- .e36 * .e5 .e327 <- .e5 * .e7 * .e91 * .e3/.e119 .e328 <- .e23 * .e22 .e329 <- .e7 * .e14 .e330 <- 0.5 * ((.e205 * .e221/.e62 + 4 * .e192)/.e14) .e331 <- 0.5 * ((.e76 * .e221/.e62 + 4 * .e191)/.e14) .e332 <- 0.5 * ((.e221/.e81 - 4 * .e200)/.e14) .e333 <- .e230 + .e60 .e334 <- .e274 - .e231 .e335 <- 2 * (t0 * .e207/.e10) .e336 <- 2 * (t0 * (.e153 * .e20 + .e47 * .e133 * .e3)/.e10) .e337 <- .e282 + .e285 .e338 <- t0 * .e217 .e340 <- .e52 * .e7/.e10 c(b2 = geno_b^2 * ((((((((.e265 - .e94) * .e69 - (.e272/2 + .e92) * .e43/.e10) * .e146 + 32 * ((((.e334/.e85 - t0 * (.e307 + .e66/.e9) * .e3)/.e10 - .e39 * (8 * (.e111 * .e10/.e14) - .e80/.e24)/.e242) * .e43 + .e69 * (tij * (.e265 - .e68/.e9) * .e3/.e10 - (.e288/.e10 + 2 * (.e59 * .e196 * .e26/.e35)) * .e26/.e82) - (.e115 * .e269/.e64 + .e3 * .e337/.e10)) * .e32 - .e286 * .e3/.e10) - .e175 * .e276/.e10) * .e3/.e156 + .e129 * (64 * ((((2 * ((.e57/.e10 - 2 * .e338) * .e3 + .e332) + 4 * (.e217 * .e3/.e10)) * .e32 - .e101 * .e240 * .e3/.e10) * .e10 + (.e30 - 2 * (.e302/.e64)) * .e101 * .e32) * .e46/.e252) - 32 * ((.e300 * .e3/.e210 + (.e302 + .e64 * .e3/.e10) * .e72 * .e46/.e251) * .e3))) * .e4 * .e43 * .e21/.e12 + ((.e216/.e9 + 96 * (.e199/(.e198 * .e10))) * .e22 - ((.e265 - .e307) * .e173 + .e151 * (2 * ((((2 * ((((.e332 - 2 * (.e338 * .e3))/.e10 - 2 * (.e111 * .e57/(.e20 * .e14))) * .e32 - .e311 * .e3/.e10)/.e20) - 4 * (.e299 * .e157/.e10)) * .e32 - .e123 * .e240 * .e3/.e10)/.e90 - (.e317 * .e3/.e10 + 2 * (.e111 * .e12/.e14)) * .e123 * .e32 * .e12 * .e46/.e253) * .e102) - (.e173/.e9 + 1024 * (.e323 * .e91/.e255)) * .e3)) * .e3/2)/.e10) * .e3 + ((128 * (.e124/.e83) + 8 * ((.e276 * .e32 + .e87 + .e88) * .e32 * .e102 * .e3/.e90)) * .e157/.e10 + (.e140 - .e54) * .e181 * .e46/.e254) * .e180 - .e209 * (2 * (((.e39/.e10 - 2 * (.e3/.e9)) * .e3 + .e274)/.e134) - ((2 * (((.e59/.e10 + .e280 * .e22) * .e3 + .e250) * .e26) + 2 * ((.e229 + .e144/.e9) * .e3/.e10) + 8 * ((.e149 - .e229 * .e10) * .e163 * .e35 * .e10/.e137))/.e137 + .e161 * (32 * ((.e9/(2 * (.e14 * .e10)) + .e11) * .e9/.e14) - .e126/.e24)/.e243))) * .e3 - 0.5 * (((.e288 * .e26 + ((.e334/.e10 - .e39 * .e3/.e9) * .e35 - .e39 * .e196 * .e26)/2)/.e10 + .e232 * .e196 * .e26/.e35)/.e35)) * .e7 + 0.5 * (.e245 * .e3 - 0.5 * (.e232/.e35))), q0 = geno_b * (((((((.e316/2 - .e92 * .e47 * .e7) * .e43/.e10 + (.e312 - .e93 * .e47 * .e7/.e10) * .e69) * .e146 + 32 * ((((.e305/.e85 + t0 * (.e316/.e24 - .e66 * .e47 * .e7/.e9)/.e10 - .e261 * (8 * (.e107 * .e10/.e14) - .e80 * .e75/.e11)/.e242) * .e43 + .e69 * (tij * (.e312 - .e68 * .e47 * .e7/.e9)/.e10 - (.e249 + (.e278 * .e22/.e10 - 2 * (.e59 * .e202/.e35)) * .e47) * .e26/.e82) - .e130 * .e337/.e10) * .e32 - .e115 * .e47 * .e104 * .e7/.e10) * .e3 + .e115 * (1 - (.e267 * .e47 * .e3/.e64 + .e44)) * .e32) - .e175 * .e47 * .e276 * .e7/.e10)/.e156 + .e129 * (32 * (((.e72 - .e300 * .e7 * .e3)/.e210 - (.e301 + .e322) * .e72 * .e46 * .e3/.e251) * .e47) + 64 * ((((2 * ((.e330 - .e336) * .e10 + .e258 * .e7/.e10) + 4 * (.e235 * .e47/.e10)) * .e32 - .e47 * .e101 * .e240 * .e7/.e10) * .e10 + (.e37 - 2 * (.e301/.e64)) * .e47 * .e101 * .e32) * .e46/.e252))) * .e4 * .e43 * .e21/.e12 - ((.e151 * (2 * ((((2 * (((.e330 - (.e258 * .e133/.e20 + .e336)) * .e32 - .e258 * .e104 * .e7/.e10)/.e20) + 4 * ((.e72 - .e299 * .e7 * .e3) * .e47/.e10)) * .e32 - .e47 * .e123 * .e240 * .e7/.e10)/.e90 - (.e317 * .e7/.e10 + .e133 * .e12) * .e47 * .e123 * .e32 * .e12 * .e46/.e253) * .e102) - 1024 * (.e47 * .e36 * .e5 * .e7 * .e91/.e255)) - ((.e75/.e11 + .e329/.e9)/.e24 + .e202/.e82) * .e47 * .e173) * .e3 + .e151 * .e153 * .e173)/.e24) * .e3 + .e228 * .e47 - (((.e47 * (2 * (((4 - (.e319 + .e195)) * .e3 - .e34)/.e10) - 8 * ((.e202 * .e10 + .e320) * .e163 * .e35 * .e10/.e137)) - 2 * ((.e287 * .e10 + .e59 * .e47 * .e7/.e10) * .e26))/.e137 + (2 * (.e305 * .e10 + .e261 * .e7/.e10) + 4 * .e47)/.e134 - .e47 * .e161 * (32 * ((.e9 * .e75/.e62 + 2 * .e7) * .e9/.e14) - .e126 * .e75/.e11)/.e243) * .e209 + (.e47 * (32 * (.e190 - 4 * .e327) - .e181 * (.e133 - 2 * .e340) * .e46/.e254) + 8 * (((1 - (.e136/.e176 + .e44)) * .e32 - .e47 * (.e104 + .e60) * .e7 * .e3/.e10) * .e32 * .e102 * .e3/.e90)) * .e180 + (16 * ((1 - (.e44 + 6 * (.e136/.e10))) * .e5 * .e91/.e83) - .e216 * .e47 * .e7/.e9) * .e22/.e10)) * .e3 + .e245 * .e47 - 0.5 * (((((.e75/.e220 - .e264/.e9) * .e47 + .e219) * .e35 + .e261 * .e202)/.e24 + .e287 * .e26 - .e232 * .e47 * .e202/.e35)/.e35)) * .e6, q2 = geno_b * geno_q * (((((((.e310/2 - 0.5 * (.e92 * .e7)) * .e43/.e10 + (.e308 - 0.5 * (.e93 * .e7/.e10)) * .e69) * .e146 + 32 * ((((.e260/.e85 + t0 * (.e310/.e24 - 0.5 * (.e66 * .e7/.e9))/.e10 - .e39 * (8 * (.e110 * .e10/.e14) - .e80 * .e76/.e11)/.e242) * .e43 + .e69 * (tij * (.e308 - 0.5 * (.e68 * .e7/.e9))/.e10 - (.e248 - 2 * (.e59 * .e201/.e35)) * .e26/.e82) - (0.5 * .e282 + 0.5 * .e285) * .e7/.e10) * .e32 - 0.5 * (.e286 * .e7/.e10)) * .e3 + .e115 * (0.5 - .e263 * .e3/.e64) * .e32) - .e175 * (0.5 * t0 + 0.5/.e12) * .e7/.e10)/.e156 + .e129 * (32 * ((0.5 * .e72 - .e293)/.e210 - (.e297 + 0.5 * .e322) * .e72 * .e46 * .e3/.e251) + 64 * ((((2 * ((.e331 - .e335) * .e10 + 0.5 * (.e57 * .e7/.e10)) + 4 * (.e207/.e10)) * .e32 - .e333 * .e101 * .e7/.e10) * .e10 + (.e53 - 2 * (.e297/.e64)) * .e101 * .e32) * .e46/.e252))) * .e4 * .e43 * .e21/.e12 - ((.e151 * (2 * ((((2 * (((.e331 - (.e57 * .e158/.e20 + .e335)) * .e32 - 0.5 * (.e311 * .e7/.e10))/.e20) + 4 * ((.e72 * .e139 - .e293)/.e10)) * .e32 - .e333 * .e123 * .e7/.e10)/.e90 - ((1 - .e283) * .e20 * .e7/.e10 + .e158 * .e12) * .e123 * .e32 * .e12 * .e46/.e253) * .e102) - 512 * (.e323 * .e7 * .e91/.e255)) - ((.e76/.e11 + .e329/.e203)/.e24 + .e201/.e82) * .e173) * .e3 + .e151 * .e273 * .e173)/.e24) * .e3 + 0.5 * .e228 - (((2 * (((1 - (.e189 + 0.5 * .e319)) * .e3 + 0.5 * .e35)/.e10) - (2 * ((.e248 * .e10 + 0.5 * (.e197/.e10)) * .e26) + 8 * ((.e201 * .e10 + 0.5 * .e320) * .e163 * .e35 * .e10/.e137)))/.e137 + (2 + 2 * (.e260 * .e10 + 0.5 * (.e264/.e10)))/.e134 - .e161 * (32 * ((.e9 * .e76/.e62 + .e7) * .e9/.e14) - .e126 * .e76/.e11)/.e243) * .e209 + .e180 * (32 * (0.5 * .e190 - 2 * .e327) + 8 * (((0.5 - 0.5 * (.e8/.e176)) * .e32 - (.e230 + .e71) * .e7 * .e3/.e10) * .e32 * .e102 * .e3/.e90) - (.e158 - .e340) * .e181 * .e46/.e254) + (16 * ((0.5 - 3 * .e8/.e203) * .e5 * .e91/.e83) - 0.5 * (.e216 * .e7/.e9)) * .e22/.e10)) * .e3 + 0.5 * .e245 - 0.5 * ((.e248 * .e26 + ((.e260 - .e264/.e203) * .e35 + .e201 * .e39)/.e24 - .e232 * .e201/.e35)/.e35)) * .e6, f0 = geno_b * (((.e129 * (32 * .e296 + 64 * (.e171 * .e101 * .e186 * .e10/.e64)) + 32 * (.e115 * .e171 * .e186 * .e3)) * .e21 + .e175 * .e171) * .e4 * .e43/.e194 - ((.e180 * (64 * .e70 + 8 * (.e32 * .e186 * .e102 * .e3/.e90)) + 32 * (.e328/.e119)) * .e171 + .e151 * (2 * ((.e171 * .e123 * .e186 + (2 * (.e57 * .e171 * .e186/.e20) + 4 * .e296) * .e32) * .e102/.e90) + 256 * (.e171 * .e5 * .e21/.e119)) * .e3/.e24)) * .e6 * .e157, f2 = geno_b * geno_f * (((.e129 * (32 * .e290 + 64 * (.e183 * .e101 * .e10/.e64)) + 32 * (.e115 * .e183 * .e3)) * .e21 + 0.5 * .e175) * .e4 * .e43/.e194 - ((.e151 * (128 * (.e23/.e119) + 2 * ((.e183 * .e123 + (2 * (.e183 * .e57/.e20) + 4 * .e290) * .e32) * .e102/.e90)) * .e3/2 + 16 * (.e328/.e83))/.e10 + .e180 * (32 * .e70 + 8 * (.e183 * .e32 * .e102 * .e3/.e90)))) * .e6 * .e157, f1 = geno_b * ((.e180 * (16 * (.e32 * .e102 * .e3/(.e90 * .e10)) + 64 * (.e21/.e36)) + .e151 * (2 * ((.e32 * (4 * (.e57/.e20) + 4 * .e318) + 2 * .e123) * .e102/.e90) + 256 * (.e21/.e83)) * .e3/.e203 + 32 * (.e21 * .e22/.e119)) * .e4 - ((.e129 * (128 * (.e101/.e64) + 32 * (.e318/.e10)) + 64 * (.e115 * .e3/.e10)) * .e5 * .e21 + .e166 + .e174) * .e43/.e194) * .e4 * .e6 * .e157) } deriv_mu_int_q0_qff1b_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e6 * .e3 .e9 <- .e7 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e17 <- geno_f * (f2 - f0)/2 .e18 <- f0 + .e17 .e19 <- .e11 + 2 * (.e10/.e14) .e20 <- tij - t0 .e21 <- .e18 - f1 .e22 <- 2 * .e10 .e23 <- .e6/.e10 .e24 <- .e7 * .e21 .e25 <- .e11^2 .e27 <- 2 * (.e3 * .e10) .e29 <- exp(2 * (.e10 * .e20)) .e31 <- 2 * (.e12/.e25) .e33 <- .e6/.e27 - .e31 .e34 <- .e18 - m0 .e36 <- 2 * (.e34 * .e10) .e37 <- .e24/.e10 .e39 <- 2 * .e37 - .e36 .e40 <- 0.5 * geno_q .e42 <- .e11 - .e19 * .e29 .e45 <- 2 * (.e33 * .e10/.e14) .e46 <- t0 * .e10 .e47 <- 2 * .e23 .e48 <- .e45 + .e47 .e49 <- 1 - .e40 .e50 <- .e22^2 .e51 <- .e3 * .e14 .e53 <- .e48/.e14 + 2 .e54 <- .e19 * .e6 .e56 <- exp(-.e46) .e57 <- 0.5 * .e23 .e59 <- exp(-(2 * .e46)) .e61 <- .e54 * .e20/.e10 .e62 <- 2 * .e61 .e63 <- t0 * .e19 .e64 <- .e12/.e3 .e66 <- .e63 * .e6/.e10 .e67 <- .e3/.e10 .e68 <- 2 * .e51 .e69 <- .e53 + .e62 .e71 <- .e3/.e42 - 0.5 .e72 <- 2 * .e66 .e74 <- .e51/.e22 + 0.5 .e75 <- .e53 - .e72 .e77 <- exp(-(tij * .e10)) .e78 <- t0 * .e39 .e79 <- .e24/.e50 .e80 <- .e69 * .e29 .e81 <- 0.5 * .e78 .e85 <- .e81 + 4 * .e79 + f0 + .e17 - m0 .e86 <- .e19 * .e50 .e87 <- 2 - .e80 .e88 <- .e33 * .e39 .e89 <- .e23 - .e64 .e90 <- .e57 - .e13 .e92 <- 2 * (.e24/.e9) .e93 <- 2 * .e34 .e99 <- 2 * (.e88 * .e3/.e12) + 2 * (.e85 * .e6/.e10) .e100 <- .e22^3 .e101 <- .e27^2 .e102 <- .e92 + .e93 .e103 <- .e21^2 .e105 <- .e19 * .e12^2 * .e59 .e106 <- t0 * .e74 .e107 <- 2 * .e67 .e110 <- .e89 * .e10/.e68 + .e23 .e113 <- .e90 * .e10/.e68 + .e57 .e114 <- .e8/.e9 .e115 <- .e67 + 1/(2 * .e14) .e117 <- 1/.e14 + .e107 .e118 <- .e56^2 .e119 <- tij * .e71 .e121 <- .e74 * .e56 + .e71 * .e77 .e126 <- 1 - (.e49 * .e48 * .e3/.e22 + .e40) .e128 <- .e106 * .e49 * .e6 .e133 <- 1 - (.e49 * .e87 * .e3/.e42 + .e40) .e135 <- .e126 * .e14/2 .e136 <- .e100 * .e10 .e137 <- .e128 - .e135 .e140 <- .e119 * .e49 * .e6/.e10 .e146 <- 2 * (.e113/.e14) .e148 <- 2 * (.e75 * .e39/.e19) + 4 * .e99 .e150 <- 2 * (.e75 * .e10) + 4 * (.e54/.e10) .e152 <- (.e4 * .e21/.e22)^2 .e154 <- .e133/.e42 - .e140 .e155 <- .e19 * .e3 .e157 <- 2 + 2 * (.e110/.e14) .e159 <- .e155 * .e20/.e10 .e160 <- .e7/.e10 .e162 <- (-(4 * (.e9/.e14)))^2 .e164 <- .e154 * .e77 - .e56 * .e137/.e10 .e165 <- 1/.e42 .e166 <- .e7 * .e103 .e167 <- .e8/.e101 .e168 <- .e8/.e10 .e170 <- .e14/.e22 + .e165 .e171 <- (2 * (.e39 * .e56 * .e3/.e12))^2 .e172 <- .e42^2 .e173 <- .e19 * .e59 .e174 <- .e5^4 .e175 <- 1/.e11 .e176 <- .e162 * .e14 .e177 <- (2 * (.e42 * .e10))^2 .e178 <- .e42 * .e6 .e180 <- .e86 * .e12 * .e59 .e181 <- 2 - 2 * .e114 .e182 <- .e121 * .e49 .e183 <- .e54/.e9 .e184 <- .e7 * .e6 .e185 <- .e150 * .e39 .e186 <- .e178/.e10 .e187 <- .e184 * .e103 .e188 <- 0.5 * geno_f .e189 <- .e148 * .e39 .e192 <- .e166/.e100 .e193 <- 1 + .e146 .e195 <- 32 * .e99 + 64 * (.e185 * .e10/.e86) .e200 <- 1 - .e114 .e201 <- 1 - .e188 .e202 <- 2 * (.e115/.e14) .e203 <- 2 * (.e117/.e14) .e205 <- 2 * (.e87 * .e10) + 2 * .e186 .e207 <- 2 * (.e48 * .e10) + 4 * .e6 .e209 <- .e22^4 .e210 <- .e174/(.e9 * .e10) .e211 <- 2/.e25 .e213 <- t0 * .e50/.e10 .e214 <- (.e61 + 1 + .e146) * .e29 .e221 <- .e160 - .e10 .e223 <- 128 * (.e187/.e136) + 2 * (.e189 * .e118 * .e3/.e105) .e224 <- 2 * ((.e23 - 2 * .e64)/.e25) .e225 <- .e202 + 2 * .e159 .e226 <- 2 * ((.e57 - .e64)/.e25) .e227 <- .e203 + 4 * .e159 .e228 <- 4/.e25 .e229 <- .e164 * .e39 .e230 <- .e182 * .e195 .e234 <- .e171/.e173 + 32 * (.e152 * .e3) .e235 <- (.e157 + .e62) * .e29 .e236 <- .e168 + .e10 .e237 <- .e51/.e9 .e239 <- 0.5 * .e168 + 0.5 * .e10 .e240 <- 1 - .e214 .e241 <- 1/.e3 .e243 <- 2 * .e160 - .e22 .e244 <- 2 * .e167 .e246 <- 32 * .e152 - .e223 * .e3 .e247 <- 4 * .e167 .e249 <- .e205/.e177 + .e207/.e176 .e250 <- 2 - .e235 .e251 <- 32 * .e229 .e253 <- .e110 * .e33 - (2 * (.e236 * .e6/.e101) + .e224) * .e10 .e255 <- .e113 * .e33 - (2 * (.e239 * .e6/.e101) + .e226) * .e10 .e256 <- .e173^2 .e259 <- .e33 * .e115 + .e175 - (.e244 + .e211) * .e3 .e262 <- .e33 * .e117 + .e241 - (.e247 + .e228) * .e3 .e263 <- .e33 * .e102 .e266 <- .e24/.e209 .e267 <- 2 * (.e200/.e10) .e268 <- 2 * (.e181/.e10) .e269 <- .e251 - .e230 .e271 <- t0 * .e102/.e10 .e272 <- t0 * .e12 .e273 <- 2 * .e9 .e274 <- .e69 * .e3 .e275 <- .e115 * .e6 .e279 <- .e181 * .e19 + 2 * (.e117 * .e6/.e14) .e280 <- .e48 * .e3 .e281 <- .e48/.e22 .e282 <- .e225 * .e29 .e283 <- .e227 * .e29 .e284 <- .e19 * (8 - 2 * .e213) .e286 <- .e193 - 0.5 * .e183 .e287 <- .e175 - 16 * .e192 .e289 <- 1/.e12 + t0 .e290 <- 2 * .e210 .e291 <- .e157 - .e183 .e292 <- ((.e89 * .e48/.e11 + 2 * .e253)/.e14 - .e290)/.e14 .e293 <- ((.e90 * .e48/.e11 + 2 * .e255)/.e14 - .e210)/.e14 .e295 <- (.e281 + 2 * .e259)/.e14 + .e267 .e297 <- (.e48/.e10 + 2 * .e262)/.e14 + .e268 .e298 <- .e282/.e172 .e299 <- .e283/.e172 .e300 <- .e237 + 1/.e22 .e301 <- 0.5 * .e102 .e303 <- 1/.e10 + 2 * .e237 .e304 <- 2 * .e102 .e305 <- 2 * .e78 .e306 <- .e176^2 .e307 <- .e164 * .e102 .e308 <- .e295/.e14 .e309 <- .e297/.e14 .e310 <- .e75 * .e102 .e312 <- .e180^2 .e313 <- .e105^2 .e314 <- .e136^2 .e316 <- .e263 * .e6/.e10 .e317 <- .e263 * .e3 .e318 <- .e33/(.e12 * .e10) .e319 <- .e33/.e12 .e322 <- .e85/.e9 .e323 <- .e193 * .e50 .e324 <- .e287/.e9 .e327 <- .e289 * .e39 + .e92 + .e93 .e331 <- (2 - .e183) * .e3 + (2 * .e275 + .e22)/.e14 .e332 <- .e280/.e9 .e333 <- .e50 * .e157 .e336 <- .e187 * .e3/.e136 .e337 <- .e166/(.e209 * .e10) .e338 <- .e7/.e50 .e339 <- .e6 * .e14 .e340 <- .e6/.e9 .e341 <- .e3^2 .e342 <- 0.5 * .e271 .e343 <- 2 - (.e80 + .e48 * .e42/.e22) .e344 <- 2 * (.e115 * .e50/.e14) .e345 <- 2 * (.e117 * .e50/.e14) .e346 <- .e102 + .e305 .e347 <- 2 * .e272 .e348 <- 32 * .e266 .e350 <- .e63 * .e3/.e10 .e351 <- t0/.e10 .e352 <- .e119/.e10 .e353 <- (.e292 + (2 * .e69 + 2 * .e291) * .e6 * .e20/.e10) * .e29 .e354 <- (.e293 + (.e69 + 2 * .e286) * .e6 * .e20/.e10) * .e29 .e357 <- .e308 + (2 * .e274 + 2 * .e331) * .e20/.e10 .e358 <- .e309 + (2 * .e279 + 4 * .e274) * .e20/.e10 .e361 <- ((1 - (.e49 * .e6 * .e3/.e9 + .e40)) * .e14 - .e89 * .e49/2)/2 .e362 <- .e89/.e11 .e363 <- (0.5 - .e240 * .e3/.e42)/.e42 .e365 <- (0.5 - .e8/.e273) * .e14 - .e90/2 .e366 <- .e90/.e11 .e367 <- .e323 + .e19 * (4 - .e213) * .e6 .e370 <- (16 - 4 * .e213) * .e19 * .e3 + .e345 .e372 <- .e284 * .e6 + .e333 .e374 <- .e284 * .e3 + .e344 .e375 <- .e246/.e9 .e377 <- 0.5 * .e39 .e379 <- 0.5 * t0 + 0.5/.e12 .e380 <- 2 * (.e253/.e14) .e381 <- 2 * (.e255/.e14) .e383 <- 2 * (.e259/.e14) + .e267 .e385 <- 2 * (.e262/.e14) + .e268 .e387 <- 2 * t0 + 2/.e12 .e388 <- 32 * .e79 .e389 <- 32 * .e192 .e390 <- 64 * (.e21/.e50) .e394 <- (.e365/2 - 0.5 * (.e106 * .e6)) * .e56/.e10 + (.e363 - 0.5 * (.e119 * .e6/.e10)) * .e77 .e397 <- .e307 * .e6/.e10 .e399 <- .e307 * .e3/.e10 .e402 <- (.e361 - .e128) * .e56/.e10 + ((1 - (.e49 * .e250 * .e3/.e42 + .e40))/.e42 - .e140) * .e77 .e405 <- (.e362 + .e339/.e9)/.e22 .e408 <- (.e366 + .e339/.e273)/.e22 .e416 <- .e154 * .e3 .e430 <- .e310 * .e6/.e10 .e432 <- .e310 * .e3/.e10 .e434 <- .e75 * .e6/.e10 .e436 <- .e75 * .e3/.e10 .e440 <- (.e298 - .e352) * .e77 - (.e300/2 + .e106) * .e56/.e10 .e442 <- (.e299 - 2 * .e352) * .e77 - (.e303/2 + 2 * .e106) * .e56/.e10 .e443 <- .e249 * .e234 .e466 <- .e300/.e22 .e467 <- .e71/.e9 .e469 <- .e170 * .e246 .e470 <- .e170 * .e6 .e472 <- .e170 * .e3/.e9 .e488 <- .e240/.e172 .e491 <- .e201 * .e7 .e493 <- (1 - .e347) * .e19 * .e50 .e497 <- .e289 * .e269 .e498 <- .e303/.e22 .e501 <- (128 * .e192 + 8 * (.e327 * .e39 * .e118 * .e3/.e105)) * .e341/.e10 + (.e202 - 2 * .e350) * .e171 * .e59/.e256 .e503 <- .e87 * .e6/.e10 .e505 <- .e87 * .e3/.e10 .e506 <- .e250/.e172 .e507 <- (2 - .e347) * .e19 .e508 <- (2 * (((.e175 - (.e319 + .e244 + .e211) * .e3) * .e39 - .e317) * .e3/.e12) + 2 * (.e85 * .e200 - (.e342 + .e348) * .e6 * .e3))/.e10 .e509 <- (2 * (((.e241 - (2 * .e319 + .e247 + .e228) * .e3) * .e39 - 2 * .e317) * .e3/.e12) + 2 * (.e85 * .e181 - (64 * .e266 + .e271) * .e6 * .e3))/.e10 .e510 <- .e148 * .e346 .e511 <- .e150 * .e346 .e513 <- .e48 * .e6/.e10 .e514 <- .e280/.e10 .e520 <- (.e203 - 4 * .e350) * .e171 * .e59/.e256 + (256 * .e192 + 8 * ((.e39 * .e387 + .e304) * .e39 * .e118 * .e3/.e105)) * .e341/.e10 .e531 <- .e178/.e9 .e533 <- .e42 * .e3/.e10 .e535 <- .e19 * .e12 * .e59 .e539 <- .e50 * .e7 * .e174 * .e103/.e314 .e542 <- .e50 * .e6 * .e3/.e314 .e545 <- (96 * .e337 - .e324) * .e6 - .e211 .e546 <- .e166/.e136 .e547 <- .e14 * .e10 .e548 <- .e137/.e9 .e551 <- .e301 + .e78 .e552 <- 0.5 * .e269 .e553 <- 1/.e9 .e555 <- 16 * (.e39 * .e118 * .e3/(.e105 * .e10)) + .e390 .e556 <- 16 * .e114 .e557 <- .e380 - (.e45 + 4 * .e23) * .e6/.e9 .e558 <- .e381 - (.e48/2 + .e23) * .e6/.e9 .e559 <- .e383 - .e332 .e560 <- .e385 - 2 * .e332 .e561 <- 2 * ((.e88 - (((.e318 + 2 * (.e236/.e101)) * .e6 + .e224) * .e39 + .e316) * .e3)/.e12) .e562 <- 2 * ((.e322 + .e342 + .e348) * .e174/.e10) .e564 <- 2 * (((0.5 * (t0 * .e243) + 4 * .e338) * .e201 + 1 - .e188) * .e6/.e10) + 2 * (.e33 * .e201 * .e243 * .e3/.e12) .e566 <- 2 * (.e221 * .e33 * .e3/.e12) + 2 * ((0.5 + 0.5 * (t0 * .e221) + 2 * .e338) * .e6/.e10) .e567 <- 2 * ((0.25 * .e271 + 0.5 * .e322 + 16 * .e266) * .e174/.e10) .e568 <- 2 * ((0.5 * .e88 - (((0.5 * .e318 + 2 * (.e239/.e101)) * .e6 + .e226) * .e39 + 0.5 * .e316) * .e3)/.e12) .e570 <- 2 * ((4/.e50 + .e351) * .e6) + 4 * (.e33 * .e3/.e12) .e571 <- .e102 + .e78 .e572 <- .e304 + 4 * .e78 .e573 <- 2 * (t0 * (.e200 * .e19 + 2 * (.e275/.e14))/.e10) .e574 <- 2 * (t0 * .e279/.e10) .e575 <- 2 * (t0 * .e286 * .e6/.e10) .e576 <- 2 * (t0 * .e291 * .e6/.e10) .e579 <- 32 * (.e152 - 4 * .e336) + 8 * (((2 * .e24 - .e327 * .e6 * .e3)/.e10 - .e36) * .e39 * .e118 * .e3/.e105) - .e171 * (.e157 - .e72) * .e59/.e256 .e580 <- .e388 + 8 * (.e221 * .e39 * .e118 * .e3/.e105) .e583 <- 32 * (0.5 * .e152 - 2 * .e336) + 8 * ((.e377 - (.e379 * .e39 + .e301) * .e6 * .e3/.e10) * .e39 * .e118 * .e3/.e105) - (.e193 - .e66) * .e171 * .e59/.e256 .e584 <- 4 * .e272 .e586 <- 64 * .e79 + 8 * (.e39 * .e243 * .e118 * .e3/.e105) c(q0 = ((((.e545 * .e6/.e10 - .e224) * .e3 + (.e340 + .e175 - .e389) * .e6/.e10 + .e362 - .e31) * .e20 + ((.e170 * .e579 - (.e405 + .e470/.e9 + .e506) * .e234)/2 + .e469/2)/.e10 - (.e443 + 0.5 * ((.e353 + (.e250 * .e48 + .e557 * .e42)/.e22 + .e343 * .e250/.e42)/.e42))) * .e49 - (((((.e405 + .e506) * .e246 + (((2 * ((((2 * (((.e292 - (.e75 * .e157/.e19 + .e576)) * .e39 - .e430)/.e19) + 4 * (.e561 - .e562)) * .e39 - .e510 * .e6/.e10) * .e3 + .e189)/.e105 - (.e507 * .e6/.e10 + .e157 * .e12) * .e148 * .e39 * .e12 * .e59 * .e3/.e313) + 2 * (.e189/.e105)) * .e118 - 1024 * .e539) * .e3 + (.e375 + 256 * .e546) * .e6) * .e170)/.e22 + ((2 * (.e503 - .e353 * .e10) + 2 * ((2 - (.e531 + .e235)) * .e6/.e10) - 8 * ((.e250 * .e10 + .e186) * .e205 * .e42 * .e10/.e177))/.e177 + 2 * (((.e380 - .e290) * .e10 + .e513)/.e176) - .e207 * (32 * ((.e9 * .e89/.e68 + 2 * .e6) * .e9/.e14) - .e162 * .e89/.e11)/.e306) * .e234 + .e249 * .e579) * .e49 + (64 * .e229 - ((.e402 * .e195 + .e182 * (32 * (.e561 - (.e372 * .e99/.e86 + .e562)) + 64 * ((((2 * ((.e292 - .e576) * .e10 + .e434) + 4 * (.e291 * .e6/.e10)) * .e39 - .e511 * .e6/.e10) * .e10 + (.e23 - 2 * (.e372 * .e10/.e86)) * .e150 * .e39)/.e86)) + .e497 * .e6/.e10 + 32 * ((((.e133 * .e250 + .e49 * (2 - ((.e353 + .e87 * .e250/.e42) * .e3 + .e80)))/.e172 + tij * ((2 - (.e49 * (4 - ((.e45 + 2 * .e110 + .e47)/.e14 + 4 + 4 * .e61) * .e29) * .e3/.e42 + geno_q))/.e42 - .e71 * .e49 * (.e553 + tij/.e10) * .e6) * .e6/.e10) * .e77 + .e164 * .e372/.e86 + (.e6 * (t0 * (.e361 + .e135 - .e128)/.e10 - .e548) + 0.5 * ((.e557 * .e3 + .e45 + .e47) * .e49 * .e14/.e22 + .e89 * .e126/.e11)) * .e56/.e10) * .e39 + .e397)) * .e3 + 2 * .e230)) * .e4 * .e56 * .e21/.e180) * .e3 + 32 * ((((.e402 * .e39 - .e182 * .e571 * .e6/.e10) * .e3 + .e182 * .e39)/.e180 - ((.e333 + 8 * .e54) * .e12 + .e493 * .e6/.e10) * .e121 * .e49 * .e39 * .e59 * .e3/.e312) * .e4 * .e56 * .e21))) * .e49, q2 = geno_q * ((((((48 * .e337 - 0.5 * .e324) * .e6 - 1/.e25) * .e6/.e10 - .e226) * .e3 + (0.5 * .e340 - 8 * .e192) * .e6/.e10 + .e366 + 0.5 * (.e287 * .e6/.e10 - .e31)) * .e20 + (.e170 * .e583 - (.e408 + .e470/.e273 + .e488) * .e234)/.e22 - (0.5 * ((.e354 + (.e240 * .e48 + .e558 * .e42)/.e22 + .e240 * .e343/.e42)/.e42) + 32 * ((((.e394 * .e39 - .e121 * (.e301 + .e81) * .e6/.e10) * .e3 + 0.5 * (.e121 * .e39))/.e180 - ((.e323 + 4 * .e54) * .e12 + (0.5 - .e272) * .e19 * .e50 * .e6/.e10) * .e121 * .e39 * .e59 * .e3/.e312) * .e4 * .e56 * .e21))) * .e49 + 0.5 * ((.e469/.e22 - .e443) * .e49 - .e269 * .e4 * .e56 * .e21 * .e3/.e180) - ((((.e408 + .e488) * .e246 + ((.e246/.e273 + 64 * .e546) * .e6 + (2 * (((((2 * (((.e293 - (.e75 * .e193/.e19 + .e575)) * .e39 - 0.5 * .e430)/.e19) + 4 * (.e568 - .e567)) * .e39 - .e551 * .e148 * .e6/.e10) * .e3 + 0.5 * .e189)/.e105 - ((1 - .e272) * .e19 * .e6/.e10 + .e193 * .e12) * .e148 * .e39 * .e12 * .e59 * .e3/.e313) * .e118) - 512 * .e539) * .e3 + 0.5 * .e223) * .e170)/.e22 + ((2 * ((1 - (.e214 + 0.5 * .e531)) * .e6/.e10) + 2 * (0.5 * .e503 - .e354 * .e10) - 8 * ((.e240 * .e10 + 0.5 * .e186) * .e205 * .e42 * .e10/.e177))/.e177 + 2 * (((.e381 - .e210) * .e10 + 0.5 * .e513)/.e176) - .e207 * (32 * ((.e9 * .e90/.e68 + .e6) * .e9/.e14) - .e162 * .e90/.e11)/.e306) * .e234 + .e249 * .e583) * .e49 + (.e552 - ((.e394 * .e195 + .e121 * (32 * (.e568 - (.e367 * .e99/.e86 + .e567)) + 64 * ((((2 * ((.e293 - .e575) * .e10 + 0.5 * .e434) + 4 * (.e286 * .e6/.e10)) * .e39 - .e551 * .e150 * .e6/.e10) * .e10 + (.e57 - 2 * (.e367 * .e10/.e86)) * .e150 * .e39)/.e86))) * .e49 + .e379 * .e269 * .e6/.e10 + 32 * (((((0.5 * .e87 - (.e354 + .e240 * .e87/.e42) * .e3) * .e49 + .e133 * .e240)/.e172 + tij * ((.e363 - 0.5 * (.e71 * .e6/.e9)) * .e49 + 0.5 * .e154) * .e6/.e10) * .e77 + .e164 * .e367/.e86 + (.e6 * (t0 * (.e365 * .e49/2 - 0.5 * .e137)/.e10 - 0.5 * .e548) + 0.5 * ((.e558 * .e3 + 0.5 * .e48) * .e49 * .e14/.e22 + .e90 * .e126/.e11)) * .e56/.e10) * .e39 + 0.5 * .e397)) * .e3) * .e4 * .e56 * .e21/.e180) * .e3), f0 = ((.e170 * (64 * (.e491 * .e21/.e50) - (2 * ((.e201 * .e148 * .e243 + (2 * (.e75 * .e201 * .e243/.e19) + 4 * .e564) * .e39) * .e118 * .e3/.e105) + 256 * (.e491 * .e6 * .e21/.e136)) * .e3)/.e22 - .e249 * .e201 * .e586 * .e3) * .e49 - (.e201 * .e269 + (32 * (.e164 * .e201 * .e243) - .e182 * (32 * .e564 + 64 * (.e201 * .e150 * .e243 * .e10/.e86))) * .e21) * .e4 * .e56 * .e3/.e180) * .e3 + (((8 - .e556) * .e4 * .e21 * .e20 - 32 * (.e121 * ((4 * .e160 - .e22) * .e21 - .e36) * .e56 * .e3/.e535)) * .e4/.e50 + .e170 * .e586 * .e3/.e22) * .e201 * .e49, f2 = geno_f * (((.e170 * (.e388 - (128 * (.e184 * .e21/.e136) + 2 * ((.e221 * .e148 + (2 * (.e75 * .e221/.e19) + 4 * .e566) * .e39) * .e118 * .e3/.e105)) * .e3)/.e22 - .e249 * .e580 * .e3) * .e49 - ((32 * (.e164 * .e221) - .e182 * (32 * .e566 + 64 * (.e221 * .e150 * .e10/.e86))) * .e21 + .e552) * .e4 * .e56 * .e3/.e180) * .e3 + (((4 - 8 * .e114) * .e4 * .e21 * .e20 - 32 * ((.e221 * .e21 + .e377) * .e121 * .e56 * .e3/.e535)) * .e4/.e50 + .e170 * .e580 * .e3/.e22) * .e49), f1 = (((((2 * ((.e39 * (4 * (.e75/.e19) + 4 * .e570) + 2 * .e148) * .e118 * .e3/.e105) + 256 * (.e6 * .e21/.e100)) * .e3/.e10 - .e390) * .e170/.e22 + .e249 * .e555 * .e3) * .e49 * .e4 - ((.e182 * (128 * (.e150/.e86) + 32 * (.e570/.e10)) - 64 * (.e164/.e10)) * .e7 * .e21 + .e230 - .e251) * .e56 * .e3/.e180) * .e3 + (((.e556 - 8) * .e21 * .e20/.e50 - .e170 * .e555 * .e3/.e22) * .e4 - 32 * (.e121 * (.e36 - 4 * .e37) * .e56 * .e3/.e180)) * .e49) * .e4, b0 = (((((((192 * .e337 - 2 * .e324) * .e6 - .e228) * .e3 + 2 * .e340 + 2 * .e287 - .e389) * .e3 - 1) * .e20 + ((.e299 - (.e498 + 2 * .e472)) * .e234 - .e520 * .e170)/2)/.e10 - (0.5 * (((.e358 - .e343 * .e227/.e42) * .e29 + (.e560 * .e42 - .e48 * .e227 * .e29)/.e22)/.e42) + 32 * (((.e442 * .e39 - .e121 * (.e304 + .e305)/.e10) * .e3/.e180 - .e121 * ((16 * .e155 + .e345) * .e12 + (2 - .e584) * .e19 * .e50 * .e3/.e10) * .e39 * .e59/.e312) * .e4 * .e56 * .e21 * .e3))) * .e49 + (((.e442 * .e195 * .e3 + .e121 * (32 * (.e509 - .e370 * .e99/.e86) + 64 * ((((2 * ((.e309 - .e574) * .e10 + 2 * .e436) + 4 * (.e279/.e10)) * .e39 - .e150 * .e572 * .e3/.e10) * .e10 + .e185 * (.e107 - 2 * (.e370 * .e10/.e86)))/.e86))) * .e49 + .e387 * .e269 * .e3/.e10 + 32 * (((((.e87 * .e227/.e42 - .e358) * .e49 * .e3 - .e133 * .e227) * .e29/.e172 + tij * (((.e299 - 2 * .e467) * .e6 * .e3 + 2 * .e71) * .e49 + 2 * .e416)/.e10) * .e77 + .e164 * .e370/.e86 + (0.5 * (((.e560 * .e14/2 - .e281) * .e49 * .e3 + 1 - .e40)/.e10) + t0 * .e49 * (2 * .e74 - .e303 * .e6 * .e3/.e22) - (2 * .e351 + 2/.e9) * .e3 * .e137) * .e56/.e10) * .e39 + 2 * .e399)) * .e4 * .e56 * .e21 * .e3/.e180 + (((.e299 - .e498) * .e246 - ((128 * (2/.e136 - 16 * .e542) + 256/.e136) * .e7 * .e103 + 2 * ((((2 * ((((.e297 - 2 * (.e75 * .e117/.e19))/.e14 - .e574) * .e39 - 2 * .e432)/.e19) + 4 * .e509) * .e39 - .e148 * .e572 * .e3/.e10)/.e105 - (.e19 * (4 - .e584) * .e3/.e10 + 2 * (.e117 * .e12/.e14)) * .e148 * .e39 * .e12 * .e59/.e313) * .e118 * .e3) + 2 * .e375) * .e170 * .e3)/.e22 + .e520 * .e249 - ((2 * ((.e181 * .e42 - .e227 * .e6 * .e29)/.e10) + 2 * (2 * .e505 - .e358 * .e29 * .e10) - 8 * (.e205 * (2 * .e533 - .e283 * .e10) * .e42 * .e10/.e177))/.e177 + (2 * (.e385 * .e10 + 2 * .e514) + 8)/.e176 - .e207 * (32 * ((.e9/.e547 + 4 * .e3) * .e9/.e14) - .e162/.e10)/.e306) * .e234) * .e49) * .e3) * (1 - 0.5 * geno_b) * .e5, b2 = geno_b * ((((.e440 * .e195 * .e3 + .e121 * (32 * (.e508 - .e374 * .e99/.e86) + 64 * ((((2 * ((.e308 - .e573) * .e10 + .e436) + 4 * (.e331/.e10)) * .e39 - .e511 * .e3/.e10) * .e10 + (.e67 - 2 * (.e374 * .e10/.e86)) * .e150 * .e39)/.e86))) * .e49 + .e497 * .e3/.e10 + 32 * (((((.e87 * .e225/.e42 - .e357) * .e49 * .e3 - .e133 * .e225) * .e29/.e172 + tij * ((((.e298 - .e467) * .e6 + .e165) * .e3 - 0.5) * .e49 + .e416)/.e10) * .e77 + .e164 * .e374/.e86 + (0.5 * ((.e126/2 + .e49 * .e559 * .e3 * .e14/2)/.e10) + t0 * ((.e14/2 - .e300 * .e6/2) * .e3/.e10 + 0.5) * .e49 - (.e553 + .e351) * .e3 * .e137) * .e56/.e10) * .e39 + .e399)) * .e4 * .e56 * .e21 * .e3/.e180 + (((.e298 - .e466) * .e246 - ((128 * (1/.e136 - 8 * .e542) + 128/.e136) * .e7 * .e103 + .e375 + 2 * ((((2 * ((((.e295 - 2 * (.e75 * .e115/.e19))/.e14 - .e573) * .e39 - .e432)/.e19) + 4 * .e508) * .e39 - .e510 * .e3/.e10)/.e105 - (.e507 * .e3/.e10 + 2 * (.e115 * .e12/.e14)) * .e148 * .e39 * .e12 * .e59/.e313) * .e118 * .e3)) * .e170 * .e3)/.e22 + .e501 * .e249 - ((2 * ((.e200 * .e42 - .e225 * .e6 * .e29)/.e10) + 2 * (.e505 - .e357 * .e29 * .e10) - 8 * ((.e533 - .e282 * .e10) * .e205 * .e42 * .e10/.e177))/.e177 + (2 * (.e383 * .e10 + .e514) + 4)/.e176 - .e207 * (32 * ((.e9/(2 * .e547) + .e11) * .e9/.e14) - .e162/.e22)/.e306) * .e234) * .e49) * .e3 + ((((.e545 * .e3 + .e340 + .e175 - .e389) * .e3 - 0.5) * .e20 + ((.e298 - (.e466 + .e472)) * .e234 - .e501 * .e170)/2)/.e10 - (0.5 * (((.e357 - .e343 * .e225/.e42) * .e29 + (.e559 * .e42 - .e48 * .e225 * .e29)/.e22)/.e42) + 32 * (((.e440 * .e39 - .e121 * .e571/.e10) * .e3/.e180 - .e121 * (.e493 * .e3/.e10 + (.e344 + 8 * .e155) * .e12) * .e39 * .e59/.e312) * .e4 * .e56 * .e21 * .e3))) * .e49) * .e5) } deriv_mu_int_q2_qff1b_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- b0 + geno_b * (b2 - b0)/2 .e6 <- .e5^2 .e7 <- .e4^2 .e8 <- .e6 * .e3 .e9 <- .e7 + 2 * .e8 .e10 <- sqrt(.e9) .e11 <- 2 * .e3 .e12 <- .e4 + .e10 .e13 <- .e12/.e11 .e14 <- r0 - .e13 .e17 <- geno_f * (f2 - f0)/2 .e18 <- f0 + .e17 .e19 <- .e11 + 2 * (.e10/.e14) .e20 <- tij - t0 .e21 <- .e18 - f1 .e22 <- 2 * .e10 .e23 <- .e7 * .e21 .e24 <- .e11^2 .e26 <- 2 * (.e3 * .e10) .e28 <- exp(2 * (.e10 * .e20)) .e29 <- .e6/.e10 .e32 <- .e6/.e26 - 2 * (.e12/.e24) .e33 <- .e18 - m0 .e35 <- 2 * (.e33 * .e10) .e36 <- .e23/.e10 .e38 <- 2 * .e36 - .e35 .e40 <- .e11 - .e19 * .e28 .e41 <- t0 * .e10 .e43 <- .e32 * .e10/.e14 .e44 <- .e22^2 .e45 <- .e43 + .e29 .e47 <- exp(-.e41) .e48 <- .e3 * .e14 .e49 <- 0.5 * .e29 .e50 <- .e19 * .e6 .e52 <- exp(-(2 * .e41)) .e53 <- .e3/.e10 .e55 <- .e50 * .e20/.e10 .e57 <- 2 * .e43 + 2 * .e29 .e58 <- t0 * .e19 .e60 <- .e3/.e40 - 0.5 .e62 <- .e58 * .e6/.e10 .e64 <- .e48/.e22 + 0.5 .e69 <- 0.5 * (.e57/.e14 + 2) - .e62 .e70 <- exp(-(tij * .e10)) .e73 <- .e45/.e14 + .e55 + 1 .e74 <- .e49 - .e13 .e75 <- t0 * .e38 .e76 <- .e73 * .e28 .e77 <- .e23/.e44 .e78 <- .e19 * .e44 .e79 <- 1 - .e76 .e80 <- 0.5 * .e75 .e84 <- .e80 + 4 * .e77 + f0 + .e17 - m0 .e85 <- .e8/.e9 .e86 <- .e32 * .e38 .e87 <- .e22^3 .e88 <- 2 * .e48 .e89 <- 2 * .e53 .e92 <- .e74 * .e10/.e88 + .e49 .e93 <- .e26^2 .e95 <- .e53 + 1/(2 * .e14) .e97 <- 1/.e14 + .e89 .e98 <- 2 * (.e23/.e9) .e99 <- 2 * .e33 .e102 <- .e86 * .e3/.e12 + .e84 * .e6/.e10 .e104 <- .e19 * .e12^2 * .e52 .e105 <- .e98 + .e99 .e106 <- .e45 * .e3 .e107 <- .e87 * .e10 .e108 <- .e47^2 .e109 <- t0 * .e64 .e110 <- tij * .e60 .e111 <- .e79 * .e3 .e112 <- .e21^2 .e114 <- .e64 * .e47 + .e60 * .e70 .e115 <- .e19 * .e3 .e117 <- 0.5 - .e111/.e40 .e120 <- (2 * (.e8/.e93) + 2/.e24) * .e3 .e122 <- .e115 * .e20/.e10 .e123 <- .e7/.e10 .e124 <- 0.5 - .e106/.e22 .e125 <- 0.5 * (.e109 * .e6) .e126 <- 0.5 * (.e110 * .e6/.e10) .e127 <- 2 * (.e92/.e14) .e131 <- .e117/.e40 - .e126 .e134 <- .e125 - .e124 * .e14/2 .e136 <- 2 * (.e69 * .e10) + 2 * (.e50/.e10) .e139 <- 2 - 2 * .e85 .e141 <- 2 * (.e69 * .e38/.e19) + 4 * .e102 .e143 <- .e131 * .e70 - .e134 * .e47/.e10 .e144 <- 1/.e40 .e146 <- (-(4 * (.e9/.e14)))^2 .e147 <- (.e4 * .e21/.e22)^2 .e149 <- .e78 * .e12 * .e52 .e151 <- .e14/.e22 + .e144 .e152 <- .e40^2 .e153 <- 0.5 * geno_f .e154 <- 1 - .e85 .e155 <- .e146 * .e14 .e158 <- (2 * (.e38 * .e47 * .e3/.e12))^2 .e159 <- (2 * (.e40 * .e10))^2 .e160 <- .e19 * .e52 .e161 <- .e7 * .e6 .e162 <- 1 - .e153 .e163 <- 2 * (.e95/.e14) .e164 <- 2 * (.e97/.e14) .e165 <- .e136 * .e38 .e166 <- .e40 * .e6 .e167 <- .e161 * .e112 .e168 <- (.e55 + 1 + .e127) * .e28 .e174 <- .e166/.e10 .e175 <- .e123 - .e10 .e176 <- .e5^4 .e177 <- 1 + .e127 .e178 <- 1/.e11 .e179 <- 1/.e3 .e180 <- .e163 + 2 * .e122 .e182 <- 2 * ((0.5 * (.e8/.e10) + 0.5 * .e10) * .e6/.e93) + 2 * ((.e49 - .e12/.e3)/.e24) .e183 <- .e164 + 4 * .e122 .e184 <- 2 * .e120 .e186 <- 32 * .e102 + 64 * (.e165 * .e10/.e78) .e189 <- .e174 + 2 * (.e79 * .e10) .e190 <- .e167/.e107 .e191 <- .e48/.e9 .e192 <- 1 - .e168 .e194 <- 2 * (.e45 * .e10) + 2 * .e6 .e196 <- 2 * .e123 - .e22 .e197 <- .e141 * .e38 .e199 <- t0 * .e44/.e10 .e201 <- .e114 * .e186 .e202 <- .e92 * .e32 .e203 <- .e32 * .e95 .e204 <- .e32 * .e97 .e205 <- .e154/.e10 .e206 <- .e139/.e10 .e210 <- .e182 * .e10 .e212 <- 2 * (.e197 * .e108 * .e3/.e104) + 64 * .e190 .e213 <- 32 * (.e143 * .e38) .e215 <- .e189/.e159 + .e194/.e155 .e220 <- .e158/.e160 + 32 * (.e147 * .e3) .e221 <- .e50/.e9 .e222 <- .e7 * .e112 .e223 <- .e176/(.e9 * .e10) .e224 <- 0.5 * .e105 .e226 <- 16 * .e147 - .e212 * .e3 .e227 <- 2 * .e9 .e228 <- 2 * .e105 .e229 <- .e213 - .e201 .e230 <- .e160^2 .e231 <- .e107^2 .e232 <- .e95 * .e6 .e236 <- .e139 * .e19 + 2 * (.e97 * .e6/.e14) .e237 <- .e180 * .e28 .e238 <- .e183 * .e28 .e239 <- .e38/.e12 .e241 <- .e23/.e22^4 .e243 <- t0 * .e105/.e10 .e244 <- t0 * .e12 .e245 <- .e202 - .e210 .e247 <- .e203 + .e178 - .e120 .e249 <- .e204 + .e179 - .e184 .e250 <- .e237/.e152 .e251 <- .e238/.e152 .e252 <- .e191 + 1/.e22 .e254 <- 1/.e10 + 2 * .e191 .e255 <- t0/.e10 .e256 <- .e106/.e9 .e257 <- .e45/.e22 .e260 <- .e177 * .e44 .e263 <- (2 * .e232 + .e22)/.e14 .e266 <- .e44 * .e6 * .e3/.e231 .e267 <- .e222/.e87 .e268 <- .e7/.e44 .e269 <- .e3^2 .e270 <- 0.5 * .e223 .e271 <- 0.5/.e9 .e272 <- 2 * (.e95 * .e44/.e14) .e273 <- 2 * (.e97 * .e44/.e14) .e275 <- .e58 * .e3/.e10 .e276 <- .e110/.e10 .e277 <- .e155^2 .e278 <- (((.e45 * .e74/.e11 + .e202 - .e210)/.e14 - .e270)/.e14 + ((.e45 + 2 * .e92)/.e14 + (.e20/.e10 - .e271) * .e19 * .e6 + 2) * .e6 * .e20/.e10) * .e28 .e280 <- ((.e257 + .e203 + .e178 - .e120)/.e14 + .e205)/.e14 + (.e263 + (2 + 2 * .e73 - .e221) * .e3) * .e20/.e10 .e282 <- ((.e45/.e10 + .e204 + .e179 - .e184)/.e14 + .e206)/.e14 + (.e236 + 4 * (.e73 * .e3)) * .e20/.e10 .e284 <- .e143 * .e105 .e285 <- .e245/.e14 .e287 <- .e247/.e14 + .e205 .e289 <- .e249/.e14 + .e206 .e290 <- .e149^2 .e291 <- .e104^2 .e292 <- (0.5 - .e192 * .e3/.e40)/.e40 .e294 <- (0.5 - .e8/.e227) * .e14 - .e74/2 .e295 <- .e69 * .e105 .e296 <- .e74/.e11 .e297 <- .e260 + .e19 * (4 - .e199) * .e6 .e300 <- (16 - 4 * .e199) * .e19 * .e3 + .e273 .e303 <- .e19 * (8 - 2 * .e199) * .e3 + .e272 .e304 <- .e21/.e44 .e306 <- 0.5 * .e38 .e308 <- 0.5 * t0 + 0.5/.e12 .e309 <- 1 - (.e76 + .e45 * .e40/.e22) .e310 <- .e177 - 0.5 * .e221 .e311 <- .e178 - .e120 .e313 <- 1/.e12 + t0 .e314 <- .e179 - .e184 .e315 <- 2 * .e75 .e317 <- 2 * t0 + 2/.e12 .e318 <- (((.e311 * .e38 - (.e239 + .e98 + .e99) * .e32 * .e3)/.e12 - (0.5 * .e243 + 32 * .e241) * .e6) * .e3 + .e84 * .e154)/.e10 .e319 <- (((.e314 * .e38 - .e32 * (2 * .e239 + .e228) * .e3)/.e12 - (64 * .e241 + .e243) * .e6) * .e3 + .e84 * .e139)/.e10 .e323 <- .e284 * .e3/.e10 .e326 <- (.e294/2 - .e125) * .e47/.e10 + (.e292 - .e126) * .e70 .e328 <- .e285 - (.e45/2 + .e49) * .e6/.e9 .e329 <- .e287 - .e256 .e331 <- .e289 - 2 * .e256 .e332 <- .e106/.e10 .e335 <- .e131 * .e3 .e336 <- (.e296 + .e6 * .e14/.e227)/.e22 .e339 <- ((0.5 * (t0 * .e196) + 4 * .e268) * .e162 + 1 - .e153) * .e6/.e10 + .e32 * .e162 * .e196 * .e3/.e12 .e350 <- (.e57/.e22 + 2 * .e247)/.e14 + 2 * .e205 .e352 <- (.e57/.e10 + 2 * .e249)/.e14 + 2 * .e206 .e354 <- (.e250 - .e276) * .e70 - (.e252/2 + .e109) * .e47/.e10 .e356 <- (.e251 - 2 * .e276) * .e70 - (.e254/2 + 2 * .e109) * .e47/.e10 .e364 <- .e175 * .e32 * .e3/.e12 + (0.5 + 0.5 * (t0 * .e175) + 2 * .e268) * .e6/.e10 .e371 <- .e252/.e22 .e372 <- .e60/.e9 .e375 <- .e151 * .e3/.e9 .e377 <- (0.25 * .e243 + 0.5 * (.e84/.e9) + 16 * .e241) * .e176/.e10 .e378 <- (0.5 * .e86 - (.e32 * (0.5 * .e239 + .e224) * .e6/.e10 + .e182 * .e38) * .e3)/.e12 .e380 <- .e295 * .e3/.e10 .e382 <- .e69 * .e3/.e10 .e387 <- .e111/.e10 .e388 <- .e192/.e152 .e391 <- .e162 * .e7 .e395 <- .e254/.e22 .e398 <- (128 * .e267 + 8 * ((.e313 * .e38 + .e98 + .e99) * .e38 * .e108 * .e3/.e104)) * .e269/.e10 + (.e163 - 2 * .e275) * .e158 * .e52/.e230 .e399 <- .e226/.e9 .e403 <- (.e164 - 4 * .e275) * .e158 * .e52/.e230 + (256 * .e267 + 8 * ((.e38 * .e317 + .e228) * .e38 * .e108 * .e3/.e104)) * .e269/.e10 .e412 <- .e40 * .e3/.e10 .e416 <- .e44 * .e7 * .e176 * .e112/.e231 .e418 <- (4/.e44 + .e255) * .e6 + 2 * (.e32 * .e3/.e12) .e422 <- .e222 * .e3/.e87 .e423 <- .e14 * .e10 .e424 <- 0.5 * (((.e74 * .e57/.e11 + 2 * .e245)/.e14 - .e223)/.e14) .e427 <- .e224 + .e75 .e428 <- 0.5 * .e229 .e430 <- 1/.e107 - 8 * .e266 .e432 <- 16 * (.e38 * .e108 * .e3/(.e104 * .e10)) + 64 * .e304 .e434 <- .e105 + .e315 .e435 <- .e228 + 4 * .e75 .e436 <- 2 * .e244 .e438 <- 2/.e107 - 16 * .e266 .e440 <- 32 * .e77 + 8 * (.e175 * .e38 * .e108 * .e3/.e104) .e443 <- 32 * (0.5 * .e147 - 2 * (.e167 * .e3/.e107)) + 8 * ((.e306 - (.e308 * .e38 + .e224) * .e6 * .e3/.e10) * .e38 * .e108 * .e3/.e104) - (.e177 - .e62) * .e158 * .e52/.e230 .e444 <- 4 * .e244 .e446 <- 64 * .e77 + 8 * (.e38 * .e196 * .e108 * .e3/.e104) .e447 <- 8 * .e190 .e448 <- 8 * .e85 .e450 <- t0 * (.e154 * .e19 + 2 * (.e232/.e14))/.e10 .e452 <- t0 * .e236/.e10 .e455 <- t0 * .e310 * .e6/.e10 c(q2 = geno_q^2 * (((32 * .e416 - 0.5 * .e182) * .e3 + 0.25 * .e223 + 0.5 * (.e296 - .e447) + 0.5 * (0.5 * .e32 - .e447)) * .e20 + 0.5 * ((.e151 * .e443 - (.e336 + .e151 * .e6/.e227 + .e388) * .e220)/.e22 - 32 * ((((.e326 * .e38 - .e114 * (.e224 + .e80) * .e6/.e10) * .e3 + 0.5 * (.e114 * .e38))/.e149 - ((.e260 + 4 * .e50) * .e12 + (0.5 - .e244) * .e19 * .e44 * .e6/.e10) * .e114 * .e38 * .e52 * .e3/.e290) * .e4 * .e47 * .e21)) + 0.5 * (.e151 * .e226/.e22 - (.e215 * .e220 + .e229 * .e4 * .e47 * .e21 * .e3/.e149)) - ((((.e336 + .e388) * .e226 + ((.e226/.e227 + 32 * (.e222/.e107)) * .e6 + (2 * (((((2 * (((.e424 - (.e69 * .e177/.e19 + .e455)) * .e38 - 0.5 * (.e295 * .e6/.e10))/.e19) + 4 * (.e378 - .e377)) * .e38 - .e427 * .e141 * .e6/.e10) * .e3 + 0.5 * .e197)/.e104 - ((1 - .e244) * .e19 * .e6/.e10 + .e177 * .e12) * .e141 * .e38 * .e12 * .e52 * .e3/.e291) * .e108) - 256 * .e416) * .e3 + 0.5 * .e212) * .e151)/.e22 + (((1 - (.e168 + 0.5 * (.e166/.e9))) * .e6/.e10 + 2 * (0.5 * (.e79 * .e6/.e10) - .e278 * .e10) - 8 * ((.e192 * .e10 + 0.5 * .e174) * .e189 * .e40 * .e10/.e159))/.e159 + 2 * (((.e285 - .e270) * .e10 + 0.5 * (.e45 * .e6/.e10))/.e155) - .e194 * (32 * ((.e9 * .e74/.e88 + .e6) * .e9/.e14) - .e146 * .e74/.e11)/.e277) * .e220 + .e215 * .e443 + (.e428 - (.e326 * .e186 + .e114 * (32 * (.e378 - (.e102 * .e297/.e78 + .e377)) + 64 * ((((2 * ((.e424 - .e455) * .e10 + 0.5 * (.e69 * .e6/.e10)) + 2 * (.e310 * .e6/.e10)) * .e38 - .e427 * .e136 * .e6/.e10) * .e10 + (.e49 - 2 * (.e297 * .e10/.e78)) * .e136 * .e38)/.e78)) + .e308 * .e229 * .e6/.e10 + 32 * ((((.e117 * .e192 + 0.5 * .e79 - (.e278 + .e79 * .e192/.e40) * .e3)/.e152 + tij * (0.5 * .e131 + 0.5 * (.e292 - 0.5 * (.e60 * .e6/.e9))) * .e6/.e10) * .e70 + .e143 * .e297/.e78 + (.e6 * (t0 * .e294/(4 * .e10) - .e134 * (0.5 * .e255 + .e271)) + 0.5 * ((.e328 * .e3 + 0.5 * .e45) * .e14/.e22 + .e124 * .e74/.e11)) * .e47/.e10) * .e38 + 0.5 * (.e284 * .e6/.e10))) * .e3) * .e4 * .e47 * .e21/.e149) * .e3 + 0.5 * ((.e278 + (.e328 * .e40 + .e45 * .e192)/.e22 + .e309 * .e192/.e40)/.e40))), f0 = geno_q * ((.e151 * (32 * (.e391 * .e21/.e44) - (128 * (.e391 * .e6 * .e21/.e107) + 2 * ((.e162 * .e141 * .e196 + (2 * (.e69 * .e162 * .e196/.e19) + 4 * .e339) * .e38) * .e108 * .e3/.e104)) * .e3)/.e22 - (.e215 * .e162 * .e446 + (.e162 * .e229 + (32 * (.e143 * .e162 * .e196) - .e114 * (32 * .e339 + 64 * (.e162 * .e136 * .e196 * .e10/.e78))) * .e21) * .e4 * .e47/.e149) * .e3) * .e3 + ((4 - .e448) * .e7 * .e21 * .e20/.e44 + 0.5 * ((.e151 * .e446/.e22 - 32 * (.e114 * ((4 * .e123 - .e22) * .e21 - .e35) * .e4 * .e47/.e149)) * .e3)) * .e162), f2 = geno_f * geno_q * ((.e151 * (16 * .e77 - (2 * ((.e175 * .e141 + (2 * (.e175 * .e69/.e19) + 4 * .e364) * .e38) * .e108 * .e3/.e104) + 64 * (.e161 * .e21/.e107)) * .e3)/.e22 + 0.5 * (.e151 * .e440/.e22 - 32 * ((.e175 * .e21 + .e306) * .e114 * .e4 * .e47/.e149)) - (.e215 * .e440 + ((32 * (.e143 * .e175) - .e114 * (32 * .e364 + 64 * (.e175 * .e136 * .e10/.e78))) * .e21 + .e428) * .e4 * .e47/.e149) * .e3) * .e3 + (2 - 4 * .e85) * .e7 * .e21 * .e20/.e44), f1 = geno_q * ((((128 * (.e6 * .e21/.e87) + 2 * ((.e38 * (4 * (.e69/.e19) + 4 * .e418) + 2 * .e141) * .e108 * .e3/.e104)) * .e3/.e10 - 32 * .e304) * .e151 * .e4/.e22 - ((((.e114 * (128 * (.e136/.e78) + 32 * (.e418/.e10)) - 64 * (.e143/.e10)) * .e7 * .e21 + .e201 - .e213) * .e47/.e149 - .e215 * .e432 * .e4) * .e3 + 0.5 * (.e151 * .e432 * .e4/.e22 + 32 * (.e114 * (.e35 - 4 * .e36) * .e47/.e149)))) * .e3 + (.e448 - 4) * .e4 * .e21 * .e20/.e44) * .e4, b0 = geno_q * ((((.e356 * .e186 + .e317 * .e229/.e10) * .e3 + .e114 * (32 * (.e319 - .e102 * .e300/.e78) + 64 * ((((2 * (.e236/.e10) + 2 * ((0.5 * (.e352/.e14) - .e452) * .e10 + 2 * .e382)) * .e38 - .e136 * .e435 * .e3/.e10) * .e10 + .e165 * (.e89 - 2 * (.e300 * .e10/.e78)))/.e78)) + 32 * (((((.e79 * .e183/.e40 - .e282) * .e3 - .e117 * .e183) * .e28/.e152 + tij * (0.5 * ((.e251 - 2 * .e372) * .e6 * .e3 + 2 * .e60) + 2 * .e335)/.e10) * .e70 + .e143 * .e300/.e78 + (0.5 * (((.e331 * .e14/2 - .e257) * .e3 + 0.5)/.e10) + 0.5 * (t0 * (2 * .e64 - .e254 * .e6 * .e3/.e22)) - .e134 * (2 * .e255 + 2/.e9) * .e3) * .e47/.e10) * .e38 + 2 * .e323)) * .e4 * .e47 * .e21 * .e3/.e149 + ((.e251 - .e395) * .e226 - ((128/.e107 + 64 * .e438) * .e7 * .e112 + 2 * ((((2 * ((((0.5 * .e352 - 2 * (.e69 * .e97/.e19))/.e14 - .e452) * .e38 - 2 * .e380)/.e19) + 4 * .e319) * .e38 - .e141 * .e435 * .e3/.e10)/.e104 - (.e19 * (4 - .e444) * .e3/.e10 + 2 * (.e97 * .e12/.e14)) * .e141 * .e38 * .e12 * .e52/.e291) * .e108 * .e3) + 2 * .e399) * .e151 * .e3)/.e22 + .e215 * .e403 - (((.e139 * .e40 - .e183 * .e6 * .e28)/.e10 + 2 * (2 * .e387 - .e282 * .e28 * .e10) - 8 * (.e189 * (2 * .e412 - .e238 * .e10) * .e40 * .e10/.e159))/.e159 + (2 * (.e289 * .e10 + 2 * .e332) + 4)/.e155 - .e194 * (32 * ((.e9/.e423 + 4 * .e3) * .e9/.e14) - .e146/.e10)/.e277) * .e220) * .e3 + ((0.5 * (.e314/.e10) - 8 * (.e438 * .e7 * .e112)) * .e3 + (0.5 * (1 - 32 * .e422) - 0.5 * .e139)/.e10) * .e20 + 0.5 * (((.e251 - (.e395 + 2 * .e375)) * .e220 - .e403 * .e151)/.e22 - 32 * (((.e356 * .e38 - .e114 * (.e228 + .e315)/.e10) * .e3/.e149 - .e114 * ((16 * .e115 + .e273) * .e12 + (2 - .e444) * .e19 * .e44 * .e3/.e10) * .e38 * .e52/.e290) * .e4 * .e47 * .e21 * .e3)) - 0.5 * (((.e282 - .e309 * .e183/.e40) * .e28 + (.e331 * .e40 - .e45 * .e183 * .e28)/.e22)/.e40)) * (1 - 0.5 * geno_b) * .e5, b2 = geno_b * geno_q * ((((.e354 * .e186 + .e313 * .e229/.e10) * .e3 + .e114 * (32 * (.e318 - .e102 * .e303/.e78) + 64 * ((((2 * (((2 - .e221) * .e3 + .e263)/.e10) + 2 * ((0.5 * (.e350/.e14) - .e450) * .e10 + .e382)) * .e38 - .e136 * .e434 * .e3/.e10) * .e10 + (.e53 - 2 * (.e303 * .e10/.e78)) * .e136 * .e38)/.e78)) + 32 * (((((.e79 * .e180/.e40 - .e280) * .e3 - .e117 * .e180) * .e28/.e152 + tij * (.e335 + 0.5 * (((.e250 - .e372) * .e6 + .e144) * .e3 - 0.5))/.e10) * .e70 + .e143 * .e303/.e78 + (0.5 * ((.e329 * .e3 * .e14/2 + .e124/2)/.e10) + 0.5 * (t0 * ((.e14/2 - .e252 * .e6/2) * .e3/.e10 + 0.5)) - .e134 * (1/.e9 + .e255) * .e3) * .e47/.e10) * .e38 + .e323)) * .e4 * .e47 * .e21 * .e3/.e149 + ((.e250 - .e371) * .e226 - (.e399 + (64 * .e430 + 64/.e107) * .e7 * .e112 + 2 * ((((2 * ((((0.5 * .e350 - 2 * (.e95 * .e69/.e19))/.e14 - .e450) * .e38 - .e380)/.e19) + 4 * .e318) * .e38 - .e141 * .e434 * .e3/.e10)/.e104 - ((2 - .e436) * .e19 * .e3/.e10 + 2 * (.e95 * .e12/.e14)) * .e141 * .e38 * .e12 * .e52/.e291) * .e108 * .e3)) * .e151 * .e3)/.e22 + .e215 * .e398 - (((.e154 * .e40 - .e180 * .e6 * .e28)/.e10 + 2 * (.e387 - .e280 * .e28 * .e10) - 8 * (.e189 * (.e412 - .e237 * .e10) * .e40 * .e10/.e159))/.e159 + (2 + 2 * (.e287 * .e10 + .e332))/.e155 - .e194 * (32 * ((.e9/(2 * .e423) + .e11) * .e9/.e14) - .e146/.e22)/.e277) * .e220) * .e3 + ((0.5 * (.e311/.e10) - 8 * (.e430 * .e7 * .e112)) * .e3 + (0.5 * (0.5 - 16 * .e422) - 0.5 * .e154)/.e10) * .e20 + 0.5 * (((.e250 - (.e371 + .e375)) * .e220 - .e398 * .e151)/.e22 - 32 * (((.e354 * .e38 - .e114 * (.e105 + .e75)/.e10) * .e3/.e149 - .e114 * ((1 - .e436) * .e19 * .e44 * .e3/.e10 + (.e272 + 8 * .e115) * .e12) * .e38 * .e52/.e290) * .e4 * .e47 * .e21 * .e3)) - 0.5 * (((.e280 - .e309 * .e180/.e40) * .e28 + (.e329 * .e40 - .e45 * .e180 * .e28)/.e22)/.e40)) * .e5) } deriv_mu_int_f0_ff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e7 <- sqrt(.e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3)) .e8 <- 2 * .e3 .e9 <- 2 * .e7 .e10 <- .e4 + .e7 .e12 <- r0 - .e10/.e8 .e13 <- t0 * .e7 .e14 <- .e8 + 2 * (.e7/.e12) .e16 <- .e9^2 .e17 <- .e5/.e7 .e18 <- exp(-.e13) .e19 <- tij - t0 .e23 <- 2 * .e17 - .e9 .e24 <- .e8 - .e14 * exp(2 * (.e7 * .e19)) .e25 <- exp(-(2 * .e13)) .e28 <- (.e3 * .e12/.e9 + 0.5) * .e18 + (.e3/.e24 - 0.5) * exp(-(tij * .e7)) .e31 <- .e14 * .e16 * .e10 * .e25 .e33 <- .e14 * .e10^2 * .e25 .e35 <- .e12/.e9 + 1/.e24 .e37 <- 1 - 0.5 * geno_f .e38 <- .e18^2 .e40 <- .e5 * .e19/.e16 .e41 <- .e5/.e16 .e42 <- .e17 - .e7 c(f0 = ((.e35 * (64 * .e41 + 8 * (.e23^2 * .e38 * .e3/.e33))/.e9 - 64 * (.e28 * .e23 * .e4 * .e18/.e31)) * .e3 + 8 * .e40) * .e37^2 * .e3, f2 = geno_f * ((.e35 * (32 * .e41 + 8 * (.e42 * .e23 * .e38 * .e3/.e33))/.e9 - .e28 * (16 * .e23 + 32 * .e42) * .e4 * .e18/.e31) * .e3 + 4 * .e40) * .e37 * .e3, f1 = ((.e28 * (32 * .e23 + 64 * .e17) * .e18/.e31 - .e35 * (16 * (.e23 * .e38 * .e3/(.e33 * .e7)) + 64/.e16) * .e4/.e9) * .e3 - 8 * (.e4 * .e19/.e16)) * .e37 * .e4 * .e3) } deriv_mu_int_f2_ff1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e7 <- sqrt(.e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3)) .e8 <- 2 * .e3 .e9 <- 2 * .e7 .e10 <- .e4 + .e7 .e12 <- r0 - .e10/.e8 .e13 <- t0 * .e7 .e14 <- .e8 + 2 * (.e7/.e12) .e15 <- .e5/.e7 .e17 <- .e9^2 .e18 <- exp(-.e13) .e19 <- tij - t0 .e23 <- 2 * .e15 - .e9 .e24 <- .e8 - .e14 * exp(2 * (.e7 * .e19)) .e25 <- exp(-(2 * .e13)) .e28 <- (.e3 * .e12/.e9 + 0.5) * .e18 + (.e3/.e24 - 0.5) * exp(-(tij * .e7)) .e31 <- .e14 * .e17 * .e10 * .e25 .e33 <- .e14 * .e10^2 * .e25 .e34 <- .e15 - .e7 .e36 <- .e12/.e9 + 1/.e24 .e37 <- .e18^2 c(f2 = geno_f^2 * ((.e36 * (16 * (.e5/.e17) + 4 * (.e34 * .e23 * .e37 * .e3/.e33))/.e9 - .e28 * (16 * .e34 + 8 * .e23) * .e4 * .e18/.e31) * .e3 + 2 * (.e5 * .e19/.e17)) * .e3, f1 = geno_f * ((.e28 * (16 * .e23 + 32 * .e15) * .e18/.e31 - .e36 * (32/.e17 + 8 * (.e23 * .e37 * .e3/(.e33 * .e7))) * .e4/.e9) * .e3 - 4 * (.e4 * .e19/.e17)) * .e4 * .e3) } deriv_mu_int_f1_f1_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e3 <- geno_q * (q2 - q0)/2 + q0 .e4 <- a0 + geno_a * (a2 - a0)/2 .e5 <- .e4^2 .e6 <- .e5 + 2 * ((b0 + geno_b * (b2 - b0)/2)^2 * .e3) .e7 <- sqrt(.e6) .e8 <- 2 * .e3 .e9 <- .e4 + .e7 .e11 <- r0 - .e9/.e8 .e12 <- 2 * .e7 .e13 <- t0 * .e7 .e14 <- .e8 + 2 * (.e7/.e11) .e16 <- .e12^2 .e17 <- exp(-.e13) .e18 <- tij - t0 .e21 <- .e8 - .e14 * exp(2 * (.e7 * .e18)) .e22 <- exp(-(2 * .e13)) (((.e11/.e12 + 1/.e21) * (32 * (.e5 * .e17^2 * .e3/(.e6 * .e14 * .e9^2 * .e22)) + 64/.e16)/2 - 128 * (((.e3 * .e11/.e12 + 0.5) * .e17 + (.e3/.e21 - 0.5) * exp(-(tij * .e7))) * .e4 * .e17/(.e14 * .e16 * .e9 * .e22))) * .e3/.e7 + 8 * (.e18/.e16)) * .e5 * .e3 } deriv_mu_int_m0_t_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e1 <- exp(t0 * theta) .e2 <- exp(theta * tij) (1 - 0.5 * geno_mu) * (tij * .e2 - ((.e2 - .e1)/theta + t0 * .e1))/theta } deriv_mu_int_m2_t_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e1 <- exp(t0 * theta) .e2 <- exp(theta * tij) 0.5 * (geno_mu * (tij * .e2 - ((.e2 - .e1)/theta + t0 * .e1))/theta) } deriv_mu_int_t_t_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij, r0, m0, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { .e1 <- exp(t0 * theta) .e2 <- exp(theta * tij) (geno_mu * (mu02 - mu00)/2 + mu00) * (tij^2 * .e2 - ((2 * (tij * .e2) - (2 * ((.e2 - .e1)/theta) + 2 * (t0 * .e1)))/theta + t0^2 * .e1))/theta } d_f_i1_a0_abqff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_a0_abqff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_a2_abqff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_a2_abqff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_b0_bqff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_b0_bqff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_b2_bqff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_b2_bqff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_q0_qff1mtb_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_q0_qff1mtb_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_q2_qff1mtb_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_q2_qff1mtb_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_f0_ff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_f0_ff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_f2_ff1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_f2_ff1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_f1_f1mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_f1_f1mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_m0_mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_m0_mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_m2_mt_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_m2_mt_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } d_f_i1_t_t_g <- function (a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) { d <- .Call('d_f_i1_t_t_g_c', a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0, r0, tau, t0, geno_a, geno_b, geno_q, geno_f, geno_mu) return(d) } hes_loglik_g <- function(param,m0,r0,tau,yij,delta,tij, n_j,t0,geno_a,geno_b,geno_q,geno_f,geno_mu) { deriv_a0_a0 <- deriv_a0_a2 <- deriv_a0_b0 <- deriv_a0_b2 <- deriv_a0_q0 <- deriv_a0_q2 <- deriv_a0_f0 <- deriv_a0_f2 <- deriv_a0_f1 <- deriv_a0_mu00 <- deriv_a0_mu02 <- deriv_a0_theta <- 0 deriv_a2_a2 <- deriv_a2_b0 <- deriv_a2_b2 <- deriv_a2_q0 <- deriv_a2_q2 <- deriv_a2_f0 <- deriv_a2_f2 <- deriv_a2_f1 <- deriv_a2_mu00 <- deriv_a2_mu02 <- deriv_a2_theta <- 0 deriv_b0_b0 <- deriv_b0_b2 <- deriv_b0_q0 <- deriv_b0_q2 <- deriv_b0_f0 <- deriv_b0_f2 <- deriv_b0_f1 <- deriv_b0_mu00 <- deriv_b0_mu02 <- deriv_b0_theta <- 0 deriv_b2_b2 <- deriv_b2_q0 <- deriv_b2_q2 <- deriv_b2_f0 <- deriv_b2_f2 <- deriv_b2_f1 <- deriv_b2_mu00 <- deriv_b2_mu02 <- deriv_b2_theta <- 0 deriv_q0_q0 <- deriv_q0_q2 <- deriv_q0_f0 <- deriv_q0_f2 <- deriv_q0_f1 <- deriv_q0_mu00 <- deriv_q0_mu02 <- deriv_q0_theta <- 0 deriv_q2_q2 <- deriv_q2_f0 <- deriv_q2_f2 <- deriv_q2_f1 <- deriv_q2_mu00 <- deriv_q2_mu02 <- deriv_q2_theta <- 0 deriv_f0_f0 <- deriv_f0_f2 <- deriv_f0_f1 <- deriv_f0_mu00 <- deriv_f0_mu02 <- deriv_f0_theta <- 0 deriv_f2_f2 <- deriv_f2_f1 <- deriv_f2_mu00 <- deriv_f2_mu02 <- deriv_f2_theta <- 0 deriv_f1_f1 <- deriv_f1_mu00 <- deriv_f1_mu02 <- deriv_f1_theta <- 0 deriv_mu00_mu00 <- deriv_mu00_mu02 <- deriv_mu00_theta <- 0 deriv_mu02_mu02 <- deriv_mu02_theta <- 0 deriv_theta_theta <- 0 a0 <- param[1] a2 <- param[2] b0 <- param[3] b2 <- param[4] q0 <- param[5] q2 <- param[6] f0 <- param[7] f2 <- param[8] f1 <- param[9] mu00 <- param[10] mu02 <- param[11] theta <- param[12] num_j <- length(yij) index <- 1:length(yij) re_1_a0 <- d_f_j1_a0_abq_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_1_a2 <- d_f_j1_a2_abq_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_1_b0 <- d_f_j1_b0_bq_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_1_b2 <- d_f_j1_b2_bq_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_1_q0 <- d_f_j1_q0_qb_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_1_q2 <- d_f_j1_q2_qb_g(a0, a2, b0, b2, q0, q2, r0[index], tij[index], t0[index], geno_a, geno_b, geno_q) re_2_a0 <- d_f_j2_a0_abqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1,m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_a2 <- d_f_j2_a2_abqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1,m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_b0 <- d_f_j2_b0_bqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_b2 <- d_f_j2_b2_bqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_q0 <- d_f_j2_q0_qff1b_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_q2 <- d_f_j2_q2_qff1b_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_f0 <- d_f_j2_f0_ff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_f2 <- d_f_j2_f2_ff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_2_f1 <- d_f_j2_f1_f1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, m0[index],r0[index],tij[index],yij[index], t0[index], geno_a, geno_b, geno_q, geno_f) re_4_a0 <- deriv_mu_int_a0_abqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_a2 <- deriv_mu_int_a2_abqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_b0 <- deriv_mu_int_b0_bqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_b2 <- deriv_mu_int_b2_bqff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_q0 <- deriv_mu_int_q0_qff1b_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_q2 <- deriv_mu_int_q2_qff1b_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_f0 <- deriv_mu_int_f0_ff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_f2 <- deriv_mu_int_f2_ff1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_f1 <- deriv_mu_int_f1_f1_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_mu00 <- deriv_mu_int_m0_t_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_mu02 <- deriv_mu_int_m2_t_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) re_4_theta <- deriv_mu_int_t_t_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, tij[index],r0[index],m0[index],t0[index], geno_a, geno_b, geno_q, geno_f, geno_mu) deriv_a0_a0 <- sum(re_1_a0[1:num_j]) + sum(re_2_a0[1:num_j]) - sum(re_4_a0[1:num_j]) deriv_a0_a2 <- sum(re_1_a0[(num_j+1):(2*num_j)]) + sum(re_2_a0[(num_j+1):(2*num_j)]) - sum(re_4_a0[(num_j+1):(2*num_j)]) deriv_a0_b0 <- sum(re_1_a0[(2*num_j+1):(3*num_j)]) + sum(re_2_a0[(2*num_j+1):(3*num_j)]) - sum(re_4_a0[(2*num_j+1):(3*num_j)]) deriv_a0_b2 <- sum(re_1_a0[(3*num_j+1):(4*num_j)]) + sum(re_2_a0[(3*num_j+1):(4*num_j)]) - sum(re_4_a0[(3*num_j+1):(4*num_j)]) deriv_a0_q0 <- sum(re_1_a0[(4*num_j+1):(5*num_j)]) + sum(re_2_a0[(4*num_j+1):(5*num_j)]) - sum(re_4_a0[(4*num_j+1):(5*num_j)]) deriv_a0_q2 <- sum(re_1_a0[(5*num_j+1):(6*num_j)]) + sum(re_2_a0[(5*num_j+1):(6*num_j)]) - sum(re_4_a0[(5*num_j+1):(6*num_j)]) deriv_a0_f0 <- sum(re_2_a0[(6*num_j+1):(7*num_j)]) - sum(re_4_a0[(6*num_j+1):(7*num_j)]) deriv_a0_f2 <- sum(re_2_a0[(7*num_j+1):(8*num_j)]) - sum(re_4_a0[(7*num_j+1):(8*num_j)]) deriv_a0_f1 <- sum(re_2_a0[(8*num_j+1):(9*num_j)]) - sum(re_4_a0[(8*num_j+1):(9*num_j)]) deriv_a2_a2 <- sum(re_1_a2[1:num_j]) + sum(re_2_a2[1:num_j]) - sum(re_4_a2[1:num_j]) deriv_a2_b0 <- sum(re_1_a2[(num_j+1):(2*num_j)]) + sum(re_2_a2[(num_j+1):(2*num_j)]) - sum(re_4_a2[(num_j+1):(2*num_j)]) deriv_a2_b2 <- sum(re_1_a2[(2*num_j+1):(3*num_j)]) + sum(re_2_a2[(2*num_j+1):(3*num_j)]) - sum(re_4_a2[(2*num_j+1):(3*num_j)]) deriv_a2_q0 <- sum(re_1_a2[(3*num_j+1):(4*num_j)]) + sum(re_2_a2[(3*num_j+1):(4*num_j)]) - sum(re_4_a2[(3*num_j+1):(4*num_j)]) deriv_a2_q2 <- sum(re_1_a2[(4*num_j+1):(5*num_j)]) + sum(re_2_a2[(4*num_j+1):(5*num_j)]) - sum(re_4_a2[(4*num_j+1):(5*num_j)]) deriv_a2_f0 <- sum(re_2_a2[(5*num_j+1):(6*num_j)]) - sum(re_4_a2[(5*num_j+1):(6*num_j)]) deriv_a2_f2 <- sum(re_2_a2[(6*num_j+1):(7*num_j)]) - sum(re_4_a2[(6*num_j+1):(7*num_j)]) deriv_a2_f1 <- sum(re_2_a2[(7*num_j+1):(8*num_j)]) - sum(re_4_a2[(7*num_j+1):(8*num_j)]) deriv_b0_b0 <- sum(re_1_b0[1:num_j]) + sum(re_2_b0[1:num_j]) - sum(re_4_b0[1:num_j]) deriv_b0_b2 <- sum(re_1_b0[(num_j+1):(2*num_j)]) + sum(re_2_b0[(num_j+1):(2*num_j)]) - sum(re_4_b0[(num_j+1):(2*num_j)]) deriv_b0_q0 <- sum(re_1_q0[(2*num_j+1):(3*num_j)]) + sum(re_2_q0[(5*num_j+1):(6*num_j)]) - sum(re_4_q0[(5*num_j+1):(6*num_j)]) deriv_b0_q2 <- sum(re_1_q2[(num_j+1):(2*num_j)]) + sum(re_2_q2[(4*num_j+1):(5*num_j)]) - sum(re_4_q2[(4*num_j+1):(5*num_j)]) deriv_b0_f0 <- sum(re_2_b0[(4*num_j+1):(5*num_j)]) - sum(re_4_b0[(4*num_j+1):(5*num_j)]) deriv_b0_f2 <- sum(re_2_b0[(5*num_j+1):(6*num_j)]) - sum(re_4_b0[(5*num_j+1):(6*num_j)]) deriv_b0_f1 <- sum(re_2_b0[(6*num_j+1):(7*num_j)]) - sum(re_4_b0[(6*num_j+1):(7*num_j)]) deriv_b2_b2 <- sum(re_1_b2[1:num_j]) + sum(re_2_b2[1:num_j]) - sum(re_4_b2[1:num_j]) deriv_b2_q0 <- sum(re_1_q0[(3*num_j+1):(4*num_j)]) + sum(re_2_q0[(6*num_j+1):(7*num_j)]) - sum(re_4_q0[(6*num_j+1):(7*num_j)]) deriv_b2_q2 <- sum(re_1_q2[(2*num_j+1):(3*num_j)]) + sum(re_2_q2[(5*num_j+1):(6*num_j)]) - sum(re_4_q2[(5*num_j+1):(6*num_j)]) deriv_b2_f0 <- sum(re_2_b2[(3*num_j+1):(4*num_j)]) - sum(re_4_b2[(3*num_j+1):(4*num_j)]) deriv_b2_f2 <- sum(re_2_b2[(4*num_j+1):(5*num_j)]) - sum(re_4_b2[(4*num_j+1):(5*num_j)]) deriv_b2_f1 <- sum(re_2_b2[(5*num_j+1):(6*num_j)]) - sum(re_4_b2[(5*num_j+1):(6*num_j)]) deriv_q0_q0 <- sum(re_1_q0[1:num_j]) + sum(re_2_q0[1:num_j]) - sum(re_4_q0[1:num_j]) deriv_q0_q2 <- sum(re_1_q0[(num_j+1):(2*num_j)]) + sum(re_2_q0[(num_j+1):(2*num_j)]) - sum(re_4_q0[(num_j+1):(2*num_j)]) deriv_q0_f0 <- sum(re_2_q0[(2*num_j+1):(3*num_j)]) - sum(re_4_q0[(2*num_j+1):(3*num_j)]) deriv_q0_f2 <- sum(re_2_q0[(3*num_j+1):(4*num_j)]) - sum(re_4_q0[(3*num_j+1):(4*num_j)]) deriv_q0_f1 <- sum(re_2_q0[(4*num_j+1):(5*num_j)]) - sum(re_4_q0[(4*num_j+1):(5*num_j)]) deriv_q2_q2 <- sum(re_1_q2[1:num_j]) + sum(re_2_q2[1:num_j]) - sum(re_4_q2[1:num_j]) deriv_q2_f0 <- sum(re_2_q2[(num_j+1):(2*num_j)]) - sum(re_4_q2[(num_j+1):(2*num_j)]) deriv_q2_f2 <- sum(re_2_q2[(2*num_j+1):(3*num_j)]) - sum(re_4_q2[(2*num_j+1):(3*num_j)]) deriv_q2_f1 <- sum(re_2_q2[(3*num_j+1):(4*num_j)]) - sum(re_4_q2[(3*num_j+1):(4*num_j)]) deriv_f0_f0 <- sum(re_2_f0[1:num_j]) - sum(re_4_f0[1:num_j]) deriv_f0_f2 <- sum(re_2_f0[(num_j+1):(2*num_j)]) - sum(re_4_f0[(num_j+1):(2*num_j)]) deriv_f0_f1 <- sum(re_2_f0[(2*num_j+1):(3*num_j)]) - sum(re_4_f0[(2*num_j+1):(3*num_j)]) deriv_f2_f2 <- sum(re_2_f2[1:num_j]) - sum(re_4_f2[1:num_j]) deriv_f2_f1 <- sum(re_2_f2[(num_j+1):(2*num_j)]) - sum(re_4_f2[(num_j+1):(2*num_j)]) deriv_f1_f1 <- sum(re_2_f1[1:num_j]) - sum(re_4_f1[1:num_j]) deriv_mu00_theta <- - sum(re_4_mu00[1:num_j]) deriv_mu02_theta <- - sum(re_4_mu02[1:num_j]) deriv_theta_theta <- - sum(re_4_theta[1:num_j]) num_i <- length(tau) for(i in 1:num_i) { if(i==1) { num_j <- n_j[1] index <- 1:num_j }else{ num_j <- n_j[i] index <- (sum(n_j[1:(i-1)])+1):sum(n_j[1:i]) } if(delta[i]>0) { sum_n_j <- sum(n_j[1:i]) re_3_a0 <- d_f_i1_a0_abqff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_a2 <- d_f_i1_a2_abqff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta, m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_b0 <- d_f_i1_b0_bqff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_b2 <- d_f_i1_b2_bqff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_q0 <- d_f_i1_q0_qff1mtb_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_q2 <- d_f_i1_q2_qff1mtb_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_f0 <- d_f_i1_f0_ff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_f2 <- d_f_i1_f2_ff1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_f1 <- d_f_i1_f1_f1mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_mu00 <- d_f_i1_m0_mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_mu02 <- d_f_i1_m2_mt_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) re_3_theta <- d_f_i1_t_t_g(a0, a2, b0, b2, q0, q2, f0, f2, f1, mu00, mu02, theta,m0[sum_n_j],r0[sum_n_j],tau[i], t0[sum_n_j], geno_a[sum_n_j], geno_b[sum_n_j], geno_q[sum_n_j], geno_f[sum_n_j], geno_mu[sum_n_j]) deriv_a0_a0 <- deriv_a0_a0 + re_3_a0[1] deriv_a0_a2 <- deriv_a0_a2 + re_3_a0[2] deriv_a0_b0 <- deriv_a0_b0 + re_3_a0[3] deriv_a0_b2 <- deriv_a0_b2 + re_3_a0[4] deriv_a0_q0 <- deriv_a0_q0 + re_3_a0[5] deriv_a0_q2 <- deriv_a0_q2 + re_3_a0[6] deriv_a0_f0 <- deriv_a0_f0 + re_3_a0[7] deriv_a0_f2 <- deriv_a0_f2 + re_3_a0[8] deriv_a0_f1 <- deriv_a0_f1 + re_3_a0[9] deriv_a0_mu00 <- deriv_a0_mu00 + re_3_a0[10] deriv_a0_mu02 <- deriv_a0_mu02 + re_3_a0[11] deriv_a0_theta <- deriv_a0_theta + re_3_a0[12] deriv_a2_a2 <- deriv_a2_a2 + re_3_a2[1] deriv_a2_b0 <- deriv_a2_b0 + re_3_a2[2] deriv_a2_b2 <- deriv_a2_b2 + re_3_a2[3] deriv_a2_q0 <- deriv_a2_q0 + re_3_a2[4] deriv_a2_q2 <- deriv_a2_q2 + re_3_a2[5] deriv_a2_f0 <- deriv_a2_f0 + re_3_a2[6] deriv_a2_f2 <- deriv_a2_f2 + re_3_a2[7] deriv_a2_f1 <- deriv_a2_f1 + re_3_a2[8] deriv_a2_mu00 <- deriv_a2_mu00 + re_3_a2[9] deriv_a2_mu02 <- deriv_a2_mu02 + re_3_a2[10] deriv_a2_theta <- deriv_a2_theta + re_3_a2[11] deriv_b0_b0 <- deriv_b0_b0 + re_3_b0[1] deriv_b0_b2 <- deriv_b0_b2 + re_3_b0[2] deriv_b0_q0 <- deriv_b0_q0 + re_3_q0[9] deriv_b0_q2 <- deriv_b0_q2 + re_3_q2[8] deriv_b0_f0 <- deriv_b0_f0 + re_3_b0[5] deriv_b0_f2 <- deriv_b0_f2 + re_3_b0[6] deriv_b0_f1 <- deriv_b0_f1 + re_3_b0[7] deriv_b0_mu00 <- deriv_b0_mu00 + re_3_b0[8] deriv_b0_mu02 <- deriv_b0_mu02 + re_3_b0[9] deriv_b0_theta <- deriv_b0_theta + re_3_b0[10] deriv_b2_b2 <- deriv_b2_b2 + re_3_b2[1] deriv_b2_q0 <- deriv_b2_q0 + re_3_q0[10] deriv_b2_q2 <- deriv_b2_q2 + re_3_q2[9] deriv_b2_f0 <- deriv_b2_f0 + re_3_b2[4] deriv_b2_f2 <- deriv_b2_f2 + re_3_b2[5] deriv_b2_f1 <- deriv_b2_f1 + re_3_b2[6] deriv_b2_mu00 <- deriv_b2_mu00 + re_3_b2[7] deriv_b2_mu02 <- deriv_b2_mu02 + re_3_b2[8] deriv_b2_theta <- deriv_b2_theta + re_3_b2[9] deriv_q0_q0 <- deriv_q0_q0 + re_3_q0[1] deriv_q0_q2 <- deriv_q0_q2 + re_3_q0[2] deriv_q0_f0 <- deriv_q0_f0 + re_3_q0[3] deriv_q0_f2 <- deriv_q0_f2 + re_3_q0[4] deriv_q0_f1 <- deriv_q0_f1 + re_3_q0[5] deriv_q0_mu00 <- deriv_q0_mu00 + re_3_q0[6] deriv_q0_mu02 <- deriv_q0_mu02 + re_3_q0[7] deriv_q0_theta <- deriv_q0_theta + re_3_q0[8] deriv_q2_q2 <- deriv_q2_q2 + re_3_q2[1] deriv_q2_f0 <- deriv_q2_f0 + re_3_q2[2] deriv_q2_f2 <- deriv_q2_f2 + re_3_q2[3] deriv_q2_f1 <- deriv_q2_f1 + re_3_q2[4] deriv_q2_mu00 <- deriv_q2_mu00 + re_3_q2[5] deriv_q2_mu02 <- deriv_q2_mu02 + re_3_q2[6] deriv_q2_theta <- deriv_q2_theta + re_3_q2[7] deriv_f0_f0 <- deriv_f0_f0 + re_3_f0[1] deriv_f0_f2 <- deriv_f0_f2 + re_3_f0[2] deriv_f0_f1 <- deriv_f0_f1 + re_3_f0[3] deriv_f0_mu00 <- deriv_f0_mu00 + re_3_f0[4] deriv_f0_mu02 <- deriv_f0_mu02 + re_3_f0[5] deriv_f0_theta <- deriv_f0_theta + re_3_f0[6] deriv_f2_f2 <- deriv_f2_f2 + re_3_f2[1] deriv_f2_f1 <- deriv_f2_f1 + re_3_f2[2] deriv_f2_mu00 <- deriv_f2_mu00 + re_3_f2[3] deriv_f2_mu02 <- deriv_f2_mu02 + re_3_f2[4] deriv_f2_theta <- deriv_f2_theta + re_3_f2[5] deriv_f1_f1 <- deriv_f1_f1 + re_3_f1[1] deriv_f1_mu00 <- deriv_f1_mu00 + re_3_f1[2] deriv_f1_mu02 <- deriv_f1_mu02 + re_3_f1[3] deriv_f1_theta <- deriv_f1_theta + re_3_f1[4] deriv_mu00_mu00 <- deriv_mu00_mu00 + re_3_mu00[1] deriv_mu00_mu02 <- deriv_mu00_mu02 + re_3_mu00[2] deriv_mu00_theta <- deriv_mu00_theta + re_3_mu00[3] deriv_mu02_mu02 <- deriv_mu02_mu02 + re_3_mu02[1] deriv_mu02_theta <- deriv_mu02_theta + re_3_mu02[2] deriv_theta_theta <- deriv_theta_theta + re_3_theta[1] }else{ } } hes <- matrix(0, 12, 12) hes[1,] <- c(deriv_a0_a0, deriv_a0_a2, deriv_a0_b0, deriv_a0_b2, deriv_a0_q0, deriv_a0_q2, deriv_a0_f0, deriv_a0_f2, deriv_a0_f1, deriv_a0_mu00, deriv_a0_mu02, deriv_a0_theta) hes[2,2:12] <- c(deriv_a2_a2, deriv_a2_b0, deriv_a2_b2, deriv_a2_q0, deriv_a2_q2, deriv_a2_f0, deriv_a2_f2, deriv_a2_f1, deriv_a2_mu00, deriv_a2_mu02, deriv_a2_theta) hes[3,3:12] <- c(deriv_b0_b0, deriv_b0_b2, deriv_b0_q0, deriv_b0_q2, deriv_b0_f0, deriv_b0_f2, deriv_b0_f1, deriv_b0_mu00, deriv_b0_mu02, deriv_b0_theta) hes[4,4:12] <- c(deriv_b2_b2, deriv_b2_q0, deriv_b2_q2, deriv_b2_f0, deriv_b2_f2, deriv_b2_f1, deriv_b2_mu00, deriv_b2_mu02, deriv_b2_theta) hes[5,5:12] <- c(deriv_q0_q0, deriv_q0_q2, deriv_q0_f0, deriv_q0_f2, deriv_q0_f1, deriv_q0_mu00, deriv_q0_mu02, deriv_q0_theta) hes[6,6:12] <- c(deriv_q2_q2, deriv_q2_f0, deriv_q2_f2, deriv_q2_f1, deriv_q2_mu00, deriv_q2_mu02, deriv_q2_theta) hes[7,7:12] <- c(deriv_f0_f0, deriv_f0_f2, deriv_f0_f1, deriv_f0_mu00, deriv_f0_mu02, deriv_f0_theta) hes[8,8:12] <- c(deriv_f2_f2, deriv_f2_f1, deriv_f2_mu00, deriv_f2_mu02, deriv_f2_theta) hes[9,9:12] <- c(deriv_f1_f1, deriv_f1_mu00, deriv_f1_mu02, deriv_f1_theta) hes[10,10:12] <- c(deriv_mu00_mu00, deriv_mu00_mu02, deriv_mu00_theta) hes[11,11:12] <- c(deriv_mu02_mu02, deriv_mu02_theta) hes[12,12] <- c(deriv_theta_theta) dia <- diag(hes) hes <- hes + t(hes) diag(hes) <- dia (-1)*hes }
fisher.pval <- function (k1, n1, k2, n2, alternative=c("two.sided", "less", "greater"), log.p=FALSE) { alternative <- match.arg(alternative) if (any(k1 < 0) || any(k1 > n1) || any(n1 <= 0)) stop("k1 and n1 must be integers with 0 <= k1 <= n1") if (any(k2 < 0) || any(k2 > n2) || any(n2 <= 0)) stop("k2 and n2 must be integers with 0 <= k2 <= n2") if (any(k1 + k2 <= 0)) stop("either k1 or k2 must be non-zero") l <- max(length(k1), length(n1), length(k2), length(n2)) if (length(k1) < l) k1 <- rep(k1, length.out=l) if (length(n1) < l) n1 <- rep(n1, length.out=l) if (length(k2) < l) k2 <- rep(k2, length.out=l) if (length(n2) < l) n2 <- rep(n2, length.out=l) k <- k1 + k2 if (alternative == "two.sided") { if (log.p) { pval <- pmin(phyper(k1 - 1, n1, n2, k, lower.tail=FALSE, log.p=TRUE), phyper(k1, n1, n2, k, lower.tail=TRUE, log.p=TRUE)) + log(2) pval <- pmin(pval, 0) } else { pval <- 2 * pmin(phyper(k1 - 1, n1, n2, k, lower.tail=FALSE), phyper(k1, n1, n2, k, lower.tail=TRUE)) pval <- pmax(0, pmin(1, pval)) } } else if (alternative == "greater") { pval <- phyper(k1 - 1, n1, n2, k, lower.tail=FALSE, log.p=log.p) } else if (alternative == "less") { pval <- phyper(k1, n1, n2, k, lower.tail=TRUE, log.p=log.p) } pval }
dx2x <- deriv(~ x^2, "x") print(dx2x) mode(dx2x) x <- -1:2 eval(dx2x) trig.exp <- expression(sin(cos(x + y^2))) ( D.sc <- D(trig.exp, "x") ) all.equal(D(trig.exp[[1]], "x"), D.sc) ( dxy <- deriv(trig.exp, c("x", "y")) ) y <- 1 eval(dxy) eval(D.sc) deriv((y ~ sin(cos(x) * y)), c("x","y"), func = TRUE) (fx <- deriv(y ~ b0 + b1 * 2^(-x/th), c("b0", "b1", "th"), function(b0, b1, th, x = 1:7){} ) ) fx(2, 3, 4) D(quote(log1p(x^2)), "x") stopifnot(identical( D(quote(log1p(x^2)), "x"), D(quote(log(1+x^2)), "x"))) D(quote(expm1(x^2)), "x") stopifnot(identical( D(quote(expm1(x^2)), "x") -> Dex1, D(quote(exp(x^2)-1), "x")), identical(Dex1, quote(exp(x^2) * (2 * x)))) D(quote(sinpi(x^2)), "x") D(quote(cospi(x^2)), "x") D(quote(tanpi(x^2)), "x") stopifnot(identical(D(quote(log2 (x^2)), "x"), quote(2 * x/(x^2 * log(2)))), identical(D(quote(log10(x^2)), "x"), quote(2 * x/(x^2 * log(10)))))
dinvpareto <- function(x, shape, scale, log = FALSE) .External(C_actuar_do_dpq, "dinvpareto", x, shape, scale, log) pinvpareto <- function(q, shape, scale, lower.tail = TRUE, log.p = FALSE) .External(C_actuar_do_dpq, "pinvpareto", q, shape, scale, lower.tail, log.p) qinvpareto <- function(p, shape, scale, lower.tail = TRUE, log.p = FALSE) .External(C_actuar_do_dpq, "qinvpareto", p, shape, scale, lower.tail, log.p) rinvpareto <- function(n, shape, scale) .External(C_actuar_do_random, "rinvpareto", n, shape, scale) minvpareto <- function(order, shape, scale) .External(C_actuar_do_dpq, "minvpareto", order, shape, scale, FALSE) levinvpareto <- function(limit, shape, scale, order = 1) .External(C_actuar_do_dpq, "levinvpareto", limit, shape, scale, order, FALSE)
svc <- paws::shield() test_that("describe_attack_statistics", { expect_error(svc$describe_attack_statistics(), NA) }) test_that("list_attacks", { expect_error(svc$list_attacks(), NA) }) test_that("list_attacks", { expect_error(svc$list_attacks(MaxResults = 20), NA) }) test_that("list_protection_groups", { expect_error(svc$list_protection_groups(), NA) }) test_that("list_protection_groups", { expect_error(svc$list_protection_groups(MaxResults = 20), NA) })
kern2 <- function(dep.y, reg.x, tol = 0.1, ftol = 0.1, gradients = FALSE, residuals = FALSE) { gr = FALSE resz = FALSE if (gradients) gr = TRUE if (residuals) resz = TRUE bw = npregbw(ydat = as.vector(dep.y), xdat = reg.x, tol = tol, ftol = ftol,regtype="ll", bwmethod="cv.aic" ) mod = npreg(bws = bw, gradients = gr, residuals = resz) return(mod) }
library(aRpsDCA) fitme.exponential.t <- seq(0, 5, 1 / 12) fitme.exponential.Np <- exponential.Np( 1000, as.nominal(0.70), fitme.exponential.t ) * rnorm(n=length(fitme.exponential.t), mean=1, sd=0.1) exponential.fit <- best.exponential.from.interval( diff(fitme.exponential.Np), fitme.exponential.t[2:length(fitme.exponential.t)]) cat(paste("SSE:", exponential.fit$sse)) dev.new() plot(fitme.exponential.Np ~ fitme.exponential.t, main="Exponential Fit", col="blue", xlab="Time", ylab="Cumulative Production") lines(arps.Np(exponential.fit$decline, fitme.exponential.t) ~ fitme.exponential.t, col="red") legend("topright", pch=c(1, NA), lty=c(NA, 1), col=c("blue", "red"), legend=c("Actual", "Fit")) fitme.hyperbolic.t <- seq(0, 5, 1 / 12) fitme.hyperbolic.Np <- hyperbolic.Np( 1000, as.nominal(0.70), 1.9, fitme.hyperbolic.t ) * rnorm(n=length(fitme.hyperbolic.t), mean=1, sd=0.1) hyperbolic.fit <- best.hyperbolic.from.interval( diff(fitme.hyperbolic.Np), fitme.hyperbolic.t[2:length(fitme.hyperbolic.t)]) cat(paste("SSE:", hyperbolic.fit$sse)) dev.new() plot(fitme.hyperbolic.Np ~ fitme.hyperbolic.t, main="Hyperbolic Fit", col="blue", xlab="Time", ylab="Cumulative Production") lines(arps.Np(hyperbolic.fit$decline, fitme.hyperbolic.t) ~ fitme.hyperbolic.t, col="red") legend("topright", pch=c(1, NA), lty=c(NA, 1), col=c("blue", "red"), legend=c("Actual", "Fit")) fitme.hyp2exp.t <- seq(0, 5, 1 / 12) fitme.hyp2exp.Np <- hyp2exp.Np( 1000, as.nominal(0.70), 1.9, as.nominal(0.15), fitme.hyp2exp.t ) * rnorm(n=length(fitme.hyp2exp.t), mean=1, sd=0.1) hyp2exp.fit <- best.hyp2exp.from.interval( diff(fitme.hyp2exp.Np), fitme.hyp2exp.t[2:length(fitme.hyp2exp.t)]) cat(paste("SSE:", hyp2exp.fit$sse)) dev.new() plot(fitme.hyp2exp.Np ~ fitme.hyp2exp.t, main="Hyperbolic-to-Exponential Fit", col="blue", xlab="Time", ylab="Cumulative Production") lines(arps.Np(hyp2exp.fit$decline, fitme.hyp2exp.t) ~ fitme.hyp2exp.t, col="red") legend("topright", pch=c(1, NA), lty=c(NA, 1), col=c("blue", "red"), legend=c("Actual", "Fit")) overall.best <- best.fit.from.interval( diff(fitme.hyp2exp.Np), fitme.hyp2exp.t[2:length(fitme.hyp2exp.t)]) cat(paste("SSE:", overall.best$sse)) dev.new() plot(fitme.hyp2exp.Np ~ fitme.hyp2exp.t, main="Overall Best Fit (h2e Data)", col="blue", xlab="Time", ylab="Rate") lines(arps.Np(overall.best$decline, fitme.hyp2exp.t) ~ fitme.hyp2exp.t, col="red") legend("topright", pch=c(1, NA), lty=c(NA, 1), col=c("blue", "red"), legend=c("Actual", "Fit"))
NULL browse_package <- function(package = NULL) { stopifnot(is.null(package) || is_string(package)) if (is.null(package)) { check_is_project() } urls <- character() details <- list() if (is.null(package) && uses_git()) { grl <- github_remote_list(these = NULL) ord <- c( which(grl$remote == "origin"), which(grl$remote == "upstream"), which(!grl$remote %in% c("origin", "upstream")) ) grl <- grl[ord, ] grl <- set_names(grl$url, nm = grl$remote) parsed <- parse_github_remotes(grl) urls <- c(urls, glue_data(parsed, "https://{host}/{repo_owner}/{repo_name}")) details <- c(details, map(parsed$name, ~ glue("{ui_value(.x)} remote"))) } desc_urls_dat <- desc_urls(package, include_cran = TRUE) urls <- c(urls, desc_urls_dat$url) details <- c( details, map( desc_urls_dat$desc_field, ~ if (is.na(.x)) "CRAN" else glue("{ui_field(.x)} field in DESCRIPTION") ) ) if (length(urls) == 0) { ui_oops("Can't find any URLs") return(invisible(character())) } if (!is_interactive()) { return(invisible(urls)) } prompt <- "Which URL do you want to visit? (0 to exit)" pretty <- purrr::map2( format(urls, justify = "left"), details, ~ glue("{.x} ({.y})") ) choice <- utils::menu(title = prompt, choices = pretty) if (choice == 0) { return(invisible(character())) } view_url(urls[choice]) } browse_project <- function() browse_package(NULL) browse_github <- function(package = NULL) { view_url(github_url(package)) } browse_github_issues <- function(package = NULL, number = NULL) { view_url(github_url(package), "issues", number) } browse_github_pulls <- function(package = NULL, number = NULL) { pull <- if (is.null(number)) "pulls" else "pull" view_url(github_url(package), pull, number) } browse_github_actions <- function(package = NULL) { view_url(github_url(package), "actions") } browse_travis <- function(package = NULL, ext = c("com", "org")) { gh <- github_url(package) ext <- arg_match(ext) travis_url <- glue("travis-ci.{ext}") view_url(sub("github.com", travis_url, gh)) } browse_circleci <- function(package = NULL) { gh <- github_url(package) circle_url <- "circleci.com/gh" view_url(sub("github.com", circle_url, gh)) } browse_cran <- function(package = NULL) { view_url(cran_home(package)) } github_url <- function(package = NULL) { stopifnot(is.null(package) || is_string(package)) if (is.null(package)) { check_is_project() url <- github_url_from_git_remotes() if (!is.null(url)) { return(url) } } desc_urls_dat <- desc_urls(package) if (is.null(desc_urls_dat)) { if (is.null(package)) { ui_stop(" Project {ui_value(project_name())} has no DESCRIPTION file and \\ has no GitHub remotes configured No way to discover URLs") } else { ui_stop(" Can't find DESCRIPTION for package {ui_value(package)} locally \\ or on CRAN No way to discover URLs") } } desc_urls_dat <- desc_urls_dat[desc_urls_dat$is_github, ] if (nrow(desc_urls_dat) > 0) { parsed <- parse_github_remotes(desc_urls_dat$url[[1]]) return(glue_data_chr(parsed, "https://{host}/{repo_owner}/{repo_name}")) } if (is.null(package)) { ui_stop(" Project {ui_value(project_name())} has no GitHub remotes configured \\ and has no GitHub URLs in DESCRIPTION") } ui_warn(" Package {ui_value(package)} has no GitHub URLs in DESCRIPTION Trying the GitHub CRAN mirror") glue_chr("https://github.com/cran/{package}") } cran_home <- function(package = NULL) { package <- package %||% project_name() glue_chr("https://cran.r-project.org/package={package}") } desc_urls <- function(package = NULL, include_cran = FALSE, desc = NULL) { maybe_desc <- purrr::possibly(desc::desc, otherwise = NULL) desc_from_cran <- FALSE if (is.null(desc)) { if (is.null(package)) { desc <- maybe_desc(file = proj_get()) if (is.null(desc)) { return() } } else { desc <- maybe_desc(package = package) if (is.null(desc)) { cran_desc_url <- glue("https://cran.rstudio.com/web/packages/{package}/DESCRIPTION") suppressWarnings( desc <- maybe_desc(text = readLines(cran_desc_url)) ) if (is.null(desc)) { return() } desc_from_cran <- TRUE } } } url <- desc$get_urls() bug_reports <- desc$get_field("BugReports", default = character()) cran <- if (include_cran && desc_from_cran) cran_home(package) else character() dat <- data.frame( desc_field = c( rep_len("URL", length.out = length(url)), rep_len("BugReports", length.out = length(bug_reports)), rep_len(NA, length.out = length(cran)) ), url = c(url, bug_reports, cran), stringsAsFactors = FALSE ) dat <- cbind(dat, re_match(dat$url, github_remote_regex)) dat$is_github <- !is.na(dat$.match) & grepl("github", dat$host) dat[c("url", "desc_field", "is_github")] }
spip_binary_path <- function() { bin_name <- paste("spip", Sys.info()["sysname"], sep = "-") if(Sys.info()["sysname"] == "Windows") { bin_name <- paste(bin_name, ".exe", sep = "") } file.path(system.file(package = "CKMRpop"), "bin", bin_name) }
NULL .lightsail$allocate_static_ip_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIpName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$allocate_static_ip_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_certificate_to_distribution_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_certificate_to_distribution_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_disk_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string")), instanceName = structure(logical(0), tags = list(type = "string")), diskPath = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_disk_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_instances_to_load_balancer_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), instanceNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_instances_to_load_balancer_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_load_balancer_tls_certificate_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_load_balancer_tls_certificate_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_static_ip_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIpName = structure(logical(0), tags = list(type = "string")), instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$attach_static_ip_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$close_instance_public_ports_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(portInfo = structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$close_instance_public_ports_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$copy_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(sourceSnapshotName = structure(logical(0), tags = list(type = "string")), sourceResourceName = structure(logical(0), tags = list(type = "string")), restoreDate = structure(logical(0), tags = list(type = "string")), useLatestRestorableAutoSnapshot = structure(logical(0), tags = list(type = "boolean")), targetSnapshotName = structure(logical(0), tags = list(type = "string")), sourceRegion = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$copy_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_certificate_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(certificateName = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), subjectAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_certificate_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(certificate = structure(list(certificateArn = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), certificateDetail = structure(list(arn = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), serialNumber = structure(logical(0), tags = list(type = "string")), subjectAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), domainValidationRecords = structure(list(structure(list(domainName = structure(logical(0), tags = list(type = "string")), resourceRecord = structure(list(name = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), requestFailureReason = structure(logical(0), tags = list(type = "string")), inUseResourceCount = structure(logical(0), tags = list(type = "integer")), keyAlgorithm = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), issuedAt = structure(logical(0), tags = list(type = "timestamp")), issuerCA = structure(logical(0), tags = list(type = "string")), notBefore = structure(logical(0), tags = list(type = "timestamp")), notAfter = structure(logical(0), tags = list(type = "timestamp")), eligibleToRenew = structure(logical(0), tags = list(type = "string")), renewalSummary = structure(list(domainValidationRecords = structure(list(structure(list(domainName = structure(logical(0), tags = list(type = "string")), resourceRecord = structure(list(name = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), renewalStatus = structure(logical(0), tags = list(type = "string")), renewalStatusReason = structure(logical(0), tags = list(type = "string")), updatedAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), revokedAt = structure(logical(0), tags = list(type = "timestamp")), revocationReason = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), supportCode = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_cloud_formation_stack_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instances = structure(list(structure(list(sourceName = structure(logical(0), tags = list(type = "string")), instanceType = structure(logical(0), tags = list(type = "string")), portInfoSource = structure(logical(0), tags = list(type = "string")), userData = structure(logical(0), tags = list(type = "string")), availabilityZone = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_cloud_formation_stack_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_contact_method_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(protocol = structure(logical(0), tags = list(type = "string")), contactEndpoint = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_contact_method_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), power = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map")), deployment = structure(list(containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerService = structure(list(containerServiceName = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), power = structure(logical(0), tags = list(type = "string")), powerId = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), currentDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), nextDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), isDisabled = structure(logical(0), tags = list(type = "boolean")), principalArn = structure(logical(0), tags = list(type = "string")), privateDomainName = structure(logical(0), tags = list(type = "string")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map")), url = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_deployment_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_deployment_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerService = structure(list(containerServiceName = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), power = structure(logical(0), tags = list(type = "string")), powerId = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), currentDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), nextDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), isDisabled = structure(logical(0), tags = list(type = "boolean")), principalArn = structure(logical(0), tags = list(type = "string")), privateDomainName = structure(logical(0), tags = list(type = "string")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map")), url = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_registry_login_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_container_service_registry_login_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(registryLogin = structure(list(username = structure(logical(0), tags = list(type = "string")), password = structure(logical(0), tags = list(type = "string")), expiresAt = structure(logical(0), tags = list(type = "timestamp")), registry = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string")), availabilityZone = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(addOnType = structure(logical(0), tags = list(type = "string")), autoSnapshotAddOnRequest = structure(list(snapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_from_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string")), diskSnapshotName = structure(logical(0), tags = list(type = "string")), availabilityZone = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(addOnType = structure(logical(0), tags = list(type = "string")), autoSnapshotAddOnRequest = structure(list(snapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), sourceDiskName = structure(logical(0), tags = list(type = "string")), restoreDate = structure(logical(0), tags = list(type = "string")), useLatestRestorableAutoSnapshot = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_from_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string")), diskSnapshotName = structure(logical(0), tags = list(type = "string")), instanceName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_disk_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_distribution_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), origin = structure(list(name = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string")), protocolPolicy = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), defaultCacheBehavior = structure(list(behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), cacheBehaviorSettings = structure(list(defaultTTL = structure(logical(0), tags = list(type = "long")), minimumTTL = structure(logical(0), tags = list(type = "long")), maximumTTL = structure(logical(0), tags = list(type = "long")), allowedHTTPMethods = structure(logical(0), tags = list(type = "string")), cachedHTTPMethods = structure(logical(0), tags = list(type = "string")), forwardedCookies = structure(list(option = structure(logical(0), tags = list(type = "string")), cookiesAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedHeaders = structure(list(option = structure(logical(0), tags = list(type = "string")), headersAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedQueryStrings = structure(list(option = structure(logical(0), tags = list(type = "boolean")), queryStringsAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")), cacheBehaviors = structure(list(structure(list(path = structure(logical(0), tags = list(type = "string")), behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), bundleId = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_distribution_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distribution = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), alternativeDomainNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), status = structure(logical(0), tags = list(type = "string")), isEnabled = structure(logical(0), tags = list(type = "boolean")), domainName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), origin = structure(list(name = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string")), protocolPolicy = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), originPublicDNS = structure(logical(0), tags = list(type = "string")), defaultCacheBehavior = structure(list(behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), cacheBehaviorSettings = structure(list(defaultTTL = structure(logical(0), tags = list(type = "long")), minimumTTL = structure(logical(0), tags = list(type = "long")), maximumTTL = structure(logical(0), tags = list(type = "long")), allowedHTTPMethods = structure(logical(0), tags = list(type = "string")), cachedHTTPMethods = structure(logical(0), tags = list(type = "string")), forwardedCookies = structure(list(option = structure(logical(0), tags = list(type = "string")), cookiesAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedHeaders = structure(list(option = structure(logical(0), tags = list(type = "string")), headersAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedQueryStrings = structure(list(option = structure(logical(0), tags = list(type = "boolean")), queryStringsAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")), cacheBehaviors = structure(list(structure(list(path = structure(logical(0), tags = list(type = "string")), behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), ableToUpdateBundle = structure(logical(0), tags = list(type = "boolean")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_domain_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_domain_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_domain_entry_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string")), domainEntry = structure(list(id = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), target = structure(logical(0), tags = list(type = "string")), isAlias = structure(logical(0), tags = list(type = "boolean")), type = structure(logical(0), tags = list(type = "string")), options = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(deprecated = TRUE, type = "map"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_domain_entry_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instance_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceSnapshotName = structure(logical(0), tags = list(type = "string")), instanceName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instance_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instances_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), availabilityZone = structure(logical(0), tags = list(type = "string")), customImageName = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), blueprintId = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), userData = structure(logical(0), tags = list(type = "string")), keyPairName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(addOnType = structure(logical(0), tags = list(type = "string")), autoSnapshotAddOnRequest = structure(list(snapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instances_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instances_from_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), attachedDiskMapping = structure(list(structure(list(structure(list(originalDiskPath = structure(logical(0), tags = list(type = "string")), newDiskName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "map")), availabilityZone = structure(logical(0), tags = list(type = "string")), instanceSnapshotName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), userData = structure(logical(0), tags = list(type = "string")), keyPairName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(addOnType = structure(logical(0), tags = list(type = "string")), autoSnapshotAddOnRequest = structure(list(snapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), sourceInstanceName = structure(logical(0), tags = list(type = "string")), restoreDate = structure(logical(0), tags = list(type = "string")), useLatestRestorableAutoSnapshot = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_instances_from_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_key_pair_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPairName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_key_pair_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPair = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), fingerprint = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), publicKeyBase64 = structure(logical(0), tags = list(type = "string")), privateKeyBase64 = structure(logical(0), tags = list(type = "string")), operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_load_balancer_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), instancePort = structure(logical(0), tags = list(type = "integer")), healthCheckPath = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), certificateDomainName = structure(logical(0), tags = list(type = "string")), certificateAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_load_balancer_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_load_balancer_tls_certificate_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), certificateDomainName = structure(logical(0), tags = list(type = "string")), certificateAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_load_balancer_tls_certificate_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), availabilityZone = structure(logical(0), tags = list(type = "string")), relationalDatabaseBlueprintId = structure(logical(0), tags = list(type = "string")), relationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), masterDatabaseName = structure(logical(0), tags = list(type = "string")), masterUsername = structure(logical(0), tags = list(type = "string")), masterUserPassword = structure(logical(0), tags = list(type = "string", sensitive = TRUE)), preferredBackupWindow = structure(logical(0), tags = list(type = "string")), preferredMaintenanceWindow = structure(logical(0), tags = list(type = "string")), publiclyAccessible = structure(logical(0), tags = list(type = "boolean")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_from_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), availabilityZone = structure(logical(0), tags = list(type = "string")), publiclyAccessible = structure(logical(0), tags = list(type = "boolean")), relationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string")), relationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), sourceRelationalDatabaseName = structure(logical(0), tags = list(type = "string")), restoreTime = structure(logical(0), tags = list(type = "timestamp")), useLatestRestorableTime = structure(logical(0), tags = list(type = "boolean")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_from_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), relationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$create_relational_database_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_alarm_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(alarmName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_alarm_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_auto_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), date = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_auto_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_certificate_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(certificateName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_certificate_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_contact_method_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(protocol = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_contact_method_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_container_image_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), image = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_container_image_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_container_service_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_container_service_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_disk_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string")), forceDeleteAddOns = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_disk_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_disk_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_disk_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_distribution_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_distribution_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_domain_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_domain_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_domain_entry_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string")), domainEntry = structure(list(id = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), target = structure(logical(0), tags = list(type = "string")), isAlias = structure(logical(0), tags = list(type = "boolean")), type = structure(logical(0), tags = list(type = "string")), options = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(deprecated = TRUE, type = "map"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_domain_entry_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_instance_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string")), forceDeleteAddOns = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_instance_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_instance_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_instance_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_key_pair_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPairName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_key_pair_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_known_host_keys_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_known_host_keys_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_load_balancer_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_load_balancer_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_load_balancer_tls_certificate_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), force = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_load_balancer_tls_certificate_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), skipFinalSnapshot = structure(logical(0), tags = list(type = "boolean")), finalRelationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_relational_database_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$delete_relational_database_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_certificate_from_distribution_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_certificate_from_distribution_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_disk_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_disk_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_instances_from_load_balancer_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), instanceNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_instances_from_load_balancer_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_static_ip_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIpName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$detach_static_ip_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$disable_add_on_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(addOnType = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$disable_add_on_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$download_default_key_pair_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$download_default_key_pair_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(publicKeyBase64 = structure(logical(0), tags = list(type = "string")), privateKeyBase64 = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$enable_add_on_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), addOnRequest = structure(list(addOnType = structure(logical(0), tags = list(type = "string")), autoSnapshotAddOnRequest = structure(list(snapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$enable_add_on_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$export_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(sourceSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$export_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_active_names_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_active_names_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(activeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_alarms_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(alarmName = structure(logical(0), tags = list(type = "string")), pageToken = structure(logical(0), tags = list(type = "string")), monitoredResourceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_alarms_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(alarms = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), monitoredResourceInfo = structure(list(arn = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), comparisonOperator = structure(logical(0), tags = list(type = "string")), evaluationPeriods = structure(logical(0), tags = list(type = "integer")), period = structure(logical(0), tags = list(type = "integer")), threshold = structure(logical(0), tags = list(type = "double")), datapointsToAlarm = structure(logical(0), tags = list(type = "integer")), treatMissingData = structure(logical(0), tags = list(type = "string")), statistic = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), unit = structure(logical(0), tags = list(type = "string")), contactProtocols = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), notificationTriggers = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), notificationEnabled = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_auto_snapshots_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_auto_snapshots_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), autoSnapshots = structure(list(structure(list(date = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), status = structure(logical(0), tags = list(type = "string")), fromAttachedDisks = structure(list(structure(list(path = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_blueprints_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(includeInactive = structure(logical(0), tags = list(type = "boolean")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_blueprints_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(blueprints = structure(list(structure(list(blueprintId = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), group = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), isActive = structure(logical(0), tags = list(type = "boolean")), minPower = structure(logical(0), tags = list(type = "integer")), version = structure(logical(0), tags = list(type = "string")), versionCode = structure(logical(0), tags = list(type = "string")), productUrl = structure(logical(0), tags = list(type = "string")), licenseUrl = structure(logical(0), tags = list(type = "string")), platform = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_bundles_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(includeInactive = structure(logical(0), tags = list(type = "boolean")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_bundles_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(bundles = structure(list(structure(list(price = structure(logical(0), tags = list(type = "float")), cpuCount = structure(logical(0), tags = list(type = "integer")), diskSizeInGb = structure(logical(0), tags = list(type = "integer")), bundleId = structure(logical(0), tags = list(type = "string")), instanceType = structure(logical(0), tags = list(type = "string")), isActive = structure(logical(0), tags = list(type = "boolean")), name = structure(logical(0), tags = list(type = "string")), power = structure(logical(0), tags = list(type = "integer")), ramSizeInGb = structure(logical(0), tags = list(type = "float")), transferPerMonthInGb = structure(logical(0), tags = list(type = "integer")), supportedPlatforms = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_certificates_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(certificateStatuses = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), includeCertificateDetails = structure(logical(0), tags = list(type = "boolean")), certificateName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_certificates_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(certificates = structure(list(structure(list(certificateArn = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), certificateDetail = structure(list(arn = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), serialNumber = structure(logical(0), tags = list(type = "string")), subjectAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), domainValidationRecords = structure(list(structure(list(domainName = structure(logical(0), tags = list(type = "string")), resourceRecord = structure(list(name = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), requestFailureReason = structure(logical(0), tags = list(type = "string")), inUseResourceCount = structure(logical(0), tags = list(type = "integer")), keyAlgorithm = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), issuedAt = structure(logical(0), tags = list(type = "timestamp")), issuerCA = structure(logical(0), tags = list(type = "string")), notBefore = structure(logical(0), tags = list(type = "timestamp")), notAfter = structure(logical(0), tags = list(type = "timestamp")), eligibleToRenew = structure(logical(0), tags = list(type = "string")), renewalSummary = structure(list(domainValidationRecords = structure(list(structure(list(domainName = structure(logical(0), tags = list(type = "string")), resourceRecord = structure(list(name = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), renewalStatus = structure(logical(0), tags = list(type = "string")), renewalStatusReason = structure(logical(0), tags = list(type = "string")), updatedAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), revokedAt = structure(logical(0), tags = list(type = "timestamp")), revocationReason = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), supportCode = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_cloud_formation_stack_records_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_cloud_formation_stack_records_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(cloudFormationStackRecords = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), sourceInfo = structure(list(structure(list(resourceType = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), destinationInfo = structure(list(id = structure(logical(0), tags = list(type = "string")), service = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_contact_methods_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(protocols = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_contact_methods_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(contactMethods = structure(list(structure(list(contactEndpoint = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), protocol = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_api_metadata_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_api_metadata_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metadata = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_images_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_images_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerImages = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), digest = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_log_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), containerName = structure(logical(0), tags = list(type = "string")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), filterPattern = structure(logical(0), tags = list(type = "string")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_log_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(logEvents = structure(list(structure(list(createdAt = structure(logical(0), tags = list(type = "timestamp")), message = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_deployments_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_deployments_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(deployments = structure(list(structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_metric_data_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), period = structure(logical(0), tags = list(type = "integer")), statistics = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_metric_data_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metricName = structure(logical(0), tags = list(type = "string")), metricData = structure(list(structure(list(average = structure(logical(0), tags = list(type = "double")), maximum = structure(logical(0), tags = list(type = "double")), minimum = structure(logical(0), tags = list(type = "double")), sampleCount = structure(logical(0), tags = list(type = "double")), sum = structure(logical(0), tags = list(type = "double")), timestamp = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_powers_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_service_powers_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(powers = structure(list(structure(list(powerId = structure(logical(0), tags = list(type = "string")), price = structure(logical(0), tags = list(type = "float")), cpuCount = structure(logical(0), tags = list(type = "float")), ramSizeInGb = structure(logical(0), tags = list(type = "float")), name = structure(logical(0), tags = list(type = "string")), isActive = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_services_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_container_services_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerServices = structure(list(structure(list(containerServiceName = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), power = structure(logical(0), tags = list(type = "string")), powerId = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), currentDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), nextDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), isDisabled = structure(logical(0), tags = list(type = "boolean")), principalArn = structure(logical(0), tags = list(type = "string")), privateDomainName = structure(logical(0), tags = list(type = "string")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map")), url = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(disk = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskSnapshot = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), progress = structure(logical(0), tags = list(type = "string")), fromDiskName = structure(logical(0), tags = list(type = "string")), fromDiskArn = structure(logical(0), tags = list(type = "string")), fromInstanceName = structure(logical(0), tags = list(type = "string")), fromInstanceArn = structure(logical(0), tags = list(type = "string")), isFromAutoSnapshot = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_snapshots_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disk_snapshots_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(diskSnapshots = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), progress = structure(logical(0), tags = list(type = "string")), fromDiskName = structure(logical(0), tags = list(type = "string")), fromDiskArn = structure(logical(0), tags = list(type = "string")), fromInstanceName = structure(logical(0), tags = list(type = "string")), fromInstanceArn = structure(logical(0), tags = list(type = "string")), isFromAutoSnapshot = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disks_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_disks_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(disks = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_bundles_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_bundles_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(bundles = structure(list(structure(list(bundleId = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), price = structure(logical(0), tags = list(type = "float")), transferPerMonthInGb = structure(logical(0), tags = list(type = "integer")), isActive = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_latest_cache_reset_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_latest_cache_reset_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(status = structure(logical(0), tags = list(type = "string")), createTime = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_metric_data_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), period = structure(logical(0), tags = list(type = "integer")), unit = structure(logical(0), tags = list(type = "string")), statistics = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distribution_metric_data_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metricName = structure(logical(0), tags = list(type = "string")), metricData = structure(list(structure(list(average = structure(logical(0), tags = list(type = "double")), maximum = structure(logical(0), tags = list(type = "double")), minimum = structure(logical(0), tags = list(type = "double")), sampleCount = structure(logical(0), tags = list(type = "double")), sum = structure(logical(0), tags = list(type = "double")), timestamp = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distributions_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_distributions_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributions = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), alternativeDomainNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), status = structure(logical(0), tags = list(type = "string")), isEnabled = structure(logical(0), tags = list(type = "boolean")), domainName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), certificateName = structure(logical(0), tags = list(type = "string")), origin = structure(list(name = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string")), protocolPolicy = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), originPublicDNS = structure(logical(0), tags = list(type = "string")), defaultCacheBehavior = structure(list(behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), cacheBehaviorSettings = structure(list(defaultTTL = structure(logical(0), tags = list(type = "long")), minimumTTL = structure(logical(0), tags = list(type = "long")), maximumTTL = structure(logical(0), tags = list(type = "long")), allowedHTTPMethods = structure(logical(0), tags = list(type = "string")), cachedHTTPMethods = structure(logical(0), tags = list(type = "string")), forwardedCookies = structure(list(option = structure(logical(0), tags = list(type = "string")), cookiesAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedHeaders = structure(list(option = structure(logical(0), tags = list(type = "string")), headersAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedQueryStrings = structure(list(option = structure(logical(0), tags = list(type = "boolean")), queryStringsAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")), cacheBehaviors = structure(list(structure(list(path = structure(logical(0), tags = list(type = "string")), behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), ableToUpdateBundle = structure(logical(0), tags = list(type = "boolean")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_domain_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_domain_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domain = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), domainEntries = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), target = structure(logical(0), tags = list(type = "string")), isAlias = structure(logical(0), tags = list(type = "boolean")), type = structure(logical(0), tags = list(type = "string")), options = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(deprecated = TRUE, type = "map"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_domains_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_domains_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domains = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), domainEntries = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), target = structure(logical(0), tags = list(type = "string")), isAlias = structure(logical(0), tags = list(type = "boolean")), type = structure(logical(0), tags = list(type = "string")), options = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(deprecated = TRUE, type = "map"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_export_snapshot_records_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_export_snapshot_records_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(exportSnapshotRecords = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), sourceInfo = structure(list(resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), fromResourceName = structure(logical(0), tags = list(type = "string")), fromResourceArn = structure(logical(0), tags = list(type = "string")), instanceSnapshotInfo = structure(list(fromBundleId = structure(logical(0), tags = list(type = "string")), fromBlueprintId = structure(logical(0), tags = list(type = "string")), fromDiskInfo = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), path = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), diskSnapshotInfo = structure(list(sizeInGb = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure"))), tags = list(type = "structure")), destinationInfo = structure(list(id = structure(logical(0), tags = list(type = "string")), service = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instance = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), blueprintId = structure(logical(0), tags = list(type = "string")), blueprintName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), isStaticIp = structure(logical(0), tags = list(type = "boolean")), privateIpAddress = structure(logical(0), tags = list(type = "string")), publicIpAddress = structure(logical(0), tags = list(type = "string")), ipv6Address = structure(logical(0), tags = list(type = "string")), hardware = structure(list(cpuCount = structure(logical(0), tags = list(type = "integer")), disks = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), ramSizeInGb = structure(logical(0), tags = list(type = "float"))), tags = list(type = "structure")), networking = structure(list(monthlyTransfer = structure(list(gbPerMonthAllocated = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure")), ports = structure(list(structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), accessFrom = structure(logical(0), tags = list(type = "string")), accessType = structure(logical(0), tags = list(type = "string")), commonName = structure(logical(0), tags = list(type = "string")), accessDirection = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), state = structure(list(code = structure(logical(0), tags = list(type = "integer")), name = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), username = structure(logical(0), tags = list(type = "string")), sshKeyName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_access_details_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string")), protocol = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_access_details_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(accessDetails = structure(list(certKey = structure(logical(0), tags = list(type = "string")), expiresAt = structure(logical(0), tags = list(type = "timestamp")), ipAddress = structure(logical(0), tags = list(type = "string")), password = structure(logical(0), tags = list(type = "string")), passwordData = structure(list(ciphertext = structure(logical(0), tags = list(type = "string")), keyPairName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), privateKey = structure(logical(0), tags = list(type = "string")), protocol = structure(logical(0), tags = list(type = "string")), instanceName = structure(logical(0), tags = list(type = "string")), username = structure(logical(0), tags = list(type = "string")), hostKeys = structure(list(structure(list(algorithm = structure(logical(0), tags = list(type = "string")), publicKey = structure(logical(0), tags = list(type = "string")), witnessedAt = structure(logical(0), tags = list(type = "timestamp")), fingerprintSHA1 = structure(logical(0), tags = list(type = "string")), fingerprintSHA256 = structure(logical(0), tags = list(type = "string")), notValidBefore = structure(logical(0), tags = list(type = "timestamp")), notValidAfter = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_metric_data_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), period = structure(logical(0), tags = list(type = "integer")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string")), statistics = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_metric_data_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metricName = structure(logical(0), tags = list(type = "string")), metricData = structure(list(structure(list(average = structure(logical(0), tags = list(type = "double")), maximum = structure(logical(0), tags = list(type = "double")), minimum = structure(logical(0), tags = list(type = "double")), sampleCount = structure(logical(0), tags = list(type = "double")), sum = structure(logical(0), tags = list(type = "double")), timestamp = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_port_states_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_port_states_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(portStates = structure(list(structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceSnapshot = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), state = structure(logical(0), tags = list(type = "string")), progress = structure(logical(0), tags = list(type = "string")), fromAttachedDisks = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), fromInstanceName = structure(logical(0), tags = list(type = "string")), fromInstanceArn = structure(logical(0), tags = list(type = "string")), fromBlueprintId = structure(logical(0), tags = list(type = "string")), fromBundleId = structure(logical(0), tags = list(type = "string")), isFromAutoSnapshot = structure(logical(0), tags = list(type = "boolean")), sizeInGb = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_snapshots_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_snapshots_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceSnapshots = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), state = structure(logical(0), tags = list(type = "string")), progress = structure(logical(0), tags = list(type = "string")), fromAttachedDisks = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), fromInstanceName = structure(logical(0), tags = list(type = "string")), fromInstanceArn = structure(logical(0), tags = list(type = "string")), fromBlueprintId = structure(logical(0), tags = list(type = "string")), fromBundleId = structure(logical(0), tags = list(type = "string")), isFromAutoSnapshot = structure(logical(0), tags = list(type = "boolean")), sizeInGb = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_state_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instance_state_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(state = structure(list(code = structure(logical(0), tags = list(type = "integer")), name = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instances_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_instances_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instances = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), blueprintId = structure(logical(0), tags = list(type = "string")), blueprintName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), isStaticIp = structure(logical(0), tags = list(type = "boolean")), privateIpAddress = structure(logical(0), tags = list(type = "string")), publicIpAddress = structure(logical(0), tags = list(type = "string")), ipv6Address = structure(logical(0), tags = list(type = "string")), hardware = structure(list(cpuCount = structure(logical(0), tags = list(type = "integer")), disks = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), addOns = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), snapshotTimeOfDay = structure(logical(0), tags = list(type = "string")), nextSnapshotTimeOfDay = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), sizeInGb = structure(logical(0), tags = list(type = "integer")), isSystemDisk = structure(logical(0), tags = list(type = "boolean")), iops = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), attachmentState = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), gbInUse = structure(logical(0), tags = list(deprecated = TRUE, type = "integer"))), tags = list(type = "structure"))), tags = list(type = "list")), ramSizeInGb = structure(logical(0), tags = list(type = "float"))), tags = list(type = "structure")), networking = structure(list(monthlyTransfer = structure(list(gbPerMonthAllocated = structure(logical(0), tags = list(type = "integer"))), tags = list(type = "structure")), ports = structure(list(structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), accessFrom = structure(logical(0), tags = list(type = "string")), accessType = structure(logical(0), tags = list(type = "string")), commonName = structure(logical(0), tags = list(type = "string")), accessDirection = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), state = structure(list(code = structure(logical(0), tags = list(type = "integer")), name = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), username = structure(logical(0), tags = list(type = "string")), sshKeyName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_key_pair_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPairName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_key_pair_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPair = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), fingerprint = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_key_pairs_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_key_pairs_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPairs = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), fingerprint = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancer = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), dnsName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), protocol = structure(logical(0), tags = list(type = "string")), publicPorts = structure(list(structure(logical(0), tags = list(type = "integer"))), tags = list(type = "list")), healthCheckPath = structure(logical(0), tags = list(type = "string")), instancePort = structure(logical(0), tags = list(type = "integer")), instanceHealthSummary = structure(list(structure(list(instanceName = structure(logical(0), tags = list(type = "string")), instanceHealth = structure(logical(0), tags = list(type = "string")), instanceHealthReason = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), tlsCertificateSummaries = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), configurationOptions = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_metric_data_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), period = structure(logical(0), tags = list(type = "integer")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string")), statistics = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_metric_data_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metricName = structure(logical(0), tags = list(type = "string")), metricData = structure(list(structure(list(average = structure(logical(0), tags = list(type = "double")), maximum = structure(logical(0), tags = list(type = "double")), minimum = structure(logical(0), tags = list(type = "double")), sampleCount = structure(logical(0), tags = list(type = "double")), sum = structure(logical(0), tags = list(type = "double")), timestamp = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_tls_certificates_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancer_tls_certificates_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(tlsCertificates = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), loadBalancerName = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean")), status = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string")), domainValidationRecords = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), type = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string")), validationStatus = structure(logical(0), tags = list(type = "string")), domainName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), failureReason = structure(logical(0), tags = list(type = "string")), issuedAt = structure(logical(0), tags = list(type = "timestamp")), issuer = structure(logical(0), tags = list(type = "string")), keyAlgorithm = structure(logical(0), tags = list(type = "string")), notAfter = structure(logical(0), tags = list(type = "timestamp")), notBefore = structure(logical(0), tags = list(type = "timestamp")), renewalSummary = structure(list(renewalStatus = structure(logical(0), tags = list(type = "string")), domainValidationOptions = structure(list(structure(list(domainName = structure(logical(0), tags = list(type = "string")), validationStatus = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")), revocationReason = structure(logical(0), tags = list(type = "string")), revokedAt = structure(logical(0), tags = list(type = "timestamp")), serial = structure(logical(0), tags = list(type = "string")), signatureAlgorithm = structure(logical(0), tags = list(type = "string")), subject = structure(logical(0), tags = list(type = "string")), subjectAlternativeNames = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancers_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_load_balancers_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancers = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), dnsName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), protocol = structure(logical(0), tags = list(type = "string")), publicPorts = structure(list(structure(logical(0), tags = list(type = "integer"))), tags = list(type = "list")), healthCheckPath = structure(logical(0), tags = list(type = "string")), instancePort = structure(logical(0), tags = list(type = "integer")), instanceHealthSummary = structure(list(structure(list(instanceName = structure(logical(0), tags = list(type = "string")), instanceHealth = structure(logical(0), tags = list(type = "string")), instanceHealthReason = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), tlsCertificateSummaries = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), configurationOptions = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operation_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operationId = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operation_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operations_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operations_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operations_for_resource_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_operations_for_resource_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageCount = structure(logical(0), tags = list(deprecated = TRUE, type = "string")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_regions_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(includeAvailabilityZones = structure(logical(0), tags = list(type = "boolean")), includeRelationalDatabaseAvailabilityZones = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_regions_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(regions = structure(list(structure(list(continentCode = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), displayName = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), availabilityZones = structure(list(structure(list(zoneName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), relationalDatabaseAvailabilityZones = structure(list(structure(list(zoneName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabase = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), relationalDatabaseBlueprintId = structure(logical(0), tags = list(type = "string")), relationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), masterDatabaseName = structure(logical(0), tags = list(type = "string")), hardware = structure(list(cpuCount = structure(logical(0), tags = list(type = "integer")), diskSizeInGb = structure(logical(0), tags = list(type = "integer")), ramSizeInGb = structure(logical(0), tags = list(type = "float"))), tags = list(type = "structure")), state = structure(logical(0), tags = list(type = "string")), secondaryAvailabilityZone = structure(logical(0), tags = list(type = "string")), backupRetentionEnabled = structure(logical(0), tags = list(type = "boolean")), pendingModifiedValues = structure(list(masterUserPassword = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), backupRetentionEnabled = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")), engine = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), latestRestorableTime = structure(logical(0), tags = list(type = "timestamp")), masterUsername = structure(logical(0), tags = list(type = "string")), parameterApplyStatus = structure(logical(0), tags = list(type = "string")), preferredBackupWindow = structure(logical(0), tags = list(type = "string")), preferredMaintenanceWindow = structure(logical(0), tags = list(type = "string")), publiclyAccessible = structure(logical(0), tags = list(type = "boolean")), masterEndpoint = structure(list(port = structure(logical(0), tags = list(type = "integer")), address = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), pendingMaintenanceActions = structure(list(structure(list(action = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), currentApplyDate = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "list")), caCertificateIdentifier = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_blueprints_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_blueprints_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(blueprints = structure(list(structure(list(blueprintId = structure(logical(0), tags = list(type = "string")), engine = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), engineDescription = structure(logical(0), tags = list(type = "string")), engineVersionDescription = structure(logical(0), tags = list(type = "string")), isEngineDefault = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_bundles_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_bundles_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(bundles = structure(list(structure(list(bundleId = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), price = structure(logical(0), tags = list(type = "float")), ramSizeInGb = structure(logical(0), tags = list(type = "float")), diskSizeInGb = structure(logical(0), tags = list(type = "integer")), transferPerMonthInGb = structure(logical(0), tags = list(type = "integer")), cpuCount = structure(logical(0), tags = list(type = "integer")), isEncrypted = structure(logical(0), tags = list(type = "boolean")), isActive = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_events_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), durationInMinutes = structure(logical(0), tags = list(type = "integer")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_events_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseEvents = structure(list(structure(list(resource = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), message = structure(logical(0), tags = list(type = "string")), eventCategories = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_log_events_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), logStreamName = structure(logical(0), tags = list(type = "string")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), startFromHead = structure(logical(0), tags = list(type = "boolean")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_log_events_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceLogEvents = structure(list(structure(list(createdAt = structure(logical(0), tags = list(type = "timestamp")), message = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextBackwardToken = structure(logical(0), tags = list(type = "string")), nextForwardToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_log_streams_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_log_streams_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(logStreams = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_master_user_password_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), passwordVersion = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_master_user_password_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(masterUserPassword = structure(logical(0), tags = list(type = "string", sensitive = TRUE)), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_metric_data_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), period = structure(logical(0), tags = list(type = "integer")), startTime = structure(logical(0), tags = list(type = "timestamp")), endTime = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string")), statistics = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_metric_data_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(metricName = structure(logical(0), tags = list(type = "string")), metricData = structure(list(structure(list(average = structure(logical(0), tags = list(type = "double")), maximum = structure(logical(0), tags = list(type = "double")), minimum = structure(logical(0), tags = list(type = "double")), sampleCount = structure(logical(0), tags = list(type = "double")), sum = structure(logical(0), tags = list(type = "double")), timestamp = structure(logical(0), tags = list(type = "timestamp")), unit = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_parameters_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_parameters_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(parameters = structure(list(structure(list(allowedValues = structure(logical(0), tags = list(type = "string")), applyMethod = structure(logical(0), tags = list(type = "string")), applyType = structure(logical(0), tags = list(type = "string")), dataType = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), isModifiable = structure(logical(0), tags = list(type = "boolean")), parameterName = structure(logical(0), tags = list(type = "string")), parameterValue = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_snapshot_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_snapshot_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseSnapshot = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), engine = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseName = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseArn = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseBlueprintId = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_snapshots_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_database_snapshots_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseSnapshots = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), engine = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), sizeInGb = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseName = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseArn = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), fromRelationalDatabaseBlueprintId = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_databases_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_relational_databases_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabases = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), relationalDatabaseBlueprintId = structure(logical(0), tags = list(type = "string")), relationalDatabaseBundleId = structure(logical(0), tags = list(type = "string")), masterDatabaseName = structure(logical(0), tags = list(type = "string")), hardware = structure(list(cpuCount = structure(logical(0), tags = list(type = "integer")), diskSizeInGb = structure(logical(0), tags = list(type = "integer")), ramSizeInGb = structure(logical(0), tags = list(type = "float"))), tags = list(type = "structure")), state = structure(logical(0), tags = list(type = "string")), secondaryAvailabilityZone = structure(logical(0), tags = list(type = "string")), backupRetentionEnabled = structure(logical(0), tags = list(type = "boolean")), pendingModifiedValues = structure(list(masterUserPassword = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), backupRetentionEnabled = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")), engine = structure(logical(0), tags = list(type = "string")), engineVersion = structure(logical(0), tags = list(type = "string")), latestRestorableTime = structure(logical(0), tags = list(type = "timestamp")), masterUsername = structure(logical(0), tags = list(type = "string")), parameterApplyStatus = structure(logical(0), tags = list(type = "string")), preferredBackupWindow = structure(logical(0), tags = list(type = "string")), preferredMaintenanceWindow = structure(logical(0), tags = list(type = "string")), publiclyAccessible = structure(logical(0), tags = list(type = "boolean")), masterEndpoint = structure(list(port = structure(logical(0), tags = list(type = "integer")), address = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), pendingMaintenanceActions = structure(list(structure(list(action = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), currentApplyDate = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "list")), caCertificateIdentifier = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_static_ip_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIpName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_static_ip_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIp = structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), ipAddress = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_static_ips_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(pageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$get_static_ips_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIps = structure(list(structure(list(name = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), supportCode = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), ipAddress = structure(logical(0), tags = list(type = "string")), attachedTo = structure(logical(0), tags = list(type = "string")), isAttached = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure"))), tags = list(type = "list")), nextPageToken = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$import_key_pair_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(keyPairName = structure(logical(0), tags = list(type = "string")), publicKeyBase64 = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$import_key_pair_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$is_vpc_peered_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$is_vpc_peered_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(isPeered = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$open_instance_public_ports_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(portInfo = structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$open_instance_public_ports_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$peer_vpc_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$peer_vpc_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$put_alarm_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(alarmName = structure(logical(0), tags = list(type = "string")), metricName = structure(logical(0), tags = list(type = "string")), monitoredResourceName = structure(logical(0), tags = list(type = "string")), comparisonOperator = structure(logical(0), tags = list(type = "string")), threshold = structure(logical(0), tags = list(type = "double")), evaluationPeriods = structure(logical(0), tags = list(type = "integer")), datapointsToAlarm = structure(logical(0), tags = list(type = "integer")), treatMissingData = structure(logical(0), tags = list(type = "string")), contactProtocols = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), notificationTriggers = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), notificationEnabled = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$put_alarm_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$put_instance_public_ports_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(portInfos = structure(list(structure(list(fromPort = structure(logical(0), tags = list(type = "integer")), toPort = structure(logical(0), tags = list(type = "integer")), protocol = structure(logical(0), tags = list(type = "string")), cidrs = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), cidrListAliases = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "list")), instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$put_instance_public_ports_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reboot_instance_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reboot_instance_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reboot_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reboot_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$register_container_image_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), label = structure(logical(0), tags = list(type = "string")), digest = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$register_container_image_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerImage = structure(list(image = structure(logical(0), tags = list(type = "string")), digest = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$release_static_ip_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(staticIpName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$release_static_ip_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reset_distribution_cache_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$reset_distribution_cache_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(status = structure(logical(0), tags = list(type = "string")), createTime = structure(logical(0), tags = list(type = "timestamp")), operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$send_contact_method_verification_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(protocol = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$send_contact_method_verification_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$start_instance_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$start_instance_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$start_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$start_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$stop_instance_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(instanceName = structure(logical(0), tags = list(type = "string")), force = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$stop_instance_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$stop_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), relationalDatabaseSnapshotName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$stop_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$tag_resource_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), resourceArn = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$tag_resource_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$test_alarm_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(alarmName = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$test_alarm_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$unpeer_vpc_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$unpeer_vpc_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$untag_resource_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(resourceName = structure(logical(0), tags = list(type = "string")), resourceArn = structure(logical(0), tags = list(type = "string")), tagKeys = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$untag_resource_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_container_service_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(serviceName = structure(logical(0), tags = list(type = "string")), power = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), isDisabled = structure(logical(0), tags = list(type = "boolean")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_container_service_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(containerService = structure(list(containerServiceName = structure(logical(0), tags = list(type = "string")), arn = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), resourceType = structure(logical(0), tags = list(type = "string")), tags = structure(list(structure(list(key = structure(logical(0), tags = list(type = "string")), value = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), power = structure(logical(0), tags = list(type = "string")), powerId = structure(logical(0), tags = list(type = "string")), state = structure(logical(0), tags = list(type = "string")), scale = structure(logical(0), tags = list(type = "integer")), currentDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), nextDeployment = structure(list(version = structure(logical(0), tags = list(type = "integer")), state = structure(logical(0), tags = list(type = "string")), containers = structure(list(structure(list(image = structure(logical(0), tags = list(type = "string")), command = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list")), environment = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map")), ports = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "map"))), tags = list(type = "structure"))), tags = list(type = "map")), publicEndpoint = structure(list(containerName = structure(logical(0), tags = list(type = "string")), containerPort = structure(logical(0), tags = list(type = "integer")), healthCheck = structure(list(healthyThreshold = structure(logical(0), tags = list(type = "integer")), unhealthyThreshold = structure(logical(0), tags = list(type = "integer")), timeoutSeconds = structure(logical(0), tags = list(type = "integer")), intervalSeconds = structure(logical(0), tags = list(type = "integer")), path = structure(logical(0), tags = list(type = "string")), successCodes = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")), createdAt = structure(logical(0), tags = list(type = "timestamp"))), tags = list(type = "structure")), isDisabled = structure(logical(0), tags = list(type = "boolean")), principalArn = structure(logical(0), tags = list(type = "string")), privateDomainName = structure(logical(0), tags = list(type = "string")), publicDomainNames = structure(list(structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "map")), url = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_distribution_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), origin = structure(list(name = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string")), protocolPolicy = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), defaultCacheBehavior = structure(list(behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), cacheBehaviorSettings = structure(list(defaultTTL = structure(logical(0), tags = list(type = "long")), minimumTTL = structure(logical(0), tags = list(type = "long")), maximumTTL = structure(logical(0), tags = list(type = "long")), allowedHTTPMethods = structure(logical(0), tags = list(type = "string")), cachedHTTPMethods = structure(logical(0), tags = list(type = "string")), forwardedCookies = structure(list(option = structure(logical(0), tags = list(type = "string")), cookiesAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedHeaders = structure(list(option = structure(logical(0), tags = list(type = "string")), headersAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure")), forwardedQueryStrings = structure(list(option = structure(logical(0), tags = list(type = "boolean")), queryStringsAllowList = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(type = "list"))), tags = list(type = "structure"))), tags = list(type = "structure")), cacheBehaviors = structure(list(structure(list(path = structure(logical(0), tags = list(type = "string")), behavior = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list")), isEnabled = structure(logical(0), tags = list(type = "boolean"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_distribution_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_distribution_bundle_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(distributionName = structure(logical(0), tags = list(type = "string")), bundleId = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_distribution_bundle_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operation = structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_domain_entry_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(domainName = structure(logical(0), tags = list(type = "string")), domainEntry = structure(list(id = structure(logical(0), tags = list(type = "string")), name = structure(logical(0), tags = list(type = "string")), target = structure(logical(0), tags = list(type = "string")), isAlias = structure(logical(0), tags = list(type = "boolean")), type = structure(logical(0), tags = list(type = "string")), options = structure(list(structure(logical(0), tags = list(type = "string"))), tags = list(deprecated = TRUE, type = "map"))), tags = list(type = "structure"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_domain_entry_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_load_balancer_attribute_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(loadBalancerName = structure(logical(0), tags = list(type = "string")), attributeName = structure(logical(0), tags = list(type = "string")), attributeValue = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_load_balancer_attribute_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_relational_database_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), masterUserPassword = structure(logical(0), tags = list(type = "string", sensitive = TRUE)), rotateMasterUserPassword = structure(logical(0), tags = list(type = "boolean")), preferredBackupWindow = structure(logical(0), tags = list(type = "string")), preferredMaintenanceWindow = structure(logical(0), tags = list(type = "string")), enableBackupRetention = structure(logical(0), tags = list(type = "boolean")), disableBackupRetention = structure(logical(0), tags = list(type = "boolean")), publiclyAccessible = structure(logical(0), tags = list(type = "boolean")), applyImmediately = structure(logical(0), tags = list(type = "boolean")), caCertificateIdentifier = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_relational_database_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_relational_database_parameters_input <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(relationalDatabaseName = structure(logical(0), tags = list(type = "string")), parameters = structure(list(structure(list(allowedValues = structure(logical(0), tags = list(type = "string")), applyMethod = structure(logical(0), tags = list(type = "string")), applyType = structure(logical(0), tags = list(type = "string")), dataType = structure(logical(0), tags = list(type = "string")), description = structure(logical(0), tags = list(type = "string")), isModifiable = structure(logical(0), tags = list(type = "boolean")), parameterName = structure(logical(0), tags = list(type = "string")), parameterValue = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) } .lightsail$update_relational_database_parameters_output <- function(...) { args <- c(as.list(environment()), list(...)) shape <- structure(list(operations = structure(list(structure(list(id = structure(logical(0), tags = list(type = "string")), resourceName = structure(logical(0), tags = list(type = "string")), resourceType = structure(logical(0), tags = list(type = "string")), createdAt = structure(logical(0), tags = list(type = "timestamp")), location = structure(list(availabilityZone = structure(logical(0), tags = list(type = "string")), regionName = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure")), isTerminal = structure(logical(0), tags = list(type = "boolean")), operationDetails = structure(logical(0), tags = list(type = "string")), operationType = structure(logical(0), tags = list(type = "string")), status = structure(logical(0), tags = list(type = "string")), statusChangedAt = structure(logical(0), tags = list(type = "timestamp")), errorCode = structure(logical(0), tags = list(type = "string")), errorDetails = structure(logical(0), tags = list(type = "string"))), tags = list(type = "structure"))), tags = list(type = "list"))), tags = list(type = "structure")) return(populate(args, shape)) }
define_strategy <- function(..., transition = define_transition(), starting_values = define_starting_values()) { states <- define_state_list_(list(...)) define_strategy_( transition = transition, states = states, starting_values = starting_values ) } define_strategy_ <- function(transition, states, starting_values) { starting_values <- check_starting_values( x = starting_values, ref = get_state_value_names(states) ) if (! get_state_number(states) == get_state_number(transition)) { stop(sprintf( "Number of state in model input (%i) differ from number of state in transition object (%i).", get_state_number(states), length(get_state_names(transition)) )) } if (! identical( as.vector(sort(get_state_names(states))), as.vector(sort(get_state_names(transition))) )) { stop("State names differ from transition object.") } structure( list( transition = transition, states = states, starting_values = starting_values ), class = "uneval_model") } get_transition <- function(x){ UseMethod("get_transition") } get_transition.default <- function(x){ x$transition } set_transition <- function(x, m) { UseMethod("set_transition") } set_transition.default <- function(x, m) { x$transition <- m x } get_states <- function(x){ UseMethod("get_states") } get_states.default <- function(x) { x$states } set_states <- function(x, s) { UseMethod("set_states") } set_states.default <- function(x, s) { x$states <- s x } get_state_value_names.uneval_model <- function(x) { get_state_value_names(get_states(x)) } get_state_names.uneval_model <- function(x, ...) { get_state_names(get_states(x)) }
lavutils_mplus_readdifftest <- function(file="deriv.dat") { raw <- scan(file, quiet=TRUE) T1 <- raw[1] ngroups <- as.integer(raw[2]) ndat <- as.integer(raw[3]) npar <- as.integer(raw[4]) pstar <- npar*(npar+1)/2 offset <- 4L delta_raw <- raw[offset + seq_len(npar*ndat)] Delta <- matrix(delta_raw, nrow=ndat, ncol=npar, byrow=TRUE) offset <- 4L + npar*ndat p1_raw <- raw[offset + seq_len(pstar)] P1 <- lav_matrix_lower2full(p1_raw) offset <- 4L + npar*ndat + pstar nacov_raw <- raw[offset + seq_len(pstar)] V1 <- lav_matrix_lower2full(nacov_raw) list(T1=T1, ngroups=ngroups, ndat=ndat, npar=npar, pstar=pstar, Delta=Delta, P1=P1, V1=V1) }
add_raster_tile_layer <- function( deckgl, id = "raster-tiles", tileServer = "https://c.tile.openstreetmap.org/", properties = list(), ... ) { properties <- utils::modifyList(raster_tile_properties(tileServer), properties) add_layer(deckgl, "TileLayer", id, data = NULL, properties = properties, ...) } raster_tile_properties <- function(tile_server) { list( opacity = 1, minZoom = 0, maxZoom = 19, tileServer = tile_server, renderSubLayers = JS("deckglWidget.renderMapTiles") ) }
read_eq <- function(...) { xx <- enexprs(...) ll <- length(xx) res <- vector("list", ll) for (i in seq_along(xx)) { children <- as.list(xx[[i]]) for (c in seq_along(children)) { if (rlang::is_call(children[[c]])) { children[[c]] <- vapply(as.list(children[[c]])[-1], function(x) { expr_text(x) }, character(1)) } else if (is.symbol(children[[c]])) { children[[c]] <- expr_text(children[[c]]) } } res[[i]] <- children } res } format_trans <- function(x) { forw <- c("`%>%`", "`>`") back <- c("`%<%`", "`<`") direc_df <- data.frame( direction = c(forw, back), names = c(rep("forward", 2), rep("backword", 2)), stringsAsFactors = F ) direct <- direc_df$names[match(x[[1]], direc_df$direction)] key_old <- x[[2]] key_new <- x[[3]] list( direction = direct, old = key_old, new = key_new ) }
iClick.VisAssetPrice <- function(dat,color4="r2b",color5="jet") { Sys.setlocale(category = "LC_ALL", locale = "English_United States.1252") yr0=unique(lubridate::year(index(dat))) if (length(yr0)>11) {dat=dat[paste0(c(last(yr0)-10),"::",last(yr0))]} else {dat=dat} y=timeSeries::as.timeSeries(zoo::as.zoo(dat)) if (ncol(y)>=2){print("Only univariate time series data is allowed");stop} YMD=time(y) yr=unique(lubridate::year(YMD)) charvec <- timeDate::timeCalendar(m = 12, d = 15:31, y = yr[1]-1, FinCenter = "GMT") fake=timeSeries::as.timeSeries(rnorm(length(charvec)),charvec) colnames(fake)=colnames(y) x=rbind(fake,y) names(x)=names(y) YMD=time(x) yr=unique(lubridate::year(YMD)) full.Date=as.Date(seq(from=YMD[1],to=YMD[length(YMD)],by="1 day")) date=as.POSIXlt(paste(full.Date,"02:00:00"),"GMT") full.Data=timeSeries::as.timeSeries(data.frame(date,1)); data.Date=as.POSIXlt(paste(YMD,"02:00:00"),"GMT") real.Data=timeSeries::as.timeSeries(data.frame(data.Date,unclass(x))) newData=cbind(full.Data,real.Data)[,-1] dat=data.frame(date,unclass(newData)) dataRefreshCode <- function(...) { type = as.integer(.oneClickCalendarPlot(obj.name = "plotType")) if (type == 1) { summaryTable=as.matrix(fBasics::basicStats(y)[-c(10:12),]) rownames(summaryTable)=rownames(fBasics::basicStats(y))[-c(10:12)] print(summaryTable) } if (type == 2) { seriesPlotX(y,ylab="Price", col = "indianred2") } if (type == 3) { print(cutAndStack(y, number=6, overlap = 0.1)) } if (type == 4) { dev.new();print(calendarHeat(y,color=color4)) } if (type == 5) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[2]),cols =color5,year=yr[2]) } if (type == 6) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[3]),cols=color5,year=yr[3]) } if (type == 7) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[4]),cols = color5,year=yr[4]) } if (type == 8) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[5]),cols = color5,year=yr[4]) } if (type == 9) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[6]),cols = color5,year=yr[6]) } if (type == 10) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[7]),cols = color5,year=yr[7]) } if (type == 11) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[8]),cols = color5,year=yr[8]) } if (type == 12) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[9]),cols = color5,year=yr[9]) } if (type == 13) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[10]),cols = color5,year=yr[10]) } if (type == 14) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[11]),cols = color5,year=yr[11]) } if (type == 15) {dev.new();openair::calendarPlot(dat,pollutant=names(dat)[2],main=paste(names(dat),"in", yr[12]),cols = color5,year=yr[12]) } } nAssets = dim(x)[2] V0=c("1 Descriptive Statistics Table", "2 Price Series Plot", "3 Breaking Plot", "4 Calender Heatmap, up to 6 years only") no=5:((length(yr)-1)+4) V1=paste(no," Calender Plot, year ", yr[-1],sep="") .oneClickCalendarPlot( dataRefreshCode, names = c("Selected Asset"), minima = c( 0), maxima = c( nAssets), resolutions = c( 1), starts = c( 0), button.functions = list( function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "1") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "2") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "3") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "4") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "5") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "6") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "7") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "8") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "9") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "10") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "11") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "12") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "13") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "14") dataRefreshCode()}, function(...){ .oneClickCalendarPlot(obj.name = "plotType", obj.value = "15") dataRefreshCode()} ), button.names =c(V0,V1), title = "1-Click Visualization: Asset Price" ) .oneClickCalendarPlot(obj.name = "type", obj.value = "1", no = 1) invisible() } .oneClickCalendarPlot.env = new.env() .oneClickCalendarPlot <- function(names, minima, maxima, resolutions, starts,button.functions, button.names, no, set.no.value, obj.name, obj.value,reset.function, title) { if(!exists(".oneClickCalendarPlot.env")) { .oneClickCalendarPlot.env <<- new.env() } if(!missing(obj.name)){ if(!missing(obj.value)) { assign(obj.name, obj.value, envir = .oneClickCalendarPlot.env) } else { obj.value <- get(obj.name, envir = .oneClickCalendarPlot.env) } return(obj.value) } if(missing(title)) { title = "Control Widget" } myPane <- tktoplevel() tkwm.title(myPane, title) tkwm.geometry(myPane, "+0+0") framed.button <- ttkframe(myPane,padding=c(3,3,12,12)) tkpack(framed.button, fill = "x") if (missing(button.names)) { button.names <- NULL } for (i in seq(button.names)) { button.fun <-button.functions[[i]] plotButtons<-tkbutton(framed.button, text = button.names[i], command = button.fun, anchor = "nw",relief="ridge",width = "45") tkconfigure(plotButtons,foreground="blue",font=tkfont.create(size=10,weight="bold")) tkpack(plotButtons,fill = "x", pady=1) } quitCMD = function() { tkdestroy(myPane) } quitButton<-tkbutton(framed.button, text = "Quit", command = quitCMD, anchor = "center",relief="ridge",width = "8") tkbind(myPane,"Q", function() tcl(quitButton,"invoke")) tkfocus(quitButton) tkconfigure(quitButton,foreground="indianred2", font=tkfont.create(weight="bold",size=10)) tkconfigure(quitButton,underline=0) tkpack(quitButton, side = "right",fill = "x",ipady=3) assign(".oneClickCalendarPlot.values.old", starts, envir = .oneClickCalendarPlot.env) invisible(myPane) }
context("cro new tests") a = set_val_lab(1:5, c(a = 1, b = 2, d = 3)) var_lab(a) = "My a" expect_identical(cro(mrset(a)), cro(a))
strstrip <- function(string, side = c("both", "left", "right")) { string <- .verifyChar(string) side <- match.arg(side) pattern <- switch(side, left = "^\\s+", right = "\\s+$", both = "^\\s+|\\s+$") OUT <- gsub(pattern, "", string) return(OUT) }
HJBiplotPage <- function(X, parent, notebook, envir) { Dim1 <- Dim2 <- Variable <- Label <- xend <- yend <- NULL Plot <- function(graph) { if(!is.null(graph$reload)) { plot(env$save$plot) return(NULL) } t <- match.fun(graph$theme) if(graph$cluster > 1) { X$data[is.na(X$data)] <- 0 kcluster <- kmeans(X$data, graph$cluster) kcluster <- kcluster$cluster kcluster <- c(rep(0, ncol(X$data)), kcluster) plotdf <- cbind(plotdf, kcluster) plotdf$kcluster <- factor(plotdf$kcluster) } if(graph$dim %in% c("dim1", "dim2")) { w <- plotdf[which(plotdf$Variable == "Rows"),] w <- w[order(w[[(if(graph$dim == "dim1") "Con1" else "Con2")]], decreasing = TRUE),] w <- rbind(plotdf[which(plotdf$Variable == "Columns"),], w[1:graph$limit,]) }else { w <- plotdf[1:(graph$limit+ncol(X$data)),] } line_alpha <- 0.50 vector_alpha <- 0.75 if(graph$alpha == 1) { vector_alpha <- 1 line_alpha <- 1 } plot <- ggplot(plotdf) + geom_vline(xintercept = 0, lty = "dashed", alpha = line_alpha) + geom_hline(yintercept = 0, lty = "dashed", alpha = line_alpha) + geom_segment(data = plotdf[which(w$Variable == "Columns"),], aes(x = 0, y = 0, xend = Dim1, yend = Dim2), arrow = arrow(length = unit(0.2, "cm")), alpha = vector_alpha, color = graph$vcolor, size = graph$vsize) + scale_shape_manual(values = c(4, 17)) plot <- plot + geom_point(data = w, aes(x = Dim1, y = Dim2, col = (if(graph$cluster < 2) Variable else kcluster), shape = Variable, label = Label), size = graph$psize) g_text <- if(graph$repel == TRUE && requireNamespace("ggrepel", quietly = TRUE)) ggrepel::geom_text_repel else geom_text if(graph$vtext == TRUE) plot <- plot + g_text(data = w[which(w$Variable == "Columns"),], aes(x = Dim1, y = Dim2, col = (if(graph$cluster < 2) Variable else kcluster), shape = Variable, label = Label), vjust = -0.5) if(graph$ptext == TRUE) plot <- plot + g_text(data = w[which(w$Variable == "Rows"),], aes(x = Dim1, y = Dim2, col = (if(graph$cluster < 2) Variable else kcluster), shape = Variable, label = Label), vjust = -0.5) if(graph$distance != "") { r <- biplot$ColCoordinates[graph$distance,] slope <- r[2] / r[1] distance <- Distance(biplot$RowCoordinates[1:graph$limit,], slope = slope) console(cmds = "slope", envir = environment()) console(cmds = "distance", envir = environment()) plot <- plot + geom_abline(intercept = 0, slope = slope, linetype = "dashed", color = graph$vcolor, alpha = vector_alpha) + geom_segment(data = distance, aes(x = Dim1, y = Dim2, xend = xend, yend = yend), inherit.aes = FALSE, linetype = "dotted") + coord_fixed() } plot <- plot + labs(x = paste0("Dim 1 (", round(biplot$inertia[1]), "%)"), y = paste0("Dim 2 (", round(biplot$inertia[2]), "%)"), title = graph$title) color <- c(graph$vcolor, graph$pcolor) if(graph$cluster > 1) color <- c(graph$vcolor, brewer.pal(n = graph$cluster, name = graph$palette)) plot <- plot + scale_color_manual(values = color) plot <- plot + t() + theme(legend.position = "none") env$save$plot <- plot assign(name, env$save, envir = toprint) plot(plot) } biplot <- tryCatch({ HJBiplot(X$data) }, error = function(cond) { tkmessageBox(title = "Error", message = "Error:", icon = "error", detail = "Some error occurred verify your data.", type = "ok") }) plotdf <- as.data.frame(biplot) plotdf$Variable <- factor(plotdf$Variable) console(cmds = "head(X$data)", envir = environment()) console(cmds = "head(biplot)", envir = environment()) console(cmds = "head(plotdf)", envir = environment()) name <- as.character(runif(1)) env = environment() env$save <- list() env$save$name <- "HJ-Biplot" env$save$table <- plotdf class(env$save) <- "save" assign(name, env$save, envir = toprint) PageGUI("HJ-Biplot", Plot, id = as.character(match.call()[[1]]), envir = envir, theme = "theme_white", limit = 100, vector_color = " title = "HJ-Biplot", vector_text = " ", point_text = " ", vector_size = 1, point_size = 2, repel = " ", dim = "all", parent = parent, notebook = notebook, to = nrow(X$data), distances = c(colnames(X$data), ""), cluster = 1, palette = "Dark2") }
excess_stats <- function(start, end, obs, mu, cov, pop, frequency, fhat = NULL, X = NULL, betacov = NULL){ mu <- matrix(mu, nrow = 1) observed <- sum(obs) expected <- sum(mu) excess <- observed - expected sd <- sqrt(mu %*% cov %*% t(mu)) res <- data.frame( start = start, end = end, obs_death_rate = observed / sum(pop) * frequency * 1000, exp_death_rate = expected / sum(pop) * frequency * 1000, sd_death_rate = sd / sum(pop) * frequency * 1000, observed = observed, expected = expected, excess = excess, sd = sd) if(!is.null(fhat)){ res$fitted <- mu %*% fhat res$se <- sqrt(mu %*% X %*% betacov %*% t(X) %*% t(mu)) } return(res) }
Standard_Normalization = function(x) { x = as.matrix(x); mean = apply(x, 2, mean) sd = apply(x, 2, sd) sd[sd==0] = 1 xNorm = t((t(x) - mean) / sd) return(xNorm) }
layout_multilevel <- function(x, layout = igraph::layout_with_fr){ if (!inherits(x, 'igraph')){ stop("Not a graph object") } else { if (is_multilevel(x)){ l = igraph::norm_coords(layout(x)) lay_multi = matrix(nrow = nrow(l), ncol = ncol(l)) lay_multi[ ,1] = l[ ,1] for (i in 1:nrow(lay_multi)){ if (igraph::V(x)$type[i] == TRUE){ if (l[i,2] >= 0){ lay_multi[i,2] = l[i,2] * 1 } else { lay_multi[i,2] = l[i,2] * -1 } } else { if (l[i,2] < 0){ lay_multi[i,2] = l[i,2] * 1 } else { lay_multi[i,2] = l[i,2] * -1 } } } return(openPlot(lay_multi)) } else { stop("The network is not multilevel") } } }
context("Test: getKingdoms()") test_that("The getKingdoms() interface works properly..",{ skip_on_cran() skip_on_travis() expect_equal( getKingdoms(), c( "archaea", "bacteria", "fungi", "invertebrate", "plant", "protozoa", "vertebrate_mammalian", "vertebrate_other", "viral" ) ) })
multslapmeg<-function(pathlist, fixed, random, grouping, subject, method = "BH", data){ if(missing(fixed)) stop('The argument fixed must be specified for all models!') if(missing(random)) stop('The argument random must be specified for all models!') if(class(pathlist)!="list") stop("Pathlist argument should be a list!") if(length(pathlist)<2) stop("Only one pathway is defined!") if(fixed[[1]]!="~") stop("The Fixed formula is not correctly specified! Check the vignette for help.") if(length(fixed)>2) stop("The Fixed formula is not correctly specified! Check the vignette for help.") if(! method %in% c("holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none")) stop("P-value correction method is not correctly specified! Check ?p.adjust.") fixed_forms<-sapply(pathlist, function(x) paste0(paste0(x,collapse="+"),"~",Reduce(paste, deparse(fixed[[2]])))) fixed_forms<-lapply(fixed_forms, function(f) as.formula(f)) slapmeg<-sapply(fixed_forms, function(forms) { mod<-slapmeg(forms, random, grouping, subject, data) return(list(mod$Globaltest[1], mod$slapmethod)) }) psize<-sapply(pathlist, function(x) length(x)) adj.ps<-round(p.adjust(slapmeg[[1]], method), 4) if(is.null(names(pathlist))) { path.nom<-paste0("Path", 1:length(adj.ps))} else path.nom<-names(pathlist) res<-data.frame(path.nom, adj.ps, psize, slapmeg[[2]],row.names = NULL) colnames(res)<-c("Path.Name",paste0("adj.P","(",paste(method),")"),"Path.size","method") class(res) <-c("mslapmeg") return(res) }
hist.mcSimulation <- function(x, breaks=100, col=NULL, xlab=NULL, main=paste("Histogram of " , xlab), ..., colorQuantile =c("GREY", "YELLOW", "ORANGE", "DARK GREEN", "ORANGE", "YELLOW", "GREY"), colorProbability=c(1.00, 0.95, 0.75, 0.55, 0.45, 0.25, 0.05), resultName=NULL){ if( is.list(x$y) ){ if( !is.null(resultName) ){ result<-x$y[[resultName]] if( is.null(xlab) ) xlab<-resultName } else { if(length(names(x$y))==1){ result<-unlist(x$y) if( is.null(xlab) ) xlab<-names(x$y)[[1]] } else stop("No component of the model function chosen!") } if( main==paste("Histogram of " , xlab)) main<-paste("Histogram of " , xlab, " Monte Carlo Simulation") } else { result<-x$y } if(!isTRUE(is.null(colorQuantile))){ resultNames<-NULL if( length(colorQuantile) != length(colorProbability) ) stop("length(colorQuantile) != length(colorProbability)") histPrepare<-hist(result, breaks=breaks, plot=FALSE) probability<-cumsum(histPrepare$density * diff(histPrepare$breaks)) color<-c() for( i in seq(along=probability) ){ for( j in seq(along=colorQuantile) ) if(probability[i] < colorProbability[j]) color[i]<-colorQuantile[j] } } else color=col hist(result, breaks=breaks, col=color, xlab=xlab, main=main,...) }
RGWAS.twostep <- function(pheno, geno, ZETA = NULL, package.MM = "gaston", covariate = NULL, covariate.factor = NULL, structure.matrix = NULL, n.PC = 0, min.MAF = 0.02, n.core = 1, parallel.method = "mclapply", check.size = 40, check.gene.size = 4, kernel.percent = 0.1, GWAS.res.first = NULL, P3D = TRUE, test.method.1 = "normal", test.method.2 = "LR", kernel.method = "linear", kernel.h = "tuned", haplotype = TRUE, num.hap = NULL, test.effect.1 = "additive", test.effect.2 = "additive", window.size.half = 5, window.slide = 1, chi0.mixture = 0.5, optimizer = "nlminb", gene.set = NULL, weighting.center = TRUE, weighting.other = NULL, sig.level = 0.05, method.thres = "BH", plot.qq.1 = TRUE, plot.Manhattan.1 = TRUE, plot.qq.2 = TRUE, plot.Manhattan.2 = TRUE, plot.method = 1, plot.col1 = c("dark blue", "cornflowerblue"), plot.col2 = 1, plot.col3 = c("red3", "orange3"), plot.type = "p", plot.pch = 16, saveName = NULL, main.qq.1 = NULL, main.man.1 = NULL, main.qq.2 = NULL, main.man.2 = NULL, plot.add.last = FALSE, return.EMM.res = FALSE, thres = TRUE, skip.check = FALSE, verbose = TRUE, verbose2 = FALSE, count = TRUE, time = TRUE) { start <- Sys.time() if (is.null(GWAS.res.first)) { if (verbose) { print("The 1st step: Performing 1st GWAS (for screening)!") } if (length(test.effect.1) >= 2) { stop("Sorry, you can assign only one test effect for the 1st GWAS!!") } if (test.method.1 == "normal") { GWAS.res.first <- RGWAS.normal(pheno = pheno, geno = geno, ZETA = ZETA, package.MM = package.MM, covariate = covariate, covariate.factor = covariate.factor, structure.matrix = structure.matrix, n.PC = n.PC, min.MAF = min.MAF, P3D = P3D, n.core = n.core, parallel.method = parallel.method, sig.level = sig.level, method.thres = method.thres, plot.qq = plot.qq.1, plot.Manhattan = plot.Manhattan.1, plot.method = plot.method, plot.col1 = plot.col1, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch, saveName = saveName, optimizer = optimizer, main.qq = main.qq.1, main.man = main.man.1, plot.add.last = FALSE, return.EMM.res = FALSE, thres = FALSE, skip.check = skip.check, verbose = verbose, verbose2 = verbose2, count = count, time = time) } else { GWAS.res.first <- RGWAS.multisnp(pheno = pheno, geno = geno, ZETA = ZETA, package.MM = package.MM, covariate = covariate, covariate.factor = covariate.factor, structure.matrix = structure.matrix, n.PC = n.PC, min.MAF = min.MAF, test.method = test.method.1, n.core = n.core, parallel.method = parallel.method, kernel.method = kernel.method, kernel.h = kernel.h, haplotype = haplotype, num.hap = num.hap, test.effect = test.effect.1, window.size.half = window.size.half, window.slide = window.slide, chi0.mixture = chi0.mixture, gene.set = gene.set, weighting.center = weighting.center, weighting.other = weighting.other, sig.level = sig.level, method.thres = method.thres, plot.qq = FALSE, plot.Manhattan = FALSE, plot.method = plot.method, plot.col1 = plot.col1, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch, saveName = saveName, main.qq = main.qq.2, main.man = main.man.2, plot.add.last = FALSE, return.EMM.res = FALSE, optimizer = optimizer, thres = FALSE, skip.check = skip.check, verbose = verbose, verbose2 = verbose2, count = count, time = time) } } else { if (verbose) { print("The 1st step has already finished because you input 'GWAS.res.first'.") } } n.pheno <- ncol(GWAS.res.first) - 3 trait.names <- colnames(GWAS.res.first)[4:(4 + n.pheno - 1)] map <- geno[, 1:3] if ((kernel.method == "linear") & (length(test.effect.2) >= 2)) { thresholds <- matrix(NA, nrow = length(test.effect.2), ncol = n.pheno) thresholds.correction <- matrix(NA, nrow = length(test.effect.2), ncol = n.pheno) rownames(thresholds) <- rep("normal", length(test.effect.2)) rownames(thresholds.correction) <- test.effect.2 colnames(thresholds) <- colnames(thresholds.correction) <- trait.names } else { thresholds <- thresholds.correction <- matrix(NA, nrow = 1, ncol = n.pheno) rownames(thresholds) <- "normal" rownames(thresholds.correction) <- kernel.method colnames(thresholds) <- colnames(thresholds.correction) <- trait.names } if ((kernel.method == "linear") & (length(test.effect.2) >= 2)) { res.all <- rep(list(GWAS.res.first), length(test.effect.2)) } else { res.all <- GWAS.res.first } for (pheno.no in 1:n.pheno) { trait.name <- trait.names[pheno.no] pheno.now <- pheno[, c(1, pheno.no + 1)] GWAS.res.first.now <- GWAS.res.first[, c(1:3, pheno.no + 3)] pval.first <- GWAS.res.first[, pheno.no + 3] ord.pval.first <- order(pval.first, decreasing = TRUE) ord.pval.ker.percent.0 <- ord.pval.first[1:round(length(pval.first) * (kernel.percent / 100), 0)] ord.pval.ker.percent <- as.numeric(rownames(GWAS.res.first)[ord.pval.ker.percent.0]) if (is.null(gene.set)) { check.obj <- "SNPs" check.size.half <- check.size / 2 checks.mat <- matrix(NA, nrow = length(ord.pval.ker.percent) * (check.size + 1), ncol = length(ord.pval.ker.percent)) for (check.no in 1:length(ord.pval.ker.percent)) { check <- sort(ord.pval.ker.percent)[check.no] checks.now <- (check - check.size.half):(check + check.size.half) checks.mat[, check.no] <- checks.now } checks <- unique(c(checks.mat)) checks <- checks[(checks >= 1) & (checks <= max(as.numeric(rownames(GWAS.res.first))))] n.checks <- length(checks) pseudo.chr <- rep(NA, n.checks) pseudo.chr[1] <- 1 for (k in 2:n.checks) { pseudo.chr.now <- pseudo.chr[k - 1] check.diff <- checks[k] - checks[k - 1] if (check.diff == 1) { pseudo.chr[k] <- pseudo.chr.now } else { pseudo.chr[k] <- pseudo.chr.now + 1 } } pseudo.marker <- as.character(map[checks, 1]) pseudo.pos <- map[checks, 3] pseudo.map <- data.frame(marker = pseudo.marker, chr = pseudo.chr, pos = pseudo.pos) rownames(pseudo.map) <- checks M.check <- geno[checks, -c(1:3)] geno.check <- cbind(pseudo.map, M.check) gene.set.now <- NULL } else { check.obj <- "genes" if (test.method.1 != "normal") { check.size.half <- check.gene.size / 2 checks.mat <- matrix(NA, nrow = length(ord.pval.ker.percent) * (check.gene.size + 1), ncol = length(ord.pval.ker.percent)) for (check.no in 1:length(ord.pval.ker.percent)) { check <- sort(ord.pval.ker.percent)[check.no] checks.now <- (check - check.size.half):(check + check.size.half) checks.mat[, check.no] <- checks.now } checks <- unique(c(checks.mat)) checks <- checks[(checks >= 1) & (checks <= max(as.numeric(rownames(GWAS.res.first))))] n.checks <- length(checks) gene.names <- as.character(unique(gene.set[, 1])) gene.names.now <- gene.names[checks] } else { check.size.half <- check.size / 2 checks.mat <- matrix(NA, nrow = length(ord.pval.ker.percent) * (check.size + 1), ncol = length(ord.pval.ker.percent)) for (check.no in 1:length(ord.pval.ker.percent)) { check <- sort(ord.pval.ker.percent)[check.no] checks.now <- (check - check.size.half):(check + check.size.half) checks.mat[, check.no] <- checks.now } checks <- unique(c(checks.mat)) checks <- checks[(checks >= 1) & (checks <= max(as.numeric(rownames(GWAS.res.first))))] match.gene.list <- match(as.character(gene.set[, 2]), as.character(map[checks, 1])) gene.names.now <- unique(as.character(gene.set[!is.na(match.gene.list), 1])) n.checks <- length(gene.names.now) } gene.set.now <- gene.set[as.character(gene.set[, 1]) %in% gene.names.now, ] geno.check <- geno } if (verbose) { print(paste("The 2nd step: Recalculating -log10(p) of", trait.name, "for", n.checks, check.obj, "by kernel-based (mutisnp) GWAS.")) } RGWAS.multisnp.res.0 <- RGWAS.multisnp(pheno = pheno.now, geno = geno.check, ZETA = ZETA, package.MM = package.MM, covariate = covariate, covariate.factor = covariate.factor, structure.matrix = structure.matrix, n.PC = n.PC, min.MAF = min.MAF, test.method = test.method.2, n.core = n.core, parallel.method = parallel.method, kernel.method = kernel.method, kernel.h = kernel.h, haplotype = haplotype, num.hap = num.hap, test.effect = test.effect.2, window.size.half = window.size.half, window.slide = window.slide, chi0.mixture = chi0.mixture, gene.set = gene.set.now, weighting.center = weighting.center, weighting.other = weighting.other, sig.level = sig.level, method.thres = method.thres, plot.qq = FALSE, plot.Manhattan = FALSE, plot.method = plot.method, plot.col1 = plot.col1, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch, saveName = saveName, main.qq = main.qq.2, main.man = main.man.2, plot.add.last = FALSE, return.EMM.res = TRUE, optimizer = optimizer, thres = FALSE, skip.check = TRUE, verbose = verbose, count = count, time = time) RGWAS.multisnp.res <- RGWAS.multisnp.res.0$D EMM.res0 <- RGWAS.multisnp.res.0$EMM.res if ((kernel.method == "linear") & (length(test.effect.2) >= 2)) { GWAS.res.merge.list <- lapply(RGWAS.multisnp.res, function(x) { colnames(x) <- colnames(GWAS.res.first.now) if (is.null(gene.set)) { x[, 1:3] <- map[match(rownames(x), rownames(map)), ] } GWAS.res.merge.0 <- rbind(x, GWAS.res.first.now) GWAS.res.merge <- GWAS.res.merge.0[!duplicated(as.character(GWAS.res.merge.0[, 1])), ] ord.GWAS.res.merge <- order(GWAS.res.merge[, 2], GWAS.res.merge[, 3]) res.correction <- GWAS.res.merge[ord.GWAS.res.merge, ] check.here <- match(1:nrow(x), ord.GWAS.res.merge) return(list(res = res.correction, check = check.here)) }) res.corrections <- rep(list(NA), length(test.effect.2)) for (test.effect.no in 1:length(test.effect.2)) { res.correction <- (GWAS.res.merge.list[[test.effect.no]])[[1]] res.corrections[[test.effect.no]] <- res.correction check.here <- (GWAS.res.merge.list[[test.effect.no]])[[2]] pval.correction <- res.correction[, 4] if (plot.qq.2) { if (verbose) { print("Now Plotting (Q-Q plot). Please Wait.") } if (is.null(saveName)) { if (length(grep("RStudio", names(dev.cur()))) == 0) { if (dev.cur() == dev.next()) { dev.new() } else { dev.set(dev.next()) } } qq(pval.correction) if (is.null(main.qq.2)) { title(main = trait.name) } else { title(main = main.qq.2) } } else { png(paste0(saveName, trait.name, "_qq_kernel.png")) qq(pval.correction) if (is.null(main.qq.2)) { title(main = trait.name) } else { title(main = main.qq.2) } dev.off() } } if (plot.Manhattan.2) { if (verbose) { print("Now Plotting (Manhattan plot). Please Wait.") } if (is.null(saveName)) { if (length(grep("RStudio", names(dev.cur()))) == 0) { if (dev.cur() == dev.next()) { dev.new() } else { dev.set(dev.next()) } } if (plot.method == 1) { manhattan(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col1 = plot.col1, plot.type = plot.type, plot.pch = plot.pch) if (!is.null(plot.col3)) { manhattan.plus(input = res.correction, checks = check.here, plot.col1 = plot.col1, plot.col3 = plot.col3, plot.type = plot.type, plot.pch = plot.pch) } } else { manhattan2(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch) } if (is.null(main.man.2)) { title(main = trait.name) } else { title(main = main.man.2) } } else { png(paste0(saveName, trait.name, "_manhattan_kernel.png"), width = 800) if (plot.method == 1) { manhattan(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col1 = plot.col1, plot.type = plot.type, plot.pch = plot.pch) if (!is.null(plot.col3)) { manhattan.plus(input = res.correction, checks = check.here, plot.col1 = plot.col1, plot.col3 = plot.col3, plot.type = plot.type, plot.pch = plot.pch) } } else { manhattan2(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch) } if (is.null(main.man.2)) { title(main = trait.name) } else { title(main = main.man.2) } if (!(plot.add.last & (pheno.no == n.pheno))) { dev.off() } } } threshold <- try(CalcThreshold(GWAS.res.first.now, sig.level = sig.level, method = method.thres), silent = TRUE) threshold.correction <- try(CalcThreshold(res.correction, sig.level = sig.level, method = method.thres), silent = TRUE) if ("try-error" %in% class(threshold)) { threshold <- NA } if ("try-error" %in% class(threshold.correction)) { threshold.correction <- NA } thresholds[test.effect.no, pheno.no] <- threshold thresholds.correction[test.effect.no, pheno.no] <- threshold.correction } for (test.effect.no in 1:length(test.effect.2)) { colnames(res.corrections[[test.effect.no]])[1:3] <- colnames(res.all[[test.effect.no]])[1:3] <- c("marker", "chrom", "pos") res.all[[test.effect.no]] <- merge(res.all[[test.effect.no]], res.corrections[[test.effect.no]], by.x = c("marker", "chrom", "pos"), by.y = c("marker", "chrom", "pos"), all.x = T, all.y = T) colnames(res.all[[test.effect.no]])[ncol(res.all[[test.effect.no]])] <- paste0(trait.name, "_correction") res.all[[test.effect.no]] <- (res.all[[test.effect.no]])[order(res.all[[test.effect.no]][, 2], res.all[[test.effect.no]][, 3]), ] } } else { colnames(RGWAS.multisnp.res) <- colnames(GWAS.res.first.now) if (is.null(gene.set)) { RGWAS.multisnp.res[, 1:3] <- map[match(rownames(RGWAS.multisnp.res), rownames(map)), ] } GWAS.res.merge.0 <- rbind(RGWAS.multisnp.res, GWAS.res.first.now) GWAS.res.merge <- GWAS.res.merge.0[!duplicated(as.character(GWAS.res.merge.0[, 1])), ] ord.GWAS.res.merge <- order(GWAS.res.merge[, 2], GWAS.res.merge[, 3]) res.correction <- GWAS.res.merge[ord.GWAS.res.merge, ] check.here <- match(1:nrow(RGWAS.multisnp.res), ord.GWAS.res.merge) pval.correction <- res.correction[, 4] if (plot.qq.2) { if (verbose) { print("Now Plotting (Q-Q plot). Please Wait.") } if (is.null(saveName)) { if (length(grep("RStudio", names(dev.cur()))) == 0) { if (dev.cur() == dev.next()) { dev.new() } else { dev.set(dev.next()) } } qq(pval.correction) if (is.null(main.qq.2)) { title(main = trait.name) } else { title(main = main.qq.2) } } else { png(paste0(saveName, trait.name, "_qq_kernel.png")) qq(pval.correction) if (is.null(main.qq.2)) { title(main = trait.name) } else { title(main = main.qq.2) } dev.off() } } if (plot.Manhattan.2) { if (verbose) { print("Now Plotting (Manhattan plot). Please Wait.") } if (is.null(saveName)) { if (length(grep("RStudio", names(dev.cur()))) == 0) { if (dev.cur() == dev.next()) { dev.new() } else { dev.set(dev.next()) } } if (plot.method == 1) { manhattan(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col1 = plot.col1, plot.type = plot.type, plot.pch = plot.pch) if (!is.null(plot.col3)) { manhattan.plus(input = res.correction, checks = check.here, plot.col1 = plot.col1, plot.col3 = plot.col3, plot.type = plot.type, plot.pch = plot.pch) } } else { manhattan2(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch) } if (is.null(main.man.2)) { title(main = trait.name) } else { title(main = main.man.2) } } else { png(paste0(saveName, trait.name, "_manhattan_kernel.png"), width = 800) if (plot.method == 1) { manhattan(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col1 = plot.col1, plot.type = plot.type, plot.pch = plot.pch) if (!is.null(plot.col3)) { manhattan.plus(input = res.correction, checks = check.here, plot.col1 = plot.col1, plot.col3 = plot.col3, plot.type = plot.type, plot.pch = plot.pch) } } else { manhattan2(input = res.correction, sig.level = sig.level, method.thres = method.thres, plot.col2 = plot.col2, plot.type = plot.type, plot.pch = plot.pch) } if (is.null(main.man.2)) { title(main = trait.name) } else { title(main = main.man.2) } if (!(plot.add.last & (pheno.no == n.pheno))) { dev.off() } } } threshold <- try(CalcThreshold(GWAS.res.first[, c(1:3, pheno.no + 3)], sig.level = sig.level, method = method.thres), silent = TRUE) threshold.correction <- try(CalcThreshold(res.correction, sig.level = sig.level, method= method.thres), silent = TRUE) if ("try-error" %in% class(threshold)) { threshold <- NA } if ("try-error" %in% class(threshold.correction)) { threshold.correction <- NA } thresholds[, pheno.no] <- threshold thresholds.correction[, pheno.no] <- threshold.correction colnames(res.correction)[1:3] <- colnames(res.all)[1:3] <- c("marker", "chrom", "pos") res.all <- merge(res.all, res.correction, by.x = c("marker", "chrom", "pos"), by.y = c("marker", "chrom", "pos"), all.x = T, all.y = T) colnames(res.all)[ncol(res.all)] <- paste0(trait.name, "_correction") res.all <- res.all[order(res.all[, 2], res.all[, 3]), ] } } thresholds.list <- list(first = thresholds, second = thresholds.correction) if (thres) { end <- Sys.time() if (time) { print(end - start) } if (return.EMM.res) { return(list(D = res.all, thres = thresholds.list, EMM.res = EMM.res0)) } else { return(list(D = res.all, thres = thresholds.list)) } } else { end <- Sys.time() if (time) { print(end - start) } if (return.EMM.res) { return(list(D = res.all, EMM.res = EMM.res0)) } else { return(res.all) } } }
[ { "title": "Annotables: R data package for annotating/converting Gene IDs", "href": "http://www.gettinggeneticsdone.com/2015/11/annotables-convert-gene-ids.html" }, { "title": "implementing reproducible research [short book review]", "href": "https://xianblog.wordpress.com/2014/07/15/implementing-reproducible-research-short-book-review/" }, { "title": "Get ROAuth to work on Windows 7", "href": "https://web.archive.org/web/http://www.gagetheory.com/2012/03/10/get-roauth-to-work-on-windows-7/" }, { "title": "A simple Big Data analysis using the RevoScaleR package in Revolution R", "href": "http://blog.revolutionanalytics.com/2011/05/big-data-analysis-in-revolution-r.html" }, { "title": "It was twenty years ago today…", "href": "http://dirk.eddelbuettel.com/blog/2015/09/08/" }, { "title": "Bringing R to the Enterprise – new white paper available", "href": "https://blogs.oracle.com/R/entry/bringing_r_to_the_enterprise" }, { "title": "Non-parametric Methods", "href": "http://www.r-tutor.com/elementary-statistics/non-parametric-methods" }, { "title": "Indexing Nested Lists", "href": "https://rappster.wordpress.com/2011/11/20/indexing-nested-lists/" }, { "title": "Can You Beat the Market with Modern Portfolio Theory? (Part 1)", "href": "https://web.archive.org/web/http://www.speakingstatistically.com/2011/06/can-you-beat-market-with-modern.html" }, { "title": "Text analysis of Trump’s tweets confirms he writes only the (angrier) Android half", "href": "http://varianceexplained.org/r/trump-tweets/" }, { "title": "Multilevel Models and Political Advertising", "href": "http://badhessian.org/2015/08/multilevel-models-and-political-advertising/" }, { "title": "Sunsets in Google Calendar using R", "href": "https://hilaryparker.com/2014/05/27/sunsets-in-google-calendar-using-r/" }, { "title": "Understanding the *apply() functions and then others in R by asking questions", "href": "http://www.manio.org/blog/understanding-the-apply-functions-and-then-others-in-by-asking-questions/?utm_source=rss&utm_medium=rss&utm_campaign=understanding-the-apply-functions-and-then-others-in-by-asking-questions" }, { "title": "A Story of Life and Death. On CRAN. With Packages.", "href": "http://dirk.eddelbuettel.com/blog/2011/11/27/" }, { "title": "random sudokus", "href": "https://xianblog.wordpress.com/2013/06/04/random-sudokus-2/" }, { "title": "Factor Attribution to improve performance of the 1-Month Reversal Strategy", "href": "https://systematicinvestor.wordpress.com/2012/07/17/factor-attribution-to-improve-performance-of-the-1-month-reversal-strategy/" }, { "title": "Interview with a Data Scientist (Hadley Wickham)", "href": "http://blog.danielemaasit.com/2015/08/02/interview-with-a-data-scientist-hadley-wickham/" }, { "title": "Soap analytics: Text mining “Goede tijden slechte tijden” plot summaries….", "href": "https://longhowlam.wordpress.com/2015/08/08/soap-analytics-text-mining-goede-tijden-slechte-tijden-plot-summaries/" }, { "title": "Hassle-free data from HTML tables with the htmltable package", "href": "http://www.r-datacollection.com/blog/Hassle-free-data-from-HTML-tables-with-the-htmltable-package/" }, { "title": "Numerical Integration/Differentiation in R: FTIR Spectra", "href": "https://casoilresource.lawr.ucdavis.edu/" }, { "title": "Win Your Fantasy Football Draft with These Shiny Apps: 2014 Update", "href": "http://fantasyfootballanalytics.net/2014/07/fantasy-football-draft-optimizer-shiny-app-2014-update.html" }, { "title": "Data Mining In Excel: Lecture Notes and Cases", "href": "https://rdatamining.wordpress.com/2012/07/10/data-mining-in-excel-lecture-notes-and-cases/" }, { "title": "Statistics and Computing and ABC", "href": "https://xianblog.wordpress.com/2011/02/23/statistics-and-computing-and-abc/" }, { "title": "More fun with the Failed States Index (and the State Fragility Index)", "href": "https://web.archive.org/web/http://nortalktoowise.com/2011/07/more-fun-with-the-failed-states-index-and-the-state-fragility-index/" }, { "title": "A simple test to predict coronary artery disease", "href": "http://blog.revolutionanalytics.com/2011/01/a-simple-test-to-predict-coronary-artery-disease.html" }, { "title": "Reader suggestions on alternative ways to create combination dotplot/boxplot", "href": "https://feedproxy.google.com/~r/SASandR/~3/7h0QobT4opo/reader-suggestions-on-alternative-ways.html" }, { "title": "What makes us happy? Let’s look at data to find out.", "href": "http://www.vikparuchuri.com/blog/what-makes-people-happy/" }, { "title": "Reshape 2 Exercises", "href": "http://r-exercises.com/2016/08/26/reshape-2-exercises/" }, { "title": "Two Y-Axes", "href": "https://kieranhealy.org/blog/archives/2016/01/16/two-y-axes/" }, { "title": "Spotting Potential Battles in F1 Races", "href": "https://blog.ouseful.info/2015/06/10/spotting-potential-battles-in-f1-races/" }, { "title": "A detailed guide to memory usage in R", "href": "http://blog.revolutionanalytics.com/2013/11/a-detailed-guide-to-memory-usage-in-r.html" }, { "title": "Getting Historical Weather Data in R and SAP HANA", "href": "http://allthingsr.blogspot.com/2012/04/getting-historical-weather-data-in-r.html" }, { "title": "JJ Allaire, the useR! 2014 interview", "href": "http://datascience.la/jj-allaire-the-user-2014-interview/" }, { "title": "Music Data Hackathon 2012 – Beginner’s view", "href": "http://machine-master.blogspot.com/2012/07/music-data-hackaton-2012-beginners-view.html" }, { "title": "R Tutorial Series: 2011 ANOVA Article Data", "href": "https://feedproxy.google.com/~r/RTutorialSeries/~3/xbytgM5u2mk/r-tutorial-series-2011-anova-article.html" }, { "title": "Getting Started with Git, EGit, Eclipse, and GitHub: Version Control for R Projects", "href": "http://jeromyanglim.blogspot.com/2010/11/getting-started-with-git-egit-eclipse.html" }, { "title": "Download and Parse NAREIT Data", "href": "https://tradeblotter.wordpress.com/2012/03/02/download-and-parse-nareit-data/" }, { "title": "Out now: Agenda of the [R] Kenntnis-Tage 2016", "href": "http://blog.eoda.de/2016/07/08/out-now-agenda-of-the-r-kenntnis-tage-2016/" }, { "title": "Review of Distance Course: Graduate Certificate in Statistics offered at Sheffield [completed: 3 June 2012]", "href": "http://vasishth-statistics.blogspot.com/2011/12/part-1-of-2-review-of-graduate.html" }, { "title": "Coefplot: New Package for Plotting Model Coefficients", "href": "http://blog.revolutionanalytics.com/2012/01/new-package-for-plotting-model-coefficients.html" }, { "title": "A new R trick … for me at least", "href": "http://oddhypothesis.blogspot.com/2013/08/a-new-r-trick-for-me-at-least.html" }, { "title": "Recent developments in the drug war", "href": "https://blog.diegovalle.net/2010/12/recent-developments-in-drug-war.html" }, { "title": "Introduction to PloTA library in the Systematic Investor Toolbox", "href": "https://systematicinvestor.wordpress.com/2011/10/04/introduction-to-plota-library-in-the-systematic-investor-toolbox/" }, { "title": "The average Stripe employee! 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listObsNotVerbose <- function(i, x, uniquevarlist, nObs) { mismatchesHead <- head(x$mismatches[[uniquevarlist[i]]], nObs) mismatchesTail <- tail(x$mismatches[[uniquevarlist[i]]], nObs) mismatchesHead$rowNo <- as.numeric(rownames(mismatchesHead)) mismatchesTail$rowNo <- as.numeric(rownames(mismatchesTail)) obslist <- unique(rbind(mismatchesHead, mismatchesTail)) obslist[,1] <- as.character(obslist[,1]) obslist[,2] <- as.character(obslist[,2]) rownames(obslist) <- NULL obslist <- unique(obslist[c(length(obslist), 1:length(obslist) - 1)]) obslist <- obslist[order(obslist[, 1]) ,] } listObsVerbose <- function(i, x) { mismatches <- x$mismatches[[i]] mismatches$rowNo <- as.numeric(rownames(mismatches)) rownames(mismatches) <-NULL obslist <- unique(mismatches[c(length(mismatches), 1:length(mismatches) - 1)]) obslist <- obslist[order(obslist[, 1]), ] } allVarMatchMessage <- function(x){ newLine <-"\n" cat("All compared variables match", newLine, "Number of rows compared:", rcompObjItemLength(x$rowMatching$inboth), newLine, "Number of columns compared:", rcompObjItemLength(x$colMatching$inboth)) }
ztable.modelSummary=function(x,digits=NULL,...){ count=ncol(x)/4 count modelNames=attr(x,"modelNames") selected=c() align=c("c") for(i in 1:count){ if(i<count) x[[paste0("s",i)]]="" start=(i-1)*4+1 selected=c(selected,start:(start+3)) align=c(align,c("c","c","c","r")) if(i<count) { selected=c(selected,ncol(x)) align=c(align,"c") } } x1 <- x %>% select(selected) class(x1)="data.frame" align=paste0(align,collapse = "") z=ztable::ztable(x1,align=align,...) newnames=c() newModelNames=c() ncgroup=c() for(i in 1:count){ newnames=c(newnames,c("Coef","SE","t","p")) newModelNames=c(newModelNames,modelNames[i]) ncgroup=c(ncgroup,4) if(i<count) { newnames=c(newnames,"") newModelNames=c(newModelNames,"") ncgroup=c(ncgroup,1) } } z <- z %>% addcgroup(cgroup=newModelNames,n.cgroup=ncgroup) %>% addcgroup(cgroup="Consequent",n.cgroup=ncol(x1),top=TRUE) %>% hlines(add=nrow(z$x)-5) colnames(z$x)=newnames for(i in 1:count){ for(j in 1:5){ z=spanCol(z,row=nrow(x1)+1-(j-1),from=2+(i-1)*5,to=5+(i-1)*5) } } z }
`plot.mvloc` <- function(x, est2=NULL, est3 = NULL, X=NULL, ...) { plotMvloc(est1=x, est2=est2, est3 = est3, X=X, ...) }
align_local <- function(a, b, match = 2L, mismatch = -1L, gap = -1L, edit_mark = " assert_that(identical(class(a), class(b))) UseMethod("align_local", a) } align_local.TextReuseTextDocument <- function(a, b, match = 2L, mismatch = -1L, gap = -1L, edit_mark = " progress = interactive()) { align_local(content(a), content(b), match = match, mismatch = mismatch, gap = gap, edit_mark = edit_mark) } align_local.default <- function(a, b, match = 2L, mismatch = -1L, gap = -1L, edit_mark = " assert_that(is.string(a), is.string(b), is_integer_like(match), is_integer_like(mismatch), is_integer_like(gap), is.string(edit_mark)) if (match <= 0 || mismatch > 0 || gap > 0 || !(str_length(edit_mark) == 1)) { stop("The scoring parameters should have the following characteristics:\n", " - `match` should be a positive integer\n", " - `mismatch` should be a negative integer or zero\n", " - `gap` should be a negative integer or zero\n", " - `edit_mark` should be a single character\n") } match <- as.integer(match) mismatch <- as.integer(mismatch) gap <- as.integer(gap) a_orig <- tokenize_words(a, lowercase = FALSE) b_orig <- tokenize_words(b, lowercase = FALSE) a <- str_to_lower(a_orig) b <- str_to_lower(b_orig) n_rows <- length(b) + 1 n_cols <- length(a) + 1 if (n_rows * n_cols < 1e7) progress <- FALSE if (progress) { message("Preparing a matrix with ", prettyNum(n_rows * n_cols, big.mark = ","), " elements.") } m <- matrix(0L, n_rows, n_cols) if (progress) message("Computing the optimal local alignment.") m <- sw_matrix(m, a, b, match, mismatch, gap, progress) alignment_score <- max(m) max_match <- which(m == alignment_score, arr.ind = TRUE, useNames = FALSE) if (nrow(max_match) > 1) { warning("Multiple optimal local alignments found; selecting only one of them.", call. = FALSE) } if (progress) message("Extracting the local alignment.") a_out <- vector(mode = "character", length = max(max_match)) b_out <- vector(mode = "character", length = max(max_match)) a_out[] <- NA_character_ b_out[] <- NA_character_ row_i <- max_match[1, 1] col_i <- max_match[1, 2] out_i <- 1L b_out[out_i] <- b_orig[row_i - 1] a_out[out_i] <- a_orig[col_i - 1] out_i = out_i + 1L while (m[row_i - 1, col_i - 1] != 0) { up <- m[row_i - 1, col_i] left <- m[row_i, col_i - 1] diagn <- m[row_i - 1, col_i - 1] max_cell <- max(up, left, diagn) if (up == max_cell) { row_i <- row_i - 1 bword <- b_orig[row_i - 1] b_out[out_i] <- bword a_out[out_i] <- mark_chars(bword, edit_mark) } else if (left == max_cell) { col_i <- col_i - 1 aword <- a_orig[col_i - 1] b_out[out_i] <- mark_chars(aword, edit_mark) a_out[out_i] <- aword } else if (diagn == max_cell) { row_i <- row_i - 1 col_i <- col_i - 1 bword <- b_orig[row_i - 1] aword <- a_orig[col_i - 1] if (str_to_lower(aword) == str_to_lower(bword)) { b_out[out_i] <- bword a_out[out_i] <- aword } else { b_out[out_i] <- bword a_out[out_i] <- mark_chars(bword, edit_mark) out_i <- out_i + 1 b_out[out_i] <- mark_chars(aword, edit_mark) a_out[out_i] <- aword } } out_i <- out_i + 1 } b_out <- str_c(rev(b_out[!is.na(b_out)]), collapse = " ") a_out <- str_c(rev(a_out[!is.na(a_out)]), collapse = " ") alignment <- list(a_edits = a_out, b_edits = b_out, score = alignment_score) class(alignment) <- c("textreuse_alignment", "list") alignment } print.textreuse_alignment <- function(x, ...) { cat("TextReuse alignment\n") cat("Alignment score:", x$score, "\n") cat("Document A:\n") cat(str_wrap(x$a_edits, width = 72)) cat("\n\nDocument B:\n") cat(str_wrap(x$b_edits, width = 72)) invisible(x) }
bootstrap.svisit <- function(object, B, type=c("nonpar", "param"), seed=NULL, ...) { type <- match.arg(type) CALL <- object$call CALL$data <- as.name("mfi") ini <- coef(object) CALL$inits <- as.name("ini") mf <- model.frame(object) n <- object$nobs if (exists("mfi", envir=parent.frame())) { assign("tmp1", get("mfi", envir=parent.frame())) on.exit(assign("mfi", tmp1, envir=parent.frame()), add=TRUE) } if (exists("ini", envir=parent.frame())) { assign("tmp2", get("ini", envir=parent.frame())) on.exit(assign("ini", tmp2, envir=parent.frame()), add=TRUE) } assign("ini", ini, envir=parent.frame()) if (type == "nonpar") { if (!is.null(seed)) set.seed(seed) b <- lapply(1:B, function(i) sample(1:n, n, replace=TRUE)) bfun <- function(i) { assign("mfi", mf[i,], envir=parent.frame()) mod <- eval(CALL, envir=parent.frame()) if (inherits(object, "svabu_nb")) c(coef(mod), log.sigma=mod$var$est) else coef(mod) } } else { mfi <- mf rid <- attr(attr(mf, "terms"), "response") sim <- simulate(object, B, seed) b <- 1:B bfun <- function(i) { mf[,rid] <- sim[,i] assign("mfi", mf, envir=parent.frame()) mod <- eval(CALL, envir=parent.frame()) if (inherits(object, "svabu_nb")) c(coef(mod), log.sigma=mod$var$est) else coef(mod) } } rval <- pbapply::pblapply(b, bfun) rm(list="ini", envir=parent.frame()) rval <- matrix(unlist(rval), length(rval[[1]]), B) cfs <- if (inherits(object, "svabu_nb")) c(coef(object), log.sigma=object$var$est) else coef(object) rval <- cbind(cfs, rval) attr(rval, "type") <- type attr(rval, "ini") <- ini attr(object, "bootstrap") <- rval object }
locglmfit_private<-function( xfit, r, m, x, h, returnH, link, guessing, lapsing, K, p, ker, maxiter, tol ) { epanechnikov<-function( x, m, s ) { X <- x / s; X[which( abs( X ) > 1 )] <- 1; return( 0.75 * ( 1 - X^2 ) / s ); } triangular<-function( x, m, s ) { X <- x / s; X[which( abs( X ) > 1 )] <- 1; return( ( 1 - abs( X ) ) / s ); } tricube<-function( x, m, s ) { X <- x / s; X[which( abs( X ) > 1 )] <- 1; return( ( ( 1 - abs( X )^3 )^3 )/ s ); } bisquare<-function( x, m, s ){ X <- x / s; X[which( abs( X ) > 1 )] <- 1; return( ( (1 - abs( X )^2 )^2) / s ); } uniform<-function( x, m, s ) { X <- x / s; return( ( abs( X ) <= 1 ) / 2 ); } if( link != "weibull_link_private" && link != "revweibull_link_private" ) { linkuser <- eval( call( link, guessing, lapsing ) ); } else{ linkuser <- eval( call( link, K, guessing, lapsing ) ); } linkl <- linkuser$linkfun; linki <- linkuser$linkinv; linkd <- linkuser$mu.eta nr<-length( r ); nx<-length( xfit ); value <- NULL; pfit <- NULL; etafit <- NULL; if( returnH ) H <- NULL; diffx<-as.vector( t( matrix( rep( xfit, nr ), nx, nr ) ) - matrix( rep( x, nx ), nr, nx ) ); if( length( h ) == 1 ) { kerx <- eval( call( ker, diffx, 0, h ) ); } else { h_mat <- as.vector(t( matrix( rep( h, nr ), nx, nr ) ) ) kerx <- eval( call( ker, diffx, 0, h_mat ) ); } tmpX0 <- matrix( rep( diffx, p + 1 ), nr * nx, p + 1 )^ t( matrix( rep( (0:p) , nr * nx), p + 1, nr * nx ) ) mu0 <- ( r + .5 ) / ( m + 1 ); eta0 <- linkl( mu0 ); Z0 <- rep( eta0, nx ); mu_eta <- linkd( eta0 ); W <- diag( rep( mu_eta / ( sqrt( mu0 * ( 1 - mu0 )/m ) ), nx ) ); KerX <- diag( sqrt( kerx ) ); WK <- W * KerX; KM <- rep( r / m, nx ); X0 <- matrix( 0, nr * nx, ( p + 1 ) * nx ); for( l in 1:nx ) { X0[(1:nr+(l-1)*nr),(1:(p+1)+(l-1)*(p+1))] = tmpX0[((1:nr)+(l-1)*nr),]; } X <- WK %*% X0; Y <- WK %*% Z0; DetXX <- det(t( X ) %*% X) warncount <- c(0,0) if( abs(DetXX) < 1e-14){ warncount[1] <- 1 } beta<- try(qr.solve( t( X ) %*% X) %*% ( t( X ) %*% Y ),TRUE); if (inherits(beta,"try-error")){ beta <- matrix(-50,nx*(p+1),1) eta <- X0 %*% beta; value$H <- matrix(NA,nx,nr) }else{ iternum <- 0; etadiff <- tol + 1; eta <- X0 %*% beta; mu_raw <- rep( mu0, nx ); M <- rep( m, nx ); score <- 1; epsilon <- 1/(50*max(m)); while ( ( iternum < maxiter ) && ( etadiff > tol ) && ( score ) ) { mu_old <- mu_raw; eta_old <- eta; mu <- linki( eta ); mu_raw <- mu; mu[which( mu >= 1 - lapsing -epsilon )] <- 1 - lapsing -epsilon; mu[( mu <= guessing + epsilon )] <- guessing+ epsilon ; mu_eta <- linkd( linkl( mu ) ); z <- eta + ( KM - mu ) / mu_eta; WK <- diag( mu_eta / ( sqrt( mu * ( 1 - mu ) / M ) ) ) * KerX; X <- WK %*% X0; Y <- WK %*% z; beta <- qr.solve( t( X ) %*% X ) %*% ( t( X ) %*% Y ); eta1 <- beta[seq(1, (p+1)*nx, by=(p+1))] eta <- (X0 %*% beta); iternum <- iternum + 1; mudiff <- max( max( abs( mu_old - mu_raw ) ) ); etadiff <- max( max( abs( eta_old - eta ) ) ); score <- !( ( mudiff < tol ) && ( max( abs( eta1 ) ) > 50 ) ); } if( maxiter == iternum ) { warncount[2] <- 1 } if( returnH ) { tmpH <- solve( t( X ) %*% X ) %*% ( t( X ) %*% WK ); tmpH <- tmpH[seq(1, (p+1)*nx, by=(p+1)),]; H <- matrix( 0, nx, nr ); for(i in 1:nx) { H[i,] <- tmpH[i,(1:nr)+(i-1)*nr]; } value$H <- H; } } etafit <- beta[seq(1, (p+1)*nx, by=(p+1))]; pfit <- linki( etafit ); value$pfit <- pfit value$etafit <- etafit value$warncount <- warncount return( value ); }
"tau_t_1" "f_t_1" "g_t_1" "p_t_1" "beta_1" "alpha_1" "sigma_matrix_1" "m_matrix_1"
civis_ml_sparse_logistic <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, penalty = c("l2", "l1"), dual = FALSE, tol = 1e-8, C = 499999950, fit_intercept = TRUE, intercept_scaling = 1, class_weight = NULL, random_state = 42, solver = c("liblinear", "newton-cg", "lbfgs", "sag"), max_iter = 100, multi_class = c("ovr", "multinomial"), fit_params = NULL, cross_validation_parameters = NULL, calibration = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "sparse_logistic" penalty <- match.arg(penalty) solver <- match.arg(solver) multi_class <- match.arg(multi_class) params <- list( penalty = penalty, dual = dual, tol = tol, C = C, fit_intercept = fit_intercept, intercept_scaling = intercept_scaling, random_state = random_state, solver = solver, max_iter = max_iter, multi_class = multi_class ) if (!is.null(class_weight)) { if (is.character(class_weight)) { stopifnot(class_weight == "balanced") } else { stopifnot(is.list(class_weight)) } params$class_weight <- class_weight } l1_solvers <- c("liblinear") if (penalty == "l1" & !(solver %in% l1_solvers)) { stop(paste0("The l1 penalty is not supported for ", solver, ".")) } multinomial_solvers <- c("newton-cg", "sag", "lbfgs") if (multi_class == "multinomial" & !(solver %in% multinomial_solvers)) { stop(paste0(solver, " does not support multinomial loss.")) } dual_solvers <- c("liblinear") if (dual & !(solver %in% dual_solvers)) { stop(paste0(solver, " does not support the dual formulation.")) } civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, calibration = calibration, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_sparse_linear_regressor <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, fit_intercept = TRUE, normalize = FALSE, fit_params = NULL, cross_validation_parameters = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "sparse_linear_regressor" params <- list( fit_intercept = fit_intercept, normalize = normalize ) if (!fit_intercept & normalize) { warning("fit_intercept = FALSE, ignoring normalize.") } civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_sparse_ridge_regressor <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, alpha = 1.0, fit_intercept = TRUE, normalize = FALSE, max_iter = NULL, tol = 0.001, solver = c('auto', 'svd', 'cholesky', 'lsqr', 'sparse_cg', 'sag'), random_state = 42, fit_params = NULL, cross_validation_parameters = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "sparse_ridge_regressor" params <- list( alpha = alpha, fit_intercept = fit_intercept, normalize = normalize, max_iter = max_iter, tol = tol, solver = match.arg(solver), random_state = random_state ) civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_gradient_boosting_classifier <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, loss = c('deviance', 'exponential'), learning_rate = 0.1, n_estimators = 500, subsample = 1.0, criterion = c('friedman_mse', 'mse', 'mae'), min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_depth = 2, min_impurity_split = 1e-7, random_state = 42, max_features = 'sqrt', max_leaf_nodes = NULL, presort = c('auto', TRUE, FALSE), fit_params = NULL, cross_validation_parameters = NULL, calibration = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "gradient_boosting_classifier" params <- list( loss = match.arg(loss), learning_rate = learning_rate, n_estimators = n_estimators, subsample = subsample, criterion = match.arg(criterion), min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_depth = max_depth, min_impurity_split = min_impurity_split, random_state = random_state, max_leaf_nodes = max_leaf_nodes, presort = match.arg(presort) ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, calibration = calibration, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_gradient_boosting_regressor <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, loss = c('ls', 'lad', 'huber', 'quantile'), learning_rate = 0.1, n_estimators = 500, subsample = 1.0, criterion = c('friedman_mse', 'mse', 'mae'), min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_depth = 2, min_impurity_split = 1e-7, random_state = 42, max_features = 'sqrt', alpha = 0.9, max_leaf_nodes = NULL, presort = c('auto', TRUE, FALSE), fit_params = NULL, cross_validation_parameters = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "gradient_boosting_regressor" params <- list( loss = match.arg(loss), learning_rate = learning_rate, n_estimators = n_estimators, subsample = subsample, criterion = match.arg(criterion), min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_depth = max_depth, min_impurity_split = min_impurity_split, random_state = random_state, alpha = alpha, max_leaf_nodes = max_leaf_nodes, presort = match.arg(presort) ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_random_forest_classifier <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, n_estimators = 500, criterion = c('gini', 'entropy'), max_depth = NULL, min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_features = 'sqrt', max_leaf_nodes = NULL, min_impurity_split = 1e-7, bootstrap = TRUE, random_state = 42, class_weight = NULL, fit_params = NULL, cross_validation_parameters = NULL, calibration = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "random_forest_classifier" params <- list( n_estimators = n_estimators, criterion = match.arg(criterion), max_depth = max_depth, min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_leaf_nodes = max_leaf_nodes, min_impurity_split = min_impurity_split, bootstrap = bootstrap, random_state = random_state ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features if (!is.null(class_weight)) { if (is.character(class_weight)) { stopifnot(class_weight == "balanced") } else { stopifnot(is.list(class_weight)) } params$class_weight <- class_weight } civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, calibration = calibration, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_random_forest_regressor <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, n_estimators = 500, criterion = c('mse', 'mae'), max_depth = NULL, min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_features = 'sqrt', max_leaf_nodes = NULL, min_impurity_split = 1e-7, bootstrap = TRUE, random_state = 42, fit_params = NULL, cross_validation_parameters = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "random_forest_regressor" params <- list( n_estimators = n_estimators, criterion = match.arg(criterion), max_depth = max_depth, min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_leaf_nodes = max_leaf_nodes, min_impurity_split = min_impurity_split, bootstrap = bootstrap, random_state = random_state ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_extra_trees_classifier <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, n_estimators = 500, criterion = c('gini', 'entropy'), max_depth = NULL, min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_features = 'sqrt', max_leaf_nodes = NULL, min_impurity_split = 1e-7, bootstrap = FALSE, random_state = 42, class_weight = NULL, fit_params = NULL, cross_validation_parameters = NULL, calibration = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "extra_trees_classifier" params <- list( n_estimators = n_estimators, criterion = match.arg(criterion), max_depth = max_depth, min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_leaf_nodes = max_leaf_nodes, min_impurity_split = min_impurity_split, bootstrap = bootstrap, random_state = random_state ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features if (!is.null(class_weight)) { if (is.character(class_weight)) { stopifnot(class_weight == "balanced") } else { stopifnot(is.list(class_weight)) } params$class_weight <- class_weight } civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, calibration = calibration, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) } civis_ml_extra_trees_regressor <- function(x, dependent_variable, primary_key = NULL, excluded_columns = NULL, n_estimators = 500, criterion = c('mse', 'mae'), max_depth = NULL, min_samples_split = 2, min_samples_leaf = 1, min_weight_fraction_leaf = 0.0, max_features = 'sqrt', max_leaf_nodes = NULL, min_impurity_split = 1e-7, bootstrap = FALSE, random_state = 42, fit_params = NULL, cross_validation_parameters = NULL, oos_scores_table = NULL, oos_scores_db = NULL, oos_scores_if_exists = c("fail", "append", "drop", "truncate"), model_name = NULL, cpu_requested = NULL, memory_requested = NULL, disk_requested = NULL, notifications = NULL, polling_interval = NULL, verbose = FALSE, civisml_version = "prod") { model_type <- "extra_trees_regressor" params <- list( n_estimators = n_estimators, criterion = match.arg(criterion), max_depth = max_depth, min_samples_split = min_samples_split, min_samples_leaf = min_samples_leaf, min_weight_fraction_leaf = min_weight_fraction_leaf, max_leaf_nodes = max_leaf_nodes, min_impurity_split = min_impurity_split, bootstrap = bootstrap, random_state = random_state ) if (is.character(max_features)) { stopifnot(max_features %in% c("sqrt", "auto", "log2")) } params$max_features <- max_features civis_ml(x = x, dependent_variable = dependent_variable, model_type = model_type, primary_key = primary_key, excluded_columns = excluded_columns, parameters = params, fit_params = fit_params, cross_validation_parameters = cross_validation_parameters, oos_scores_table = oos_scores_table, oos_scores_db = oos_scores_db, oos_scores_if_exists = oos_scores_if_exists, model_name = model_name, cpu_requested = cpu_requested, memory_requested = memory_requested, disk_requested = disk_requested, notifications = notifications, polling_interval = polling_interval, verbose = verbose, civisml_version = civisml_version) }
context("solarized") test_that("theme_solarized_works", { expect_is(theme_solarized(), "theme") expect_is(theme_solarized(light = FALSE), "theme") }) test_that("theme_solarized_2_works", { expect_is(theme_solarized_2(), "theme") expect_is(theme_solarized_2(light = FALSE), "theme") }) test_that("scale_colour_solarized works", { expect_is(scale_colour_solarized(), "ScaleDiscrete") }) test_that("scale_color_solarized works", { expect_eqNe(scale_colour_solarized(), scale_color_solarized()) }) test_that("scale_fill_solarized works", { expect_is(scale_fill_solarized(), "ScaleDiscrete") }) test_that("solarized_pal works", { pal <- solarized_pal() expect_is(pal, "function") n <- 5L values <- pal(n) expect_is(values, "character") expect_eqNe(length(values), n) })
simdiffT=function(N,a,mv,sv,ter,vp=1,max.iter=19999,eps=1e-15){ rt=p=matrix(,N,1) for(jj in 1:N){ drift=rnorm(1,mv,sv) p[jj]=exp(a*drift)/(1+exp(a*drift)) M=pi*vp^2/a^2 * (exp(a*drift/(2*vp^2))+exp(-a*drift/(2*vp^2))) * 1/ (drift^2/(2*vp^2)+pi^2*vp^2 / (2*a^2)) lmb = drift^2/(2*vp^2) +pi^2*vp^2/(2*a^2) ou=c() rej=0 while(length(ou)<1){ v=runif(1); u=runif(1); FF=pi^2*vp^4 * 1/(pi^2*vp^4+drift^2*a^2) sh1=1 sh2=0 sh3=0 i=0 while(abs(sh1-sh2)>eps | abs(sh2-sh3)>eps){ sh1=sh2 sh2=sh3 i=i+1 sh3= sh2 + (2*i+1)*(-1)^i*(1-u)^(FF*(2*i+1)^2) } eval=1+(1-u)^-FF * sh3 if(v<=eval) ou=c(ou,1/lmb*abs(log(1-u))) else rej=rej+1 if(rej==max.iter) stop("Rejection algorithm failed. Increase the 'max.iter' argument or try different true parameter values.") } rt[jj]=ou+ter } x=(p>matrix(runif(N)))*1 return(list(rt=rt,x=x)) }
plot.light_profile <- function(x, swap_dim = FALSE, facet_scales = "free_x", rotate_x = x$type != "partial dependence", show_points = TRUE, ...) { value_name <- getOption("flashlight.value_name") label_name <- getOption("flashlight.label_name") q1_name <- getOption("flashlight.q1_name") q3_name <- getOption("flashlight.q3_name") type_name <- getOption("flashlight.type_name") data <- x$data nby <- length(x$by) multi <- is.light_profile_multi(x) ndim <- nby + multi if (ndim > 2L) { stop("Plot method not defined for more than two by variables or multiflashlight with more than one by variable.") } if (length(x$v) >= 2L) { stop("No plot method defined for two or higher dimensional grids.") } if (x$stats == "quartiles") { p <- ggplot(x$data, aes_string(y = value_name, x = x$v, ymin = q1_name, ymax = q3_name)) } else { p <- ggplot(x$data, aes_string(y = value_name, x = x$v)) } if (ndim == 0L) { if (x$stats == "quartiles") { p <- p + geom_crossbar(...) } else { p <- p + geom_line(aes(group = 1), ...) if (show_points) { p <- p + geom_point(...) } } } else if (ndim == 1L) { first_dim <- if (multi) label_name else x$by[1] if (!swap_dim) { if (x$stats == "quartiles") { p <- p + geom_crossbar(aes_string(color = first_dim), position = "dodge", ...) } else { p <- p + geom_line(aes_string(color = first_dim, group = first_dim), ...) if (show_points) { p <- p + geom_point(aes_string(color = first_dim), ...) } } } else { p <- p + facet_wrap(reformulate(first_dim), scales = facet_scales) if (x$stats == "quartiles") { p <- p + geom_crossbar(...) } else { p <- p + geom_line(aes(group = 1), ...) if (show_points) { p <- p + geom_point(...) } } } } else { second_dim <- if (multi) label_name else x$by[2] wrap_var <- if (swap_dim) x$by[1] else second_dim col_var <- if (swap_dim) second_dim else x$by[1] if (x$stats == "quartiles") { p <- p + geom_crossbar(aes_string(color = col_var), position = "dodge", ...) } else { p <- p + geom_line(aes_string(color = col_var, group = col_var), ...) if (show_points) { p <- p + geom_point(aes_string(color = col_var), ...) } } p <- p + facet_wrap(wrap_var, scales = facet_scales) } if (rotate_x) { p <- p + theme(axis.text.x = element_text(angle = 45, hjust = 1, vjust = 1)) } p + ylab(x$type) }
expected <- structure(8.33333333333333, units = "mins", .Names = "a", class = "difftime") test(id=0, code={ argv <- structure(list(x = structure(500, units = "secs", class = "difftime", .Names = "a"), value = "mins"), .Names = c("x", "value")) do.call('units<-', argv); }, o = expected);
rgcca <- function(A, C = 1-diag(length(A)), tau = rep(1, length(A)), ncomp = rep(1, length(A)), scheme = "centroid", scale = TRUE , init="svd", bias = TRUE, tol = 1e-8, verbose=TRUE) { if (any(ncomp < 1)) stop("Compute at least one component per block!") pjs <- sapply(A, NCOL) nb_row <- NROW(A[[1]]) if (any(ncomp-pjs > 0)) stop("For each block, choose a number of components smaller than the number of variables!") if (mode(scheme) != "function") { if ((scheme != "horst" ) & (scheme != "factorial") & (scheme != "centroid")) { stop("Choose one of the three following schemes: horst, centroid, factorial or design the g function") } if (verbose) cat("Computation of the RGCCA block components based on the", scheme, "scheme \n") } if (mode(scheme) == "function" & verbose) { cat("Computation of the RGCCA block components based on the g scheme \n") } if (scale == TRUE) { A = lapply(A, function(x) scale2(x, bias = bias)) A = lapply(A, function(x) x/sqrt(NCOL(x))) } if (!is.numeric(tau) & verbose) { cat("Optimal Shrinkage intensity paramaters are estimated \n") } else { if (is.numeric(tau) & verbose) { cat("Shrinkage intensity paramaters are chosen manually \n") } } AVE_X = list() AVE_outer <- vector() ndefl <- ncomp-1 N <- max(ndefl) nb_ind <- NROW(A[[1]]) J <- length(A) primal_dual = rep("primal", J) primal_dual[which(nb_row<pjs)] = "dual" if (N == 0) { result <- rgccak(A, C, tau=tau , scheme=scheme, init = init, bias = bias, tol = tol, verbose=verbose) Y <- NULL for (b in 1:J) Y[[b]] <- result$Y[,b, drop = FALSE] for (j in 1:J) AVE_X[[j]] = mean(cor(A[[j]], Y[[j]])^2) AVE_outer <- sum(pjs * unlist(AVE_X))/sum(pjs) AVE <- list(AVE_X = AVE_X, AVE_outer = AVE_outer, AVE_inner = result$AVE_inner) a <- lapply(result$a, cbind) for (b in 1:J) { rownames(a[[b]]) = colnames(A[[b]]) rownames(Y[[b]]) = rownames(A[[b]]) colnames(Y[[b]]) = "comp1" } out <- list(Y=Y, a =a, astar=a, C=C, tau=result$tau, scheme=scheme, ncomp=ncomp, crit=result$crit, primal_dual = primal_dual, AVE=AVE) class(out) <- "rgcca" return(out) } Y <- NULL crit = list() AVE_inner <- rep(NA,max(ncomp)) R <- A P <- a <- astar <- NULL if (is.numeric(tau)) tau_mat = tau else tau_mat = matrix(NA, max(ncomp), J) for (b in 1:J) P[[b]] <- a[[b]] <- astar[[b]] <- matrix(NA,pjs[[b]],N+1) for (b in 1:J) Y[[b]] <- matrix(NA,nb_ind,N+1) for (n in 1:N) { if (verbose) cat(paste0("Computation of the RGCCA block components if(is.vector(tau)) rgcca.result <- rgccak(R, C, tau = tau , scheme=scheme, init = init, bias = bias, tol = tol, verbose=verbose) else rgcca.result <- rgccak(R, C, tau = tau[n, ] , scheme=scheme, init = init, bias = bias, tol = tol, verbose=verbose) if (!is.numeric(tau)) tau_mat[n, ] = rgcca.result$tau AVE_inner[n] <- rgcca.result$AVE_inner crit[[n]] <- rgcca.result$crit for (b in 1:J) Y[[b]][,n] <- rgcca.result$Y[ , b] defla.result <- defl.select(rgcca.result$Y, R, ndefl, n, nbloc = J) R <- defla.result$resdefl for (b in 1:J) P[[b]][,n] <- defla.result$pdefl[[b]] for (b in 1:J) a[[b]][,n] <- rgcca.result$a[[b]] if (n==1) { for (b in 1:J) astar[[b]][,n] <- rgcca.result$a[[b]] } else { for (b in 1:J) astar[[b]][,n] <- rgcca.result$a[[b]] - astar[[b]][,(1:n-1), drop=F] %*% drop( t(a[[b]][,n]) %*% P[[b]][,1:(n-1),drop=F] ) } } if (verbose) cat(paste0("Computation of the RGCCA block components if(is.vector(tau)) rgcca.result <- rgccak(R, C, tau = tau , scheme=scheme, init = init, bias = bias, tol = tol, verbose=verbose) else rgcca.result <- rgccak(R, C, tau = tau[N+1, ] , scheme=scheme, init = init, bias = bias, tol = tol, verbose=verbose) crit[[N+1]] <- rgcca.result$crit if (!is.numeric(tau)) tau_mat[N+1, ] = rgcca.result$tau AVE_inner[max(ncomp)] <- rgcca.result$AVE_inner for (b in 1:J) { Y[[b]][,N+1] <- rgcca.result$Y[ ,b] a[[b]][,N+1] <- rgcca.result$a[[b]] astar[[b]][,N+1] <- rgcca.result$a[[b]] - astar[[b]][,(1:N),drop=F] %*% drop( t(a[[b]][,(N+1)]) %*% P[[b]][,1:(N),drop=F] ) rownames(a[[b]]) = rownames(astar[[b]]) = colnames(A[[b]]) rownames(Y[[b]]) = rownames(A[[b]]) colnames(Y[[b]]) = paste0("comp", 1:max(ncomp)) } shave.matlist <- function(mat_list, nb_cols) mapply(function(m, nbcomp) m[, 1:nbcomp, drop = FALSE], mat_list, nb_cols,SIMPLIFY=FALSE) shave.veclist <- function(vec_list, nb_elts) mapply(function(m, nbcomp) m[1:nbcomp], vec_list, nb_elts, SIMPLIFY=FALSE) for (j in 1:J) AVE_X[[j]] = apply(cor(A[[j]], Y[[j]])^2, 2, mean) outer = matrix(unlist(AVE_X), nrow = max(ncomp)) for (j in 1:max(ncomp)) AVE_outer[j] <- sum(pjs * outer[j, ])/sum(pjs) Y = shave.matlist(Y, ncomp) AVE_X = shave.veclist(AVE_X, ncomp) AVE <- list(AVE_X = AVE_X, AVE_outer_model = AVE_outer, AVE_inner_model = AVE_inner) out <- list(Y = shave.matlist(Y, ncomp), a = shave.matlist(a, ncomp), astar = shave.matlist(astar, ncomp), C = C, tau = tau_mat, scheme = scheme, ncomp=ncomp, crit = crit, primal_dual = primal_dual, AVE = AVE) class(out) <- "rgcca" return(out) }
plot_puberty_stages <- function(data) { plot <- maturation_cm(data) %>% ggplot2::ggplot(ggplot2::aes(x = `Maturity Offset (years)`, y = `% Adult Height`, label = Athlete)) + ggplot2::annotate("rect", xmin = -Inf, xmax = 4.5, ymin = 100, ymax = 102, fill = "black") + ggplot2::annotate("rect", xmin = -Inf, xmax = 4.5, ymin = -Inf, ymax = 88, fill = "gray", alpha = 0.4) + ggplot2::annotate("rect", xmin = -Inf, xmax = 4.5, ymin = 88, ymax = 95, fill = "gray", alpha = 0.6) + ggplot2::annotate("rect", xmin = -Inf, xmax = 4.5, ymin = 95, ymax = 100, fill = "gray", alpha = 0.8) + ggplot2::annotate("rect", xmin = 4.5, xmax = Inf, ymin = -Inf, ymax = Inf, fill = "white") + ggplot2::annotate("text", x = 0, y = 101, label = "Growth Spurt", size = 3, color = "white") + ggplot2::annotate("text", x = -2.7, y = 101, label = "Pre-Puberty", size = 3, color = "white") + ggplot2::annotate("text", x = 2.7, y = 101, label = "Post-Puberty", size = 3, color = "white") + ggplot2::annotate("text", x = -4, y = 85, label = "< 88%", size = 3, color = "black") + ggplot2::annotate("text", x = -4, y = 91.5, label = "88-95%", size = 3, color = "black") + ggplot2::annotate("text", x = -4, y = 97.5, label = "> 95%", size = 3, color = "black") + ggplot2::geom_vline(xintercept = -1, color = "white") + ggplot2::geom_vline(xintercept = 1, color = "white") + ggrepel::geom_text_repel(nudge_x = 6, direction = "y", angle = 0, hjust = -1, segment.size = 0.01, point.padding = 1, segment.alpha = 0.1, size = 3, color = "black") + ggplot2::geom_point(size = 2.5, alpha = 0.5, color = "red", shape = 21) + ggplot2::ylim (83, 102) + ggplot2::scale_x_continuous(limits = c(-4,5.5), breaks = seq(-4, 4, by = 1)) + ggplot2::ylab("% Adult Height \n") + ggplot2::xlab("\n Maturity Offset (Years)") + ggplot2::ggtitle("\n % Predicted Adult Height", subtitle = " Maturity Offset \n") + ggplot2::theme_light() + ggplot2::theme(panel.grid = ggplot2::element_blank(), panel.border = ggplot2::element_blank(), axis.title.x = ggplot2::element_text(color = "grey", hjust = 0.8), axis.title.y = ggplot2::element_text(color = "grey", hjust = 0.8), axis.text.y = ggplot2::element_blank(), axis.ticks.y = ggplot2::element_blank(), plot.subtitle = ggplot2::element_text(color = "darkgray"), legend.title = ggplot2::element_blank()) plot }
gemOLGFTwoFirms <- function(...) sdm2(...)
context("filterKinMatrix") library(testthat) ped <- nprcgenekeepr::qcPed ped$gen <- findGeneration(ped$id, ped$sire, ped$dam) kmat <- kinship(ped$id, ped$sire, ped$dam, ped$gen, sparse = FALSE) ids <- ped$id[c(189, 192, 194, 195)] ncols <- ncol(kmat) nrows <- nrow(kmat) kmatFiltered <- filterKinMatrix(ids, kmat) test_that("filterKinMatrix retains the correct rows and columns", { expect_equal(kmatFiltered[1, 2], kmat[189, 192]) expect_equal(kmatFiltered[1, 3], kmat[189, 194]) expect_equal(kmatFiltered[1, 4], kmat[189, 195]) expect_equal(kmatFiltered[2, 3], kmat[192, 194]) }) ids <- c("C1ICXL", "2KULR3", "RI0O7F", "7M51X5", "170ZTZ", "Y7PPEZ", "CFPEEU", "ZC5SCR", "218FOV", "2IXJ2N", "CAST4W", "JGPN6K", "HOYW0S", "DD1U77", "0DAV0I", "HLI95R", "TZ5NUB", "DR5GXB", "EUG3WE", "FHV13N", "OUM6QF", "6Z7MD9", "309VM2", "8KM1MP", "I9TQ0T", "INGWI7") kmatFiltered <- filterKinMatrix(ids, kmat) test_that("filterKinMatrix leaves the correct rows", { expect_equal(nrow(kmatFiltered), length(ids)) expect_equal(ncol(kmatFiltered), length(ids)) expect_equal(kmat[(seq_len(nrow(kmat)))[rownames(kmat) %in% ids[20:23]], (seq_len(ncol(kmat)))[colnames(kmat) %in% ids[20:23]]], kmatFiltered[20:23, 20:23]) } )
geomcp <- function(X,penalty='MBIC',pen.value=0,test.stat='Normal',msl=2,nquantiles=1,MAD=FALSE,ref.vec='Default',ref.vec.value=0){ if(!is.matrix(X)){ if(is.data.frame(X)){ X <- as.matrix(X) }else{ stop("Data type must be a matrix or data frame") } } if(length(X[1,])<2){ stop('Univariate changepoint analysis is not supported') } if(anyNA(X)){ stop("Missing value: NA is not allowed in the data") } if(!is.numeric(X)){ stop("Only numeric data allowed") } penalty <- toupper(penalty) if(!(penalty %in% c('MBIC','BIC','SIC','MANUAL','HANNAN-QUINN'))){ stop('Univariate penalty choice not recognized; should be "MBIC", "BIC", "SIC","Hannan-Quinn" or "Manual"') }else if(penalty=='MANUAL'){ penalty <- 'Manual' }else if(penalty=='HANNAN-QUINN'){ penalty <- 'Hannan-Quinn' } test.stat <- toupper(test.stat) if(!((test.stat=='NORMAL')||(test.stat=="EMPIRICAL"))){ stop('Invalid test statistic, must be Normal or Empirical') }else if(test.stat=='NORMAL'){ test.stat='Normal' }else{ test.stat='Empirical' } if(msl<1|msl>floor(length(X[,1])/2)){ stop('Minimum segment length must be between 1 and half the no. of time points (rounded down)') } nquantiles <- as.integer(nquantiles) if((nquantiles<1)){ stop("Number of quantiles must be a positive integer") } if((nquantiles==1)&&(test.stat=='Empirical')){ nquantiles <- ceiling(4*log(length(X[,1]))) } if((nquantiles!=1)&&(test.stat=='Normal')){ nquantiles <- 1 warning('nquantiles is not used with a Normal test statistic') } if(!is.logical(MAD)){ stop('MAD should be logical; TRUE or FALSE.') } ref.vec <- toupper(ref.vec) if(ref.vec=='DEFAULT'){ ref.vec.value <- rep(1,length(X[1,])) ref.vec <- 'Default' }else if(ref.vec=='MANUAL'){ if(!is.numeric(ref.vec.value)){ stop("Reference vector value should be a vector of type numeric") }else if(length(ref.vec.value)!=length(X[1,])){ stop('Length of reference vector is not the same as number of series in data') }else if(isTRUE(all.equal(ref.vec.value,rep(0,length(X[1,]))))){ stop('Reference vector cannot be the origin as angle undefined.') }else{ ref.vec <- 'Manual' } }else{ stop('Reference vector type not recognized; should be "Default" or "Manual".') } X.original <- X if(MAD){ X <- apply(X,2,function(x){(x-median(x))/mad(x)}) if(sum(is.nan(X))>0){ stop('Unable to perform MAD transformation') } } min.X <- apply(X,2,min)-ref.vec.value X <- t(apply(X,1,function(x){x-min.X})) X.dist <- distance.mapping(X,ref.vec.value) X.ang <- angle.mapping(X,ref.vec.value) if(test.stat=='Normal'){ dist.cpts.ans <- cpt.meanvar(X.dist,penalty=penalty,pen.value=pen.value,method='PELT',param.estimates=FALSE,minseglen=msl,class=TRUE) ang.cpts.ans <- cpt.meanvar(X.ang,penalty=penalty,pen.value=pen.value,method='PELT',param.estimates=FALSE,minseglen=msl,class=TRUE) } else if(test.stat=='Empirical'){ dist.cpts.ans <- cpt.np(X.dist,penalty=penalty,pen.value=pen.value,method='PELT',minseglen=msl,nquantiles=nquantiles,class=TRUE) ang.cpts.ans <- cpt.np(X.ang,penalty=penalty,pen.value=pen.value,method='PELT',minseglen=msl,nquantiles=nquantiles,class=TRUE) } out <- class_input(data.set=X.original,distance=X.dist,angle=X.ang,penalty=penalty,pen.value=pen.value(dist.cpts.ans),test.stat=test.stat,msl=msl,nquantiles=nquantiles,dist.cpts=cpts(dist.cpts.ans),ang.cpts=cpts(ang.cpts.ans)) return(out) }
unseiji_ST61_C <- list( rt.y = 20, ecj = c(3, 4.5), section.y = c(0:5, 6.33, 7.67, 9.00, 10.33, 11.67, 13:20), t.start = 0.375, t.end = 12.1, section = data.frame( age = c(0.7, 1.3, 1.8, 2.4, 3.0, 3.7, 4.5, 5.3, 6.0, 6.8, 7.6, 8.3, 8.9, 9.5, 10.0, 10.6, 11.2, 11.8), d13C = c(-19.2, -18.7, -18.9, -19.0, -19.1, -19.2, -19.3, -19.3, -19.3, -19.2, -19.1, -19.1, -19.1, -19.1, -19.1, -19.3, -19.5, -19.6), d15N = c(12.9, 12.5, 12.1, 12.1, 12.4, 11.9, 11.7, 11.4, 11.5, 11.5, 11.4, 11.5, 11.7, 11.6, 11.7, 11.9, 12.1, 12.6))) unseiji_ST61_M1 <- list( rt.y = 18, ecj = c(5, 5.5), section.y = c(0:15, 18), t.start = 0.0, t.end = 10.0, section = data.frame( age = c(0.3, 0.8, 1.4, 1.9, 2.5, 3.1, 3.6, 4.2, 4.7, 5.3, 5.8, 6.4, 6.9, 7.5, 8.1, 9.2), d13C = c(-18.9, -19.1, -19.0, -18.7, -18.9, -18.8, -19.0, -19.1, -19.1, -19.0, -19.2, -19.3, -19.2, -19.3, -19.4, -19.4), d15N = c(14.5, 12.6, 12.2, 12.2, 12.4, 12.1, 12.0, 11.7, 11.4, 11.6, 11.7, 11.7, 11.6, 12.0, 12.3, 14.1)))
"absval.iwres.vs.ipred" <- function(object, ylb = "|iWRES|", type="p", ids = FALSE, idsdir = "up", smooth = TRUE, ...) { if(is.null(xvardef("iwres",object)) || is.null(xvardef("ipred",object))) { cat("The required variables are not set in the data base\n") return() } xplot <- xpose.plot.default(xvardef("ipred",object), xvardef("iwres",object), ylb = ylb, funy = "abs", type= type, ids = ids, idsdir=idsdir, smooth=smooth, object, ...) return(xplot) }
g2tests_perm <- function(data,x,y,dc,nperm) { .Call(Rfast_g2tests_perm,data,x,y,dc,nperm) } g2Test_univariate <- function(data,dc) { .Call(Rfast_g2Test_univariate,data,dc) } g2Test_perm <- function(data,x,y,cs,dc,nperm) { .Call(Rfast_g2Test_perm,data,x,y,cs,dc,nperm) } g2tests <- function(data,x,y,dc) { .Call(Rfast_g2tests,data,x,y,dc) } g2Test_univariate_perm <- function(data,dc,nperm) { .Call(Rfast_g2Test_univariate_perm,data,dc,nperm) } g2Test <- function(data,x,y,cs,dc) { .Call(Rfast_g2Test,data,x,y,cs,dc) }
zijderveld <- function(dec, inc, int, xh = "WE", xv = xh, centre = F, xlim = NA, ylim = NA, unit = NA, xlab = "", ylab = "", labels = NA, nlabels = 1, h = list(pch = 19), v = list(pch = 21, bg = "white"), f = list(pch = 21, bg = "white", cex = 1.5), t = list(pos = 3, offset = 0.5), l = list(), anchored = T, style = "branches", tcl = 0.2, orientation = TRUE, scientific = NA, decimals = 10, add = FALSE) { cart <- transphere(dec = dec, inc = inc, int = int) if(xh == "SN"){ xhi <- cart$x yhi <- -cart$y } else if(xh == "WE"){ xhi <- cart$y yhi <- cart$x } else { stop("The xh parameter should be 'SN' or 'WE'.") } yvi <- -cart$z if(xv == "SN"){ xvi <- cart$x } else if (xv == "WE"){ xvi <- cart$y } else if(xv == "modified"){ xvi <- sqrt(cart$x^2 + cart$y^2) } else { stop("The xh parameter should be 'SN', 'WE' or 'modified'.") } if(!add){ if(orientation){ if(xh == xv){ if(xh == "WE") { xcap <- c("W","E") ycap <- c("S, Down", "N, Up") } else if(xh == "SN"){ xcap <- c("S","N") ycap <- c("E, Down", "W, Up") } } else { if(xv == "WE") { xcap <- c("S, W","N, E") ycap <- c("E, Down", "W, Up") } else if(xv == "SN"){ xcap <- c("W, S","E, N") ycap <- c("S, Down", "N, Up") } else if(xv == "modified"){ if(xh == "WE") { xcap <- c("W, mod","E, mod") ycap <- c("S, Down", "N, Up") } else if(xh == "SN"){ xcap <- c("S, mod","N, mod") ycap <- c("E, Down", "W, Up") } } } } if(centre){ xmax <- max(abs(c(xhi,xvi))) xtlim <- c(-xmax,xmax) } else { xmax <- max(c(xhi,xvi,0)) xmin <- min(c(xhi,xvi,0)) xtlim <- c(xmin,xmax) } if(centre){ ymax <- max(abs(c(yhi,yvi))) ytlim <- c(-ymax,ymax) } else { ymax <- max(c(yhi,yvi,0)) ymin <- min(c(yhi,yvi,0)) ytlim <- c(ymin,ymax) } if(is.na(unit)[[1]]){ px <- pretty(xtlim) py <- pretty(ytlim) mult <- min(c((px[2] - px[1]), (py[2] - py[1]))) if(!is.na(xlim[[1]]) & length(xlim) == 2 & class(xlim) == "numeric"){ pxn <- pretty(xlim) mult <- min(mult, (pxn[2] - pxn[1])) } if(!is.na(ylim[[1]]) & length(ylim) == 2 & class(ylim) == "numeric"){ pyn <- pretty(ylim) mult <- min(mult, (pyn[2] - pyn[1])) } } else if((class(unit) == "numeric" | class(unit) == "integer") & length(unit) == 1 & !is.na(unit) & unit > 0){ mult <- unit } else { stop(paste("The 'unit' parameter should be NA or a positive", " non zero numeric of length one.", sep = "")) } xlcas <- encase(xtlim[1] - mult, xtlim[2] + mult, mult) ylcas <- encase(ytlim[1] - mult, ytlim[2] + mult, mult) if(is.na(xlim[[1]])){ xlim <- xlcas } if(is.na(ylim[[1]])){ ylim <- ylcas } plot(0, 0, asp = 1, xlim = xlim, ylim = ylim, type = "n", xlab = "", ylab = "", axes = F) pusr <- par("usr") if(style == "box0" | style == "box1" | style == "box2"){ box() xcas <- encase(pusr[1], pusr[2], mult) ycas <- encase(pusr[3], pusr[4], mult) xtic <- seq(xcas[1], xcas[2], mult) ytic <- seq(ycas[1], ycas[2], mult) if(!is.na(scientific[[1]])) { if(scientific){ xtic <- formatC(xtic, format = "e", digits = decimals) ytic <- formatC(ytic, format = "e", digits = decimals) } else if (!scientific){ xtic <- formatC(unique(round(xtic, decimals)),decimals, format = "f") ytic <- formatC(unique(round(ytic, decimals)),decimals, format = "f") } axis(1, labels = xtic, lwd = 0, lwd.ticks = 1, tcl = -tcl, at = xtic) axis(2, labels = ytic, lwd = 0, lwd.ticks = 1, tcl = -tcl, las = 1, at = ytic) } else { axis(1, lwd = 0, lwd.ticks = 1, tcl = -tcl, at = xtic) axis(2, lwd = 0, lwd.ticks = 1, tcl = -tcl, las = 1, at = ytic) } if((style == "box0" | style == "box1") & orientation){ text(xlcas, 0, labels = xcap) text(0, ylcas, labels = ycap) } if(style == "box2" & orientation){ axis(3, pos = 0, labels = xcap, lwd = 0, las = 1, at = xlcas, padj = 0.5) axis(4, pos = 0, labels = ycap, lwd = 0, las = 1, at = ylcas, hadj = 0.2) } if(style == "box1") points(0,0,pch = 3,cex = 1.5) if(style == "box2" ) abline(v = 0,h = 0) } else if(style == "branches"){ xtic <- seq(xlcas[1], xlcas[2], mult) ytic <- seq(ylcas[1], ylcas[2], mult) if(!is.na(scientific[[1]])) { if(scientific){ xtic <- formatC(xtic, format = "e", digits = decimals) ytic <- formatC(ytic, format = "e", digits = decimals) } else if (!scientific){ xtic <- formatC(unique(round(xtic, decimals)),decimals, format = "f") ytic <- formatC(unique(round(ytic, decimals)),decimals, format = "f") } xmar <- c(xtic[1], xtic[length(xtic)]) ymar <- c(ytic[1], ytic[length(ytic)]) axis(1, pos = 0, labels = xmar, lwd = 0, at = xmar) axis(2, pos = 0, labels = ymar, lwd = 0, las = 1, at = ymar) } else { xmar <- c(xtic[1], xtic[length(xtic)]) ymar <- c(ytic[1], ytic[length(ytic)]) axis(1, pos = 0, lwd = 0, at = xmar) axis(2, pos = 0, lwd = 0, las = 1, at = ymar) } axis(1, pos = 0, labels = F, lwd = 1, lwd.ticks = 0, at = xlcas) axis(1, pos = 0, labels = F, lwd = 0, lwd.ticks = 1, tcl = -tcl, at = xtic) axis(1, pos = 0, labels = F, lwd = 0, lwd.ticks = 1, tcl = tcl, at = xtic) axis(3, pos = 0, labels = xcap, lwd = 0, las = 1, at = c(xtic[1], xtic[length(xtic)])) axis(2, pos = 0, labels = F, lwd = 1, lwd.ticks = 0, at = ylcas) axis(2, pos = 0, labels = F, lwd = 0, lwd.ticks = 1, tcl = -tcl, at = ytic) axis(2, pos = 0, labels = F, lwd = 0, lwd.ticks = 1, tcl = tcl, at = ytic) axis(4, pos = 0, labels = ycap, lwd = 0, las = 1, at = c(ytic[1], ytic[length(ytic)])) } else { stop(paste("The 'style' parameter should be 'box0',", " 'box1', 'box2' or 'branches'.", sep = "")) } } hi <- merge_list(h, list(pch = 19)) vi <- merge_list(v, list(pch = 21, bg = "white")) fi <- merge_list(f, list(pch = 21, bg = "white", cex = 1.5)) hi <- c(list(x = xhi, y = yhi), hi) vi <- c(list(x = xvi, y = yvi), vi) fi <- c(list(x = c(xhi[1],xvi[1]), y = c(yhi[1],yvi[1])), fi) if(anchored){ xlhi <- c(xhi,0) ylhi <- c(yhi,0) xlvi <- c(xvi,0) ylvi <- c(yvi,0) } else { xlhi <- xhi ylhi <- yhi xlvi <- xvi ylvi <- yvi } lhi <- c(list(x = xlhi, y = ylhi), l) lvi <- c(list(x = xlvi, y = ylvi), l) do.call(lines, lhi) do.call(lines, lvi) do.call(points, fi) do.call(points, hi) do.call(points, vi) if(!(length(labels) == 1 & is.na(labels[[1]]))){ labels <- every_nth(labels, nlabels, inverse = TRUE) ti <- merge_list(t, list(pos = 3, offset = 0.5)) thi <- c(list(x = xhi, y = yhi, labels = labels), ti) tvi <- c(list(x = xvi, y = yvi, labels = labels), ti) do.call(text,thi) do.call(text,tvi) } }
twocor <- function(x1, y1, x2, y2, corfun = "pbcor", nboot = 599, tr = 0.2, beta = 0.2, ...){ cl <- match.call() alpha <- .05 corfun <- match.arg(corfun, c("pbcor", "wincor"), several.ok = FALSE) data1<-matrix(sample(length(y1),size=length(y1)*nboot,replace=TRUE),nrow=nboot) if (corfun == "pbcor") bvec1 <- apply(data1, 1, function(xx) pbcor(x1[xx], y1[xx], beta = beta, ci = FALSE)$cor) if (corfun == "wincor") bvec1 <- apply(data1, 1, function(xx) wincor(x1[xx], y1[xx], tr = tr, ci = FALSE)$cor) data2<-matrix(sample(length(y2),size=length(y2)*nboot,replace=TRUE),nrow=nboot) if (corfun == "pbcor") bvec2 <- apply(data2, 1, function(xx) pbcor(x2[xx], y2[xx], beta = beta,ci = FALSE)$cor) if (corfun == "wincor") bvec2 <- apply(data2, 1, function(xx) wincor(x2[xx], y2[xx], tr = tr,ci = FALSE)$cor) bvec<-bvec1-bvec2 bsort<-sort(bvec) nboot <- length(bsort) term<-alpha/2 ilow<-round((alpha/2) * nboot) ihi<-nboot - ilow ilow<-ilow+1 corci<-1 corci[1]<-bsort[ilow] corci[2]<-bsort[ihi] pv<-(sum(bsort<0)+.5*sum(bsort==0))/nboot pv=2*min(c(pv,1-pv)) if (corfun == "pbcor") { r1<-pbcor(x1,y1, beta,ci = FALSE)$cor r2<-pbcor(x2,y2, beta,ci = FALSE)$cor } if (corfun == "wincor") { r1<-wincor(x1,y1, tr,ci = FALSE)$cor r2<-wincor(x2,y2, tr,ci = FALSE)$cor } result <- list(r1=r1, r2 = r2, ci = corci, p.value = pv, call = cl) class(result) <- "twocor" result }
x <- 1:3 A %*% x as.matrix(x)
fullup <- function(sA) { if(is(sA, 'sparseMatrix')){ A <- as.matrix(sA) } else { A <- full(rbind(sA,cbind(sA[,2],sA[,1],sA[,3]))) } return(A) }