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if (!require("shiny")) stop("This demo requires shiny.") library(rgl) options(rgl.useNULL = TRUE) ui <- fluidPage( mainPanel( tabsetPanel( tabPanel("red", rglwidgetOutput('thewidget1')), tabPanel("green", rglwidgetOutput('thewidget2')) )) ) server <- function(input, output, session) { x <- rnorm(100) y <- 2*rnorm(100) z <- 10*rnorm(100) open3d() plot3d(x, y, z, col = "red") scene1 <- scene3d() plot3d(z, y, x, col = "green") scene2 <- scene3d() close3d() save <- options(rgl.inShiny = TRUE) on.exit(options(save)) output$thewidget1 <- renderRglwidget( rglwidget(scene1) ) output$thewidget2 <- renderRglwidget( rglwidget(scene2) ) } if (interactive()) shinyApp(ui = ui, server = server)
acontext("Segment size") df <- data.frame(x=c(0, 0), y=c(0, 1), xend=c(1, 1), yend=c(1, 0), size=c(5, 10)) test_that("segment size translates to stroke-width", { viz <- list(segs=ggplot()+ geom_segment(aes(x, y, xend=xend, yend=yend), data=df, size=1)) info <- animint2HTML(viz) expect_styles(info$html, list("stroke-width"="^1[a-z]*$")) }) test_that("segment size range translates to stroke-width", { viz <- list(segs=ggplot()+ geom_segment(aes(x, y, xend=xend, yend=yend, size=size), data=df)+ scale_size_identity()) info <- animint2HTML(viz) expect_styles(info$html, list("stroke-width"=c("^5[a-z]*$", "^10[a-z]*$"))) })
flash_clean_sprint_events <- function(df, wide_format_sprint) { if (wide_format_sprint == FALSE) { df <- df %>% data.frame() %>% dplyr::mutate(Time = stringr::str_remove(Time, "(?<!D)[Q|q]")) %>% dplyr::mutate(dplyr::across( dplyr::matches("[0-9]"), ~ stringr::str_remove(.x, " ?\\[(.*)\\]") )) varying_cols <- names(df)[grep("(^X\\d)|(^Lap)|(^L\\d)", names(df))] if (length(varying_cols) > 0) { df <- flash_pivot_longer(df, varying = varying_cols) } } else { df <- df %>% flash_col_names() %>% dplyr::mutate(dplyr::across( dplyr::matches("Split_"), ~ stringr::str_remove(.x, " ?\\[(.*)\\]") )) } clean_sprint_data <- df %>% dplyr::mutate(Time = stringr::str_remove(Time, "(?<!D)[Q|q]")) %>% dplyr::rename("Result" = "Time") %>% dplyr::mutate( Tiebreaker = dplyr::case_when( stringr::str_detect(Result, "\\(\\d{1,2}\\.\\d{3}\\)") == TRUE ~ stringr::str_extract(Result, "\\d{1,2}\\.\\d{3}"), TRUE ~ "NA" ) ) %>% dplyr::mutate(Result = stringr::str_remove(Result, "\\(\\d{1,2}\\.\\d{3}\\)")) %>% dplyr::mutate(Result = stringr::str_remove(Result, "\\\n[:upper:]{1,2}")) %>% dplyr::na_if("NA") %>% dplyr::mutate(dplyr::across(where(is.character), stringr::str_trim)) if ("Team" %in% names(clean_sprint_data) == FALSE) { clean_sprint_data <- clean_sprint_data %>% dplyr::mutate( Team = stringr::str_split_fixed(Name, "\\\n", 3)[, 2], Name = stringr::str_split_fixed(Name, "\\\n", 3)[, 1] ) } return(clean_sprint_data) } sprint_events <- flash_clean_sprint_events
methods::setClass("dbartsTreePrior") methods::setClass("dbartsCGMPrior", contains = "dbartsTreePrior", slots = list(power = "numeric", base = "numeric")) methods::setValidity("dbartsCGMPrior", function(object) { if (object@power <= 0.0) return("'power' must be positive") if (object@base <= 0.0 || object@base >= 1.0) return("'base' must be in (0, 1)") TRUE }) methods::setClass("dbartsNodeHyperprior") methods::setClass("dbartsChiHyperprior", contains = "dbartsNodeHyperprior", slots = list(degreesOfFreedom = "numeric", scale = "numeric")) methods::setValidity("dbartsChiHyperprior", function(object) { if (object@degreesOfFreedom <= 0.0) return("'degreesOfFreedom' must be positive") if (object@scale <= 0.0) return("'scale' must be positive") TRUE }) methods::setClass("dbartsFixedHyperprior", contains = "dbartsNodeHyperprior", slots = list(k = "numeric"), prototype = list(k = 2)) methods::setValidity("dbartsFixedHyperprior", function(object) { if (object@k <= 0.0) return("'k' must be positive") TRUE }) methods::setClass("dbartsNodePrior") methods::setClass("dbartsNormalPrior", contains = "dbartsNodePrior") methods::setClass("dbartsResidPrior") methods::setClass("dbartsChiSqPrior", contains = "dbartsResidPrior", slots = list(df = "numeric", quantile = "numeric")) methods::setValidity("dbartsChiSqPrior", function(object) { if (object@df <= 0.0) return("'df' must be positive") if (object@quantile <= 0.0) return("'quantile' must be positive") TRUE }) methods::setClass("dbartsFixedPrior", contains = "dbartsResidPrior", slots = list(value = "numeric")) methods::setValidity("dbartsFixedPrior", function(object) { if (object@value <= 0.0) return("'value' must be positive") TRUE }) methods::setClass("dbartsControl", slots = list(binary = "logical", verbose = "logical", keepTrainingFits = "logical", useQuantiles = "logical", keepTrees = "logical", n.samples = "integer", n.burn = "integer", n.trees = "integer", n.chains = "integer", n.threads = "integer", n.thin = "integer", printEvery = "integer", printCutoffs = "integer", rngKind = "character", rngNormalKind = "character", rngSeed = "integer", updateState = "logical", call = "language"), prototype = list(binary = FALSE, verbose = FALSE, keepTrainingFits = TRUE, useQuantiles = FALSE, keepTrees = FALSE, n.samples = NA_integer_, n.burn = 200L, n.trees = 75L, n.chains = 4L, n.threads = 1L, n.thin = 1L, printEvery = 100L, printCutoffs = 0L, rngKind = "default", rngNormalKind = "default", rngSeed = NA_integer_, updateState = TRUE, call = quote(call("NA"))) ) methods::setValidity("dbartsControl", function(object) { if (length(object@verbose) != 1L) return("'verbose' must be of length 1") if (length(object@keepTrainingFits) != 1L) return("'keepTrainingFits' must be of length 1") if (length(object@useQuantiles) != 1L) return("'useQuantiles' must be of length 1") if (length(object@keepTrees) != 1L) return("'keepTrees' must be of length 1") if (length([email protected]) != 1L) return("'n.burn' must be of length 1") if (length([email protected]) != 1L) return("'n.trees' must be of length 1") if (length([email protected]) != 1L) return("'n.threads' must be of length 1") if (length([email protected]) != 1L) return("'n.thin' must be of length 1") if (length(object@printEvery) != 1L) return("'printEvery' must be of length 1") if (length(object@printCutoffs) != 1L) return("'printCutoffs' must be of length 1") if (length(object@updateState) != 1L) return("'updateState' must be of length 1") if (length([email protected]) != 1L) return("'n.samples' must be of length 1") if (length(object@rngSeed) != 1L) return("'rngSeed' must be of length 1") if (is.na(object@verbose)) return("'verbose' must be TRUE/FALSE") if (is.na(object@keepTrainingFits)) return("'keepTrainingFits' must be TRUE/FALSE") if (is.na(object@useQuantiles)) return("'useQuantiles' must be TRUE/FALSE") if (is.na(object@keepTrees)) return("'keepTrees' must be TRUE/FALSE") if ([email protected] < 0L) return("'n.burn' must be a non-negative integer") if ([email protected] <= 0L) return("'n.trees' must be a positive integer") if ([email protected] <= 0L) return("'n.chains' must be a positive integer") if ([email protected] <= 0L) return("'n.threads' must be a positive integer") if ([email protected] < 0L) return("'n.thin' must be a non-negative integer") if (object@printEvery < 0L) return("'printEvery' must be a non-negative integer") if (object@printCutoffs < 0L) return("'printCutoffs' must be a non-negative integer") rngKind <- parse(text = deparse(RNGkind)[-1L])[[1L]] rngKinds <- character(0L) rngNormalKinds <- character(0L) for (i in seq_along(rngKind)) { rngKind.i <- as.character(rngKind[[i]]) if (any(grepl("Mersenne", rngKind.i))) rngKinds <- eval(parse(text = rngKind.i[which(grepl("Mersenne", rngKind.i))])) if (any(grepl("Inversion", rngKind.i))) rngNormalKinds <- eval(parse(text = rngKind.i[which(grepl("Inversion", rngKind.i))])) } if (length(rngKinds) == 0L || length(rngNormalKinds) == 0L) { oldKind <- RNGkind() oldSeed <- .Random.seed tryResult <- tryCatch(RNGkind(object@rngKind, object@rngNormalKind), error = function(e) e) if (inherits(tryResult, "error")) return(paste0("unrecognized rng kind ('", object@rngKind, "', '", object@rngNormalKind, "')")) object@rngKind <- RNGkind()[1L] object@rngNormalKind <- RNGkind()[2L] RNGkind(oldKind[1L], oldKind[2L]) .Random.seed <- oldSeed } else { if (!(object@rngKind %in% rngKinds)) return(paste0("unrecognized rng kind '", object@rngKind, "'")) if (!(object@rngNormalKind %in% rngNormalKinds)) return(paste0("unrecognized rng normal kind '", object@rngNormalKind, "'")) } if (is.na(object@updateState)) return("'updateState' must be TRUE/FALSE") if (!is.na([email protected]) && [email protected] < 0L) return("'n.samples' must be a non-negative integer") TRUE }) methods::setClass("dbartsModel", slots = list(p.birth_death = "numeric", p.swap = "numeric", p.change = "numeric", p.birth = "numeric", node.scale = "numeric", tree.prior = "dbartsTreePrior", node.prior = "dbartsNodePrior", node.hyperprior = "dbartsNodeHyperprior", resid.prior = "dbartsResidPrior"), prototype = list(p.birth_death = 1.0, p.swap = 0.0, p.change = 0.0, p.birth = 0.5, node.scale = 0.5, tree.prior = new("dbartsCGMPrior"), node.prior = new("dbartsNormalPrior"), node.hyperprior = new("dbartsFixedHyperprior"), resid.prior = new("dbartsChiSqPrior"))) methods::setValidity("dbartsModel", function(object) { proposalProbs <- c([email protected]_death, [email protected], [email protected]) if (any(proposalProbs < 0.0) || any(proposalProbs > 1.0)) return("rule proposal probabilities must be in [0, 1]") if (abs(sum(proposalProbs) - 1.0) >= 1e-10) return("rule proposal probabilities must sum to 1") if ([email protected] <= 0.0 || [email protected] >= 1.0) return("birth probability for birth/death step must be in (0, 1)") if ([email protected] <= 0.0) return("node.scale must be > 0") TRUE }) methods::setClassUnion("matrixOrNULL", c("matrix", "NULL")) methods::setClassUnion("numericOrNULL", c("numeric", "NULL")) methods::setClass("dbartsData", slots = list(y = "numeric", x = "matrix", varTypes = "integer", x.test = "matrixOrNULL", weights = "numericOrNULL", offset = "numericOrNULL", offset.test = "numericOrNULL", n.cuts = "integer", sigma = "numeric", testUsesRegularOffset = "logical"), prototype = list(y = numeric(0), x = matrix(0, 0, 0), varTypes = integer(0), x.test = NULL, weights = NULL, offset = NULL, offset.test = NULL, n.cuts = integer(0), sigma = NA_real_, testUsesRegularOffset = NA ) ) methods::setValidity("dbartsData", function(object) { numObservations <- length(object@y) if (nrow(object@x) != numObservations) return("number of rows of 'x' must equal length of 'y'") if (length(object@varTypes) > 0 && any(object@varTypes != ORDINAL_VARIABLE & object@varTypes != CATEGORICAL_VARIABLE)) return("variable types must all be ordinal or categorical") if (!is.null([email protected]) && ncol([email protected]) != ncol(object@x)) return("'x.test' must be null or have number of columns equal to 'x'") if (!is.null(object@weights)) { if (length(object@weights) != numObservations) return("'weights' must be null or have length equal to that of 'y'") if (anyNA(object@weights)) return("'weights' cannot be NA") if (any(object@weights < 0.0)) return("'weights' must all be non-negative") if (any(object@weights == 0.0)) warning("'weights' of 0 will be ignored but increase computation time") } if (!is.null(object@offset) && length(object@offset) != numObservations) return("'offset' must be null or have length equal to that of 'y'") if (!anyNA([email protected]) && length([email protected]) != ncol(object@x)) return("length of 'n.cuts' must equal number of columns in 'x'") if (!is.na(object@sigma) && object@sigma <= 0.0) return("'sigma' must be positive") TRUE }) methods::setClass("dbartsState", slots = list(trees = "integer", treeFits = "numeric", savedTrees = "integer", sigma = "numeric", k = "numericOrNULL", rng.state = "integer"))
knitr::opts_chunk$set( collapse = TRUE, comment = " ) fam <- binomial() class(fam) names(fam) set.seed(1) x <- matrix(rnorm(500), ncol = 5) y <- rowSums(x[, 1:2]) + rnorm(100) library(glmnet) oldfit <- glmnet(x, y, family = "gaussian") newfit <- glmnet(x, y, family = gaussian()) thresh <- 1e-18 oldfit <- glmnet(x, y, family="gaussian", thresh = thresh) newfit <- glmnet(x, y, family = gaussian(), thresh = thresh) library(testthat) for (key in c("a0", "beta", "df", "dim", "lambda", "dev.ratio", "nulldev", "offset", "nobs")) { expect_equal(oldfit[[key]], newfit[[key]]) } biny <- ifelse(y > 0, 1, 0) cnty <- ceiling(exp(y)) oldfit <- glmnet(x, biny, family = "binomial") newfit <- glmnet(x, biny, family = binomial()) oldfit <- glmnet(x, cnty, family = "poisson") newfit <- glmnet(x, cnty, family = poisson()) newfit <- glmnet(x, biny, family = binomial(link = "probit")) newfit <- glmnet(x, cnty, family = quasipoisson()) class(newfit) fit <- glmnet(x, y, family = "gaussian") class(fit) set.seed(2020) n <- 100 p <- 4 x <- matrix(runif(n * p, 5, 10), n) y <- rpois(n, exp(rowMeans(x))) glmfit <- glm(y ~ x - 1, family = poisson) coef(glmfit) oldfit <- glmnet(x, y, family = "poisson", standardize = FALSE, intercept = FALSE, lambda = 0) coef(oldfit) glmnet.control(mxitnr = 50) newfit <- glmnet(x, y, family = poisson(), standardize = FALSE, intercept = FALSE, lambda = 0) coef(newfit) thresh <- 1e-15 glmfit <- glm(y ~ x-1, family = poisson, control = list(epsilon = thresh, maxit = 100)) newfit <- glmnet(x, y, family = poisson(), standardize = FALSE, intercept = FALSE, lambda = 0, thresh = thresh) expect_equal(as.numeric(coef(glmfit)), as.numeric(coef(newfit))[2:5])
'ursa_read' <- function(fname,verbose=FALSE) { if (envi_exists(fname)) { return(read_envi(fname)) } if (!.lgrep("\\.zip$",fname)) { return(read_gdal(fname=fname,verbose=verbose)) } list1 <- unzip(fname,exdir=tempdir());on.exit(file.remove(list1)) ind <- .grep("\\.tif(f)*$",list1) if (length(ind)) { aname <- .gsub("\\.tif(f)*","",basename(list1[ind])) if (TRUE) { res <- vector("list",length(aname)) names(res) <- aname res <- lapply(list1[ind],.read_gdal,verbose=verbose) names(res) <- aname g <- lapply(res,ursa_grid) if (all(sapply(head(g,-1),function(g2) all.equal(g[[1]],g2)))) res <- as.ursa(res) return(res) } for (i in sample(seq_along(aname))) { a <- .read_gdal(fname=list1[ind][i],verbose=verbose) if (!exists("res")) res <- ursa(bandname=aname) res[i] <- a } return(res) } NULL } 'read_gdal' <- function(fname,resetGrid=TRUE,band=NULL ,engine=c("native","rgdal","sf"),verbose=FALSE,...) { engine <- match.arg(engine) if (accepted_changes <- TRUE) { if ((!is.null(band))||(engine %in% c("native","rgdal")[1:2])) { isSF <- FALSE } else if (engine %in% c("native","sf")[2]) isSF <- TRUE else { loaded <- loadedNamespaces() if ("sf" %in% loaded) isSF <- TRUE else if (("sp" %in% loaded)||("rgdal" %in% loaded)) isSF <- FALSE else isSF <- requireNamespace("sf",quietly=.isPackageInUse()) } } else isSF <- FALSE if (verbose) print(c(isSF=isSF)) if (isSF) { res <- as_ursa(sf::gdal_read(fname)) } else { obj <- open_gdal(fname,verbose=verbose) if (is.null(obj)) return(NULL) res <- if (!is.null(band)) obj[band] else obj[] close(obj) } if (T & length(grep("^\\d{8}\\.s1ab\\.1km\\.n\\.mos[13]d\\.jpg$",basename(fname)))) { g0 <- ursa_grid(res) if ((g0$columns==4500L)&&(g0$rows==5500L)) { xy <- .project(c(-176.682000,61.327000),spatial_crs(3413)) g1 <- .grid.skeleton() g1$resx <- g1$resy <- 1004.1 g1$crs <- spatial_crs(3413) g1$columns <- g0$columns g1$rows <- g0$rows g1$minx <- round(xy[,1])-g1$resx/2 g1$maxy <- round(xy[,2]) g1$maxx <- g1$minx+g1$resx*g1$columns g1$miny <- g1$maxy-g1$resy*g1$rows ursa_grid(res) <- g1 } } if (resetGrid) session_grid(res) res } '.read_gdal' <- function(fname,fileout=NULL,verbose=!FALSE,...) { if (!is.character(fname)) return(NULL) requireNamespace("rgdal",quietly=.isPackageInUse()) if (verbose) .elapsedTime("rgdal has been loaded") op <- options(warn=0-!verbose) a <- try(rgdal::GDALinfo(fname,returnStats=FALSE,returnRAT=FALSE ,returnColorTable=TRUE,returnCategoryNames=TRUE)) options(op) if (inherits(a,"try-error")) { fname <- normalizePath(fname) op <- options(warn=0-!verbose) a <- try(rgdal::GDALinfo(fname,returnStats=FALSE,returnRAT=FALSE ,returnColorTable=TRUE,returnCategoryNames=TRUE)) options(op) if (verbose) str(a) if (inherits(a,"try-error")) { if (verbose) { message("It looks like file ",.dQuote(fname) ," is not found or not GDAL-recognized") } return(NULL) } } a1 <- as.numeric(a) g1 <- regrid() g1$rows <- as.integer(a1[1]) g1$columns <- as.integer(a1[2]) nl <- as.integer(a1[3]) g1$minx <- a1[4] g1$miny <- a1[5] g1$resx <- a1[6] g1$resy <- a1[7] g1$maxx <- with(g1,minx+resx*columns) g1$maxy <- with(g1,miny+resy*rows) g1$crs <- attr(a,"projection") if (is.na(g1$crs)) g1$crs <- "" b1 <- attr(a,"mdata") ln <- .gsub("^Band_\\d+=\\t*(.+)$","\\1",.grep("band",b1,value=TRUE)) c1 <- attr(a,"df") hasndv <- unique(c1$hasNoDataValue) nodata <- unique(c1$NoDataValue) nodata <- if ((length(hasndv)==1)&&(length(nodata)==1)&&(hasndv)) nodata else NA ct <- attr(a,"ColorTable") if ((length(ct))&&(!is.null(ct[[1]]))) { ct <- ct[[1]] ca <- attr(a,"CATlist") if ((length(ca))&&(!is.null(ca[[1]]))) { nval <- ca[[1]] ct <- ct[seq(length(nval))] } else nval <- NULL names(ct) <- nval } else ct <- character() class(ct) <- "ursaColorTable" session_grid(g1) dset <- methods::new("GDALReadOnlyDataset",fname) if (!length(ln)) { dima <- dim(dset) ln <- paste("Band",if (length(dima)==3) seq(dima[3]) else 1L) } if (!is.character(fileout)) { val <- rgdal::getRasterData(dset) dima <- dim(val) if (length(dima)==2) dim(val) <- c(dima,1L) val <- val[,rev(seq(dim(val)[2])),,drop=FALSE] res <- as.ursa(value=val,bandname=ln,ignorevalue=nodata) } else { res <- create_envi(fileout,bandname=ln,ignorevalue=nodata,...) for (i in seq_along(ln)) { res[i]$value[] <- rgdal::getRasterData(dset,band=i) } } rgdal::closeDataset(dset) res$colortable <- ct class(res$value) <- ifelse(length(ct),"ursaCategory","ursaNumeric") res }
move_jitter_grob <- function(loon.grob, index, swap, jitterxy, temporary, ...) { obj <- character(0) class(obj) <- names(loon.grob$children) UseMethod("move_jitter_grob", obj) } move_jitter_grob.l_plot <- function(loon.grob, index, swap, jitterxy, temporary = FALSE, ...) { if(length(index) == 0) return(loon.grob) args <- list(...) pointsTreeName <- args$pointsTreeName if(pointsTreeName != "points: missing glyphs") { x <- jitterxy$x y <- jitterxy$y newGrob <- grid::getGrob(loon.grob, pointsTreeName) if(!temporary & swap) { lapply(index, function(i) { if(grepl(newGrob$children[[i]]$name,pattern = "primitive_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], y = unit(x[which(index %in% i)], "native"), x = unit(y[which(index %in% i)], "native") ) } else if(grepl(newGrob$children[[i]]$name, pattern = "serialaxes_glyph")) { polyline_grob <- grid::getGrob(newGrob$children[[i]], "polyline") if(is.null(polyline_grob)) { polyline_grob <- grid::getGrob(newGrob$children[[i]], "polyline: showArea") polyline_grob_name <- "polyline: showArea" } else polyline_grob_name <- "polyline" polyline_grob <- grid::editGrob( polyline_grob, y = unit(x[which(index %in% i)], "native") + get_unit(polyline_grob$x, is.unit = FALSE, as.numeric = FALSE), x = unit(y[which(index %in% i)], "native") + get_unit(polyline_grob$y, is.unit = FALSE, as.numeric = FALSE) ) newGrob$children[[i]] <<- grid::setGrob( gTree = newGrob$children[[i]], gPath = polyline_grob_name, newGrob = polyline_grob ) } else if(grepl(newGrob$children[[i]]$name, pattern = "polygon_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], y = unit(x[which(index %in% i)], "native") + get_unit(newGrob$children[[i]]$x, is.unit = FALSE, as.numeric = FALSE), x = unit(y[which(index %in% i)], "native") + get_unit(newGrob$children[[i]]$y, is.unit = FALSE, as.numeric = FALSE) ) } else if(grepl(newGrob$children[[i]]$name, pattern = "pointrange_glyph")) { pointGrob <- grid::getGrob(newGrob$children[[i]], "point") line_grob <- grid::getGrob(newGrob$children[[i]], "range") pointGrob <- grid::editGrob( pointGrob, y = unit(x[which(index %in% i)], "native"), x = unit(y[which(index %in% i)], "native") ) range <- diff(sort(as.numeric(line_grob$x)))/2 line_grob <- grid::editGrob( line_grob, y = unit(rep(x[which(index %in% i)], 2), "native"), x = unit(c(y[which(index %in% i)] - range, y[which(index %in% i)] + range), "native") ) tmpGrob <- grid::setGrob( gTree = newGrob$children[[i]], gPath = "point", newGrob = pointGrob ) newGrob$children[[i]] <<- grid::setGrob( gTree = tmpGrob, gPath = "range", newGrob = line_grob ) } else if(grepl(newGrob$children[[i]]$name, pattern = "text_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], y = unit(x[which(index %in% i)], "native"), x = unit(y[which(index %in% i)], "native") ) } else if(grepl(newGrob$children[[i]]$name, pattern = "image_glyph")) { imageBorderGrob <- grid::getGrob(newGrob$children[[i]], "image_border") imageGrob <- grid::getGrob(newGrob$children[[i]], "image") imageBorderGrob <- grid::editGrob( imageBorderGrob, y = unit(x[which(index %in% i)], "native"), x = unit(y[which(index %in% i)], "native") ) imageGrob <- grid::editGrob( imageGrob, y = unit(x[which(index %in% i)], "native"), x = unit(y[which(index %in% i)], "native") ) tmpGrob <- grid::setGrob( gTree = newGrob$children[[i]], gPath = "image_border", newGrob = imageBorderGrob ) newGrob$children[[i]] <<- grid::setGrob( gTree = tmpGrob, gPath = "image", newGrob = imageGrob ) } else stop("not implemented") } ) } else { lapply(index, function(i) { if(grepl(newGrob$children[[i]]$name, pattern = "primitive_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], x = unit(x[which(index %in% i)], "native"), y = unit(y[which(index %in% i)], "native") ) } else if(grepl(newGrob$children[[i]]$name, pattern = "serialaxes_glyph")) { polyline_grob <- grid::getGrob(newGrob$children[[i]], "polyline") if(is.null(polyline_grob)) { polyline_grob <- grid::getGrob(newGrob$children[[i]], "polyline: showArea") polyline_grob_name <- "polyline: showArea" } else polyline_grob_name <- "polyline" polyline_grob <- grid::editGrob( polyline_grob, x = unit(x[which(index %in% i)], "native") + get_unit(polyline_grob$x, is.unit = FALSE, as.numeric = FALSE), y = unit(y[which(index %in% i)], "native") + get_unit(polyline_grob$y, is.unit = FALSE, as.numeric = FALSE) ) newGrob$children[[i]] <<- grid::setGrob( gTree = newGrob$children[[i]], gPath = polyline_grob_name, newGrob = polyline_grob ) } else if(grepl(newGrob$children[[i]]$name, pattern = "polygon_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], x = unit(x[which(index %in% i)], "native") + get_unit(newGrob$children[[i]]$x, is.unit = FALSE, as.numeric = FALSE), y = unit(y[which(index %in% i)], "native") + get_unit(newGrob$children[[i]]$y, is.unit = FALSE, as.numeric = FALSE) ) } else if(grepl(newGrob$children[[i]]$name, pattern = "pointrange_glyph")) { pointGrob <- grid::getGrob(newGrob$children[[i]], "point") line_grob <- grid::getGrob(newGrob$children[[i]], "range") pointGrob <- grid::editGrob( pointGrob, x = unit(x[which(index %in% i)], "native"), y = unit(y[which(index %in% i)], "native") ) range <- diff(sort(as.numeric(line_grob$y)))/2 line_grob <- grid::editGrob( line_grob, x = unit(rep(x[which(index %in% i)], 2), "native"), y = unit(c(y[which(index %in% i)] - range, y[which(index %in% i)] + range), "native") ) tmpGrob <- grid::setGrob( gTree = newGrob$children[[i]], gPath = "point", newGrob = pointGrob ) newGrob$children[[i]] <<- grid::setGrob( gTree = tmpGrob, gPath = "range", newGrob = line_grob ) } else if(grepl(newGrob$children[[i]]$name, pattern = "text_glyph")) { newGrob$children[[i]] <<- grid::editGrob( grob = newGrob$children[[i]], x = unit(x[which(index %in% i)], "native"), y = unit(y[which(index %in% i)], "native") ) } else if(grepl(newGrob$children[[i]]$name, pattern = "image_glyph")) { imageBorderGrob <- grid::getGrob(newGrob$children[[i]], "image_border") imageGrob <- grid::getGrob(newGrob$children[[i]], "image") imageBorderGrob <- grid::editGrob( imageBorderGrob, x = unit(x[which(index %in% i)], "native"), y = unit(y[which(index %in% i)], "native") ) imageGrob <- grid::editGrob( imageGrob, x = unit(x[which(index %in% i)], "native"), y = unit(y[which(index %in% i)], "native") ) tmpGrob <- grid::setGrob( gTree = newGrob$children[[i]], gPath = "image_border", newGrob = imageBorderGrob ) newGrob$children[[i]] <<- grid::setGrob( gTree = tmpGrob, gPath = "image", newGrob = imageGrob ) } else stop("not implemented") } ) } grid::setGrob( gTree = loon.grob, gPath = pointsTreeName, newGrob = newGrob ) } else loon.grob } move_jitter_grob.l_graph <- function(loon.grob, index, swap, jitterxy, temporary = FALSE, ...) { if(length(index) == 0) return(loon.grob) jx <- jitterxy$x jy <- jitterxy$y nodesGrob <- grid::getGrob(loon.grob, "graph nodes") labelsGrob <- grid::getGrob(loon.grob, "graph labels") edgesGrob <- grid::getGrob(loon.grob, "graph edges") if(!temporary & swap) { lapply(index, function(i) { nodesGrob$children[[i]] <<- grid::editGrob( grob = nodesGrob$children[[i]], x = unit(jy[which(index == i)], "native"), y = unit(jx[which(index == i)], "native") ) } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph nodes", newGrob = nodesGrob ) if(!grepl(grobName(labelsGrob), pattern = "null")) { lapply(index, function(i) { grobi <- labelsGrob$children[[i]] labelsGrob$children[[i]] <<- grid::editGrob( grob = grobi, x = unit(jy[which(index == i)], "native") + get_unit(grobi$y, is.unit = FALSE, as.numeric = FALSE), y = unit(jx[which(index == i)], "native") + get_unit(grobi$x, is.unit = FALSE, as.numeric = FALSE) ) } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph labels", newGrob = labelsGrob ) } lapply(1:length(edgesGrob$children), function(i) { grobi <- edgesGrob$children[[i]] if(!grepl(grobi$name,pattern = "missing")) { to_id <- grobi$id num_line <- length(to_id)/2 edgesGrob$children[[i]] <<- if(i %in% index) { x <- c(rep(jy[which(index == i)], num_line), c(grobi$x)[(num_line + 1) : (2*num_line)]) y <- c(rep(jx[which(index == i)], num_line), c(grobi$y)[(num_line + 1) : (2*num_line)]) change_id <- which(to_id %in% index)[which(to_id %in% index) > num_line] if(length(change_id) > 0) { x[change_id] <- jy[which(index %in% to_id[change_id])] y[change_id] <- jx[which(index %in% to_id[change_id])] grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } else { grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } } else { change_id <- which(to_id %in% index)[which(to_id %in% index) > num_line] x <- c(grobi$x) y <- c(grobi$y) if(length(change_id) > 0) { x[change_id] <- jy[which(index %in% to_id[change_id])] y[change_id] <- jx[which(index %in% to_id[change_id])] grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } else grobi } } } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph edges", newGrob = edgesGrob ) } else { lapply(index, function(i) { nodesGrob$children[[i]] <<- grid::editGrob( grob = nodesGrob$children[[i]], x = unit(jx[which(index == i)], "native"), y = unit(jy[which(index == i)], "native") ) } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph nodes", newGrob = nodesGrob ) if(!grepl(grobName(labelsGrob),pattern = "null")) { lapply(index, function(i) { grobi <- labelsGrob$children[[i]] labelsGrob$children[[i]] <<- grid::editGrob( grob = grobi, y = unit(jy[which(index == i)], "native") + get_unit(grobi$y, is.unit = FALSE, as.numeric = FALSE), x = unit(jx[which(index == i)], "native") + get_unit(grobi$x, is.unit = FALSE, as.numeric = FALSE) ) } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph labels", newGrob = labelsGrob ) } lapply(1:length(edgesGrob$children), function(i) { grobi <- edgesGrob$children[[i]] if(!grepl(grobi$name, pattern = "missing")) { to_id <- grobi$id num_line <- length(to_id)/2 edgesGrob$children[[i]] <<- if(i %in% index) { y <- c(rep(jy[which(index == i)], num_line), c(grobi$y)[(num_line + 1) : (2*num_line)]) x <- c(rep(jx[which(index == i)], num_line), c(grobi$x)[(num_line + 1) : (2*num_line)]) change_id <- which(to_id %in% index)[which(to_id %in% index) > num_line] if(length(change_id) > 0) { x[change_id] <- jx[which(index %in% to_id[change_id])] y[change_id] <- jy[which(index %in% to_id[change_id])] grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } else { grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } } else { change_id <- which(to_id %in% index)[which(to_id %in% index) > num_line] x <- c(grobi$x) y <- c(grobi$y) if(length(change_id) > 0) { x[change_id] <- jx[which(index %in% to_id[change_id])] y[change_id] <- jy[which(index %in% to_id[change_id])] grid::editGrob( grobi, x = unit(x, "native"), y = unit(y, "native") ) } else grobi } } } ) loon.grob <- grid::setGrob( gTree = loon.grob, gPath = "graph edges", newGrob = edgesGrob ) } loon.grob } jitter_coord <- function(x, y, index) { if(length(index) == 1) { jitter_x <- x[index] jitter_y <- y[index] } else { diff_x <- diff(sort(x[index])) diff_y <- diff(sort(y[index])) diff_x <- diff_x[diff_x > 1e-2] diff_y <- diff_y[diff_y > 1e-2] dx <- if(length(diff_x) == 0) 1e-2 else min(diff_x) dy <- if(length(diff_y) == 0) 1e-2 else min(diff_y) jitter_x <- rnorm(length(index), x[index], dx/5) jitter_y <- rnorm(length(index), y[index], dx/5) } list( x = jitter_x, y = jitter_y ) }
library(RagGrid) m = data.frame(a = 1, b = 2, c = 3) aggrid(m) aggrid(as.matrix(m))
library(LearnBayes) data(cancermortality) mycontour(betabinexch0,c(.0001,.003,1,20000),cancermortality, xlab="eta",ylab="K") S=readline(prompt="Type <Return> to continue : ") windows() mycontour(betabinexch,c(-8,-4.5,3,16.5),cancermortality, xlab="logit eta",ylab="log K")
multiverse_engine <- function(options) { if(is.null(options$inside)) stop("A multiverse object should be specified with", "a multiverse code block using the `inside` argument") .multiverse_name = options$inside if (is.character(.multiverse_name)) { if ( !(.multiverse_name %in% ls(envir = knit_global()))) { stop( "Multiverse object `", .multiverse_name, "` was not found.\n", "You may need to execute `", .multiverse_name, " <- multiverse()` to create the multiverse\n", "before executing a multiverse code block." ) } .multiverse = get(.multiverse_name, envir = knit_global()) } else if (is.multiverse(.multiverse_name)) { .multiverse = .multiverse_name } .c = multiverse_block_code(.multiverse, options$label, options$code) if(is.null(getOption("knitr.in.progress"))) { if (!is.null(getOption("execute"))) { if (getOption("execute") == "all") { execute_multiverse(.multiverse) } else if (getOption("execute") == "default") { execute_universe(.multiverse) } } multiverse_default_block_exec(.c, options) } else { multiverse_default_block_exec(options$code, options, TRUE) } } multiverse_block_code <- function(.multiverse, .label, .code) { if (strsplit(.label, "-[0-9]+") == "unnamed-chunk") { stop("Please provide a label to your multiverse code block") } if (!is(.multiverse, "multiverse")) { stop("Objects passed to inside should be a multiverse object") } pasted <- paste(.code, collapse = "\n") .expr <- parse(text = c("{", pasted, "}"), keep.source = FALSE)[[1]] add_and_parse_code(.multiverse, .expr, .label) .m_list = attr(.multiverse, "multiverse")$multiverse_diction$as_list() if ( is.list(parameters(.multiverse)) & length(parameters(.multiverse)) == 0 ) { .c = get_code_universe(.m_list = .m_list, .uni = 1, .level = length(.m_list)) } else { idx = 1 .c = get_code_universe(.m_list = .m_list, .uni = idx, .level = length(.m_list)) } deparse(.c[[.label]]) } multiverse_default_block_exec <- function(.code, options, knit = FALSE) { if (knit && options$eval) { .multiverse = options$inside options$engine = "R" options$comment = "" options$dev = 'png' options_list <- lapply(1:size(.multiverse), function(x) { temp_options <- options temp_options$code = tidy_source(text = map_chr( tail(head(deparse(expand(.multiverse)[[".code"]][[x]][[options$label]]), -1), -1), ~ gsub(pattern = " ", replacement = "", x = .) ))$text.tidy if (x == 1) { temp_options$class.source = paste0("multiverse universe-", x, " default") temp_options$class.output = paste0("multiverse universe-", x, " default") } else { temp_options$class.source = paste0("multiverse universe-", x, "") temp_options$class.output = paste0("multiverse universe-", x, "") } temp_options }) eng_r = knit_engines$get("R") unlist(lapply(options_list, eng_r)) } else { code = .code[-c(1, length(.code))] outputs = evaluate::evaluate( code, new_device = FALSE, envir = knit_global() ) outputs[sapply(outputs, function(x) is.character(x) || is_condition(x))] } } knitr::knit_engines$set(multiverse = multiverse_engine)
test_that("function_to_pmml('1+2') outputs correct xml", { current <- function_to_pmml("1 + 2") node <- newXMLNode(name = "Apply", attrs = c("function" = "+")) c1 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "1") c2 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "2") expected <- addChildren(node, kids = c(c1, c2)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) }) test_that("function_to_pmml('foo(bar(baz))') outputs correct xml", { current <- function_to_pmml("foo(bar(baz))") node <- newXMLNode(name = "Apply", attrs = c("function" = "foo")) c1 <- newXMLNode(name = "Apply", attrs = c("function" = "bar")) c2 <- newXMLNode(name = "FieldRef", attrs = c("field" = "baz")) expected <- addChildren(node, addChildren(c1, c2)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) }) test_that("function_to_pmml('1(2)') throws unexpected end of input error", { expect_error(function_to_pmml("1(2"), regexp = "unexpected end of input") }) test_that("function_to_pmml('-3') outputs correct xml", { current <- function_to_pmml("-3") node <- newXMLNode(name = "Apply", attrs = c("function" = "-")) c1 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "0") c2 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "3") expected <- addChildren(node, kids = c(c1, c2)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) }) test_that("function_to_pmml('-(44*a)') outputs correct xml", { current <- function_to_pmml("-(44*a)") node <- newXMLNode(name = "Apply", attrs = c("function" = "-")) c1 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "0") c1node <- newXMLNode(name = "Apply", attrs = c("function" = "*")) c2 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "44") c3 <- newXMLNode(name = "FieldRef", attrs = c("field" = "a")) addChildren(c1node, kids = c(c2, c3)) expected <- addChildren(node, kids = c(c1, c1node)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) }) test_that("function_to_pmml('-a') outputs correct xml", { current <- function_to_pmml("-a") node <- newXMLNode(name = "Apply", attrs = c("function" = "-")) c1 <- newXMLNode(name = "Constant", attrs = c("dataType" = "double"), text = "0") c2 <- newXMLNode(name = "FieldRef", attrs = c("field" = "a")) expected <- addChildren(node, kids = c(c1, c2)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) }) test_that("function_to_pmml('?3') throws error when ? is * or /", { expect_error(function_to_pmml("*3"), regexp = "<text>:1:1: unexpected '*'") expect_error(function_to_pmml("/3"), regexp = "<text>:1:1: unexpected '/'") }) test_that("function_to_pmml outputs boolean TRUE/FALSE for if function", { current <- function_to_pmml("if(out < t){TRUE} else {FALSE}") c0node <- newXMLNode(name = "Apply", attrs = c("function" = "if")) c1node <- newXMLNode(name = "Apply", attrs = c("function" = "lessThan")) c2 <- newXMLNode(name = "FieldRef", attrs = c("field" = "out")) c3 <- newXMLNode(name = "FieldRef", attrs = c("field" = "t")) addChildren(c1node, kids = c(c2, c3)) c3 <- newXMLNode(name = "Constant", attrs = c("dataType" = "boolean"), text = TRUE) c4 <- newXMLNode(name = "Constant", attrs = c("dataType" = "boolean"), text = FALSE) expected <- addChildren(c0node, kids = c(c1node, c3, c4)) current_split <- strsplit(saveXML(current), split = "")[[1]] expected_split <- strsplit(saveXML(expected), split = "")[[1]] expect_equal(current_split, expected_split) })
sar_mmf <- function(data, start = NULL, grid_start = "partial", grid_n = NULL, normaTest = "none", homoTest = "none", homoCor = "spearman", verb = TRUE){ .Deprecated() if (!(is.matrix(data) | is.data.frame(data))) stop('data must be a matrix or dataframe') if (is.matrix(data)) data <- as.data.frame(data) if (anyNA(data)) stop('NAs present in data') normaTest <- match.arg(normaTest, c('none', 'shapiro', 'kolmo', 'lillie')) homoTest <- match.arg(homoTest, c('none', 'cor.area', 'cor.fitted')) if (homoTest != 'none'){ homoCor <- match.arg(homoCor, c('spearman', 'pearson', 'kendall')) } if (!(grid_start %in% c('none', 'partial', 'exhaustive'))){ stop('grid_start should be one of none, partial or exhaustive') } if (grid_start == 'exhaustive'){ if (!is.numeric(grid_n)) stop('grid_n should be numeric if grid_start == exhaustive') } if (!is.logical(verb)){ stop('verb should be logical') } data <- data[order(data[,1]),] colnames(data) <- c('A','S') xr <- range(data$S)/mean(data$S) if (isTRUE(all.equal(xr[1], xr[2]))) { if (data$S[1] == 0){ warning('All richness values are zero: parameter estimates of', ' non-linear models should be interpreted with caution') } else{ warning('All richness values identical') }} model <- list( name=c("MMF"), formula=expression(S==d/(1+c*A^(-z))), exp=expression(d/(1+c*A^(-z))), shape="convex/sigmoid", asymp=function(pars)pars["d"], parLim = c("Rplus","Rplus","Rplus"), custStart=function(data)c(max(data$S),5,.25), init=function(data){ if(any(data$S==0)){data=data[data$S!=0,]} d=(max(data$S)*4) newVar = log((d/data$S) - 1) reg = stats::lm(newVar~log(data$A)) c=exp(reg$coefficients[1]) z=-reg$coefficients[2] c(d,c,z) } ) model <- compmod(model) fit <- get_fit(model = model, data = data, start = start, grid_start = grid_start, grid_n = grid_n, algo = 'Nelder-Mead', normaTest = normaTest, homoTest = homoTest, homoCor = homoCor, verb = verb) if(is.na(fit$value)){ return(list(value = NA)) }else{ obs <- obs_shape(fit, verb = verb) fit$observed_shape <- obs$fitShape fit$asymptote <- obs$asymp fit$neg_check <- any(fit$calculated < 0) class(fit) <- 'sars' attr(fit, 'type') <- 'fit' return(fit) } }
delay.pert<-function(duration,prec1and2=matrix(0),prec3and4=matrix(0),observed.duration,delta=NULL,cost.function=NULL){ or1<-order(organize(prec1and2,prec3and4)$Order[,2]) or2<-organize(prec1and2,prec3and4)$Order[,2] precedence<-organize(prec1and2,prec3and4)$Precedence duration<-duration[or2] observed.duration<-observed.duration[or2] activities<-1:length(duration) n<-length(activities) SD<-numeric(length(activities)) w<-numeric(2^n-1) tiempo.early<-rep(0,n) ii<-as.logical(colSums(precedence)) iii<-activities[ii] nn<-length(iii) if(nn>0){ prec<-matrix(0,nrow=nn,ncol=n-1) for(j in 1:length(iii)){ prec[j,1:length(which(precedence[,iii[j]]==1))]<-which(precedence[,iii[j]]==1) } prec<-prec[,as.logical(colSums(prec)),drop=FALSE] for(i in 1:length(iii)) { tiempo.early[iii[i]]=max(tiempo.early[prec[i,]]+duration[prec[i,]]); } } tiempo<-max(tiempo.early+duration) if(is.null(delta)==FALSE){tiempo<-delta} if(nn>0){ for(i in 1:nn) { tiempo.early[iii[i]]=max(tiempo.early[prec[i,]]+observed.duration[prec[i,]]); } } tiempo.observado<-max(tiempo.early+observed.duration) { if(is.null(cost.function)==FALSE){ cat("There has been a delay of = ", cost.function(tiempo.observado), "\n") Prop<-((observed.duration-duration)/sum(observed.duration-duration))*(cost.function(tiempo.observado)) TProp<-(pmin(observed.duration-duration,cost.function(tiempo.observado))/sum(pmin(observed.duration-duration,cost.function(tiempo.observado))))*(cost.function(tiempo.observado)) } else{ cat("There has been a delay of = ", tiempo.observado-tiempo, "\n") Prop<-((observed.duration-duration)/sum(observed.duration-duration))*(tiempo.observado-tiempo) TProp<-(pmin(observed.duration-duration,tiempo.observado-tiempo)/sum(pmax(observed.duration-duration,tiempo.observado-tiempo)))*(tiempo.observado-tiempo) } } for(j in 1:length(activities)){ duracion1<-duration duracion1[j]<-observed.duration[j] if(nn>0){ for(i in 1:nn) { tiempo.early[iii[i]]=max(tiempo.early[prec[i,]]+duracion1[prec[i,]]); } } if(is.null(cost.function)==FALSE){w[j]<-cost.function(max(tiempo.early+duracion1))} SD[j]<-max(tiempo.early+duracion1) } { if(length(activities)>10){ cat("shapley need some time to compute a", n, "player game \n") cat("Continue calculation of the Shapley value based on sampling? (Y = Yes, N = No) \n") continue <- scan(what = "character", n = 1) if(continue=="Y"){ contador<-0 sh<-numeric(length(activities)) while(contador<=1000){ x<-sample(length(activities)) for(i in 1:n){ duracion1<-duration duracion1[x[1:i]]<-observed.duration[x[1:i]] if(nn>0){ for(j in 1:nn) { tiempo.early[iii[j]]=max(tiempo.early[prec[j,]]+duracion1[prec[j,]]) } } { if(is.null(cost.function)==FALSE){ tiempo2[i]<-cost.function(max(tiempo.early+duracion1)) } else{ tiempo2[i]<-max(tiempo.early+duracion1)-tiempo } } } sh[x[1]]<-sh[x[1]]+tiempo2[1] sh[x[2:n]]<-sh[x[2:n]]+tiempo2[2:n]-tiempo2[1:(n-1)] contador<-contador+1 } sh<-sh/contador } } else{ v<-numeric(2^n-1) v[1:n]<-SD[1:n] continue<-"Y" p<-n+1 for(j in 2:n){ con<-as.matrix(combn(c(1:n),j)) for(z in 1:dim(con)[2]){ duracion1<-duration duracion1[con[,z]]<-observed.duration[con[,z]] if(nn>0){ for(i in 1:length(iii)) { tiempo.early[iii[i]]=max(tiempo.early[prec[i,]]+duracion1[prec[i,]]) } } if(is.null(cost.function)==FALSE){w[p]<-cost.function(max(tiempo.early+duracion1))} v[p]<-max(tiempo.early+duracion1) p<-p+1 } } v<-v-tiempo { if(is.null(cost.function)==FALSE){ z<-as.matrix(DefineGame(n,w)$Lex) z<-as.vector(z) coalitions <- set.func(c(0, z)) sh <- Shapley.value(coalitions) } else{ z<-as.matrix(DefineGame(n,v)$Lex) z<-as.vector(z) coalitions <- set.func(c(0, z)) sh <- Shapley.value(coalitions) } } } } { if(continue=="Y"){ A<-matrix(c(Prop[or1],TProp[or1],sh[or1]),ncol=length(activities),byrow=TRUE) colnames(A)=c(activities) rownames(A)=c("The proportional payment ","The truncated proportional payment ", "Shapley rule") cat(" ","\n") return(round(A,5)) } else{ A<-matrix(c(Prop[or1],TProp[or1]),ncol=length(activities),byrow=TRUE) colnames(A)=c(activities) rownames(A)=c("The proportional payment ","The truncated proportional payment ") cat(" ","\n") return(round(A,5)) } } }
summary.mvProbitMargEff <- function( object, ... ) { nObs <- nrow( object ) nMargEff <- ncol( object ) result <- matrix( NA, nrow = nObs * nMargEff, ncol = 4 ) if( nObs == 1 ) { rownames( result ) <- colnames( object ) } else { rownames( result ) <- paste( rep( rownames( object ), each = nMargEff ), ": ", rep( colnames( object ), nObs ), sep = "" ) } colnames( result ) <- c( "Estimate", "Std. error", "z value", "Pr(> z)" ) result[ , 1 ] <- c( t( as.matrix( object ) ) ) margEffVCov <- attr( object, "vcov" ) if( !is.null( margEffVCov ) ) { for( i in 1:nObs ) { result[ ( (i-1) * nMargEff + 1 ):( i * nMargEff ), 2 ] <- sqrt( diag( margEffVCov[ i, , ] ) ) } result[ , 3 ] <- result[ , 1 ] / result[ , 2 ] result[ , 4 ] <- 2 * pnorm( -abs( result[ , 3 ] ) ) } class( result ) <- c( "summary.mvProbitMargEff", class( result ) ) return( result ) }
getEurostatRaw <- function(kod = "educ_iste", rowRegExp=NULL, colRegExp=NULL, strip.white = TRUE) { adres <- paste("http://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2F",kod,".tsv.gz",sep="") tfile <- tempfile() download.file(adres, tfile) dat <- read.table(gzfile(tfile), sep="\t", na.strings = ": ", header=FALSE, stringsAsFactors=FALSE, strip.white = strip.white) unlink(tfile) colnames(dat) <- as.character(dat[1,]) dat <- dat[-1,] if (!is.null(rowRegExp)) { dat <- dat[grep(dat[,1], pattern=rowRegExp),,drop=FALSE] } if (!is.null(colRegExp)) { dat <- dat[,union(1, grep(colnames(dat), pattern=colRegExp)),drop=FALSE] } for (i in 2:ncol(dat)) { tmp <- sapply(strsplit(as.character(dat[,i]), split = ' '), `[`, 1) tmp[tmp==":"] = NA dat[,i] <-as.numeric(tmp) } dat }
PipeOpEncodeImpact = R6Class("PipeOpEncodeImpact", inherit = PipeOpTaskPreprocSimple, public = list( initialize = function(id = "encodeimpact", param_vals = list()) { ps = ParamSet$new(params = list( ParamDbl$new("smoothing", 0, Inf, tags = c("train", "required")), ParamLgl$new("impute_zero", tags = c("train", "required")) )) ps$values = list(smoothing = 1e-4, impute_zero = FALSE) super$initialize(id, param_set = ps, param_vals = param_vals, tags = "encode", feature_types = c("factor", "ordered")) } ), private = list( .get_state_dt = function(dt, levels, target) { task_type = if (is.numeric(target)) "regr" else "classif" state = list() smoothing = self$param_set$values$smoothing list(impact = switch(task_type, classif = sapply(dt, function(col) sapply(levels(target), function(tl) { tprop = (sum(target == tl) + smoothing) / (length(target) + 2 * smoothing) tplogit = log(tprop / (1 - tprop)) map_dbl(c(stats::setNames(levels(col), levels(col)), c(.TEMP.MISSING = NA)), function(cl) { if (!self$param_set$values$impute_zero && is.na(cl)) return(NA_real_) condprob = (sum(target[is.na(cl) | col == cl] == tl, na.rm = TRUE) + smoothing) / (sum(is.na(cl) | col == cl, na.rm = TRUE) + 2 * smoothing) cplogit = log(condprob / (1 - condprob)) cplogit - tplogit }) }), simplify = FALSE), regr = { meanimp = mean(target) sapply(dt, function(col) t(t(c(sapply(levels(col), function(lvl) { (sum(target[col == lvl], na.rm = TRUE) + smoothing * meanimp) / (sum(col == lvl, na.rm = TRUE) + smoothing) - meanimp }), if (self$param_set$values$impute_zero) c(.TEMP.MISSING = 0) else c(.TEMP.MISSING = NA)))), simplify = FALSE) })) }, .transform_dt = function(dt, levels) { impact = self$state$impact imap(dt, function(curdat, idx) { curdat = as.character(curdat) curdat[is.na(curdat)] = ".TEMP.MISSING" curdat[curdat %nin% rownames(impact[[idx]])] = ".TEMP.MISSING" impact[[idx]][match(curdat, rownames(impact[[idx]])), , drop = is.null(colnames(impact[[idx]]))] }) } ) ) mlr_pipeops$add("encodeimpact", PipeOpEncodeImpact)
require(graph) require(eulerian) g <- new("graphNEL", nodes=as.character(1:10), edgemode="directed") g <- addEdge(graph=g, from="1", to="10") g <- addEdge(graph=g, from="2", to="1") g <- addEdge(graph=g, from="2", to="6") g <- addEdge(graph=g, from="3", to="2") g <- addEdge(graph=g, from="4", to="2") g <- addEdge(graph=g, from="5", to="4") g <- addEdge(graph=g, from="6", to="5") g <- addEdge(graph=g, from="6", to="8") g <- addEdge(graph=g, from="7", to="9") g <- addEdge(graph=g, from="8", to="7") g <- addEdge(graph=g, from="9", to="6") g <- addEdge(graph=g, from="10", to="3") testNum <- 1 cat("Test-", testNum, ": ", sep="") has <- hasEulerianPath(g) msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianCycle(g) msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- eulerian(g) msg <- ifelse(length(epath)==numEdges(g)+1, "passed", "failed!!!") cat(msg, "\n") cat(" g <- addEdge(graph=g, from="5", to="6") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g) msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "5") msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "6") msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianCycle(g) msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- eulerian(g, "5") msg <- ifelse(length(epath)==numEdges(g)+1, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- tryCatch(eulerian(g, "7"), error = function(e) NA); msg <- ifelse(is.na(epath), "passed", "failed!!!") cat(msg, "\n") cat(" g <- new("graphNEL", nodes=LETTERS[6:1], edgemode="undirected") g <- addEdge(graph=g, from=c("A","B","B","C","D"), to=c("B","C","D","E","E")) cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g) msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "A") msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "B") msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "C") msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g, "F") msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianCycle(g) msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- eulerian(g, "B") msg <- ifelse(length(epath)==numEdges(g)+1 && epath[1]=="B", "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- tryCatch(eulerian(g, "C"), error = function(e) NA); msg <- ifelse(is.na(epath), "passed", "failed!!!") cat(msg, "\n") cat(" g <- new("graphNEL", nodes=LETTERS[1:4], edgemode="undirected") g <- addEdge(graph=g, from=c("A","B","C","D"), to=c("B","A","D","C")) cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g) msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianCycle(g) msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- tryCatch(eulerian(g, "C"), error = function(e) NA); msg <- ifelse(is.na(epath), "passed", "failed!!!") cat(msg, "\n") cat(" g <- new("graphNEL", nodes=LETTERS[1:5], edgemode="undirected") g <- addEdge(graph=g, from=c("A","B","B","C", "C", "D", "C","C"), to=c("B","C","D","E", "C", "E","C","C")) cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianPath(g) msg <- ifelse(has==TRUE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") has <- hasEulerianCycle(g) msg <- ifelse(has==FALSE, "passed", "failed!!!") cat(msg, "\n") cat("Test-", testNum <- testNum + 1, ": ", sep="") epath <- tryCatch(eulerian(g, "B"), error = function(e) NA); msg <- ifelse(length(epath)==numEdges(g)+1 && epath[1]=="B", "passed", "failed!!!") cat(msg, "\n")
"greenhouse_gases"
na.bootstrap <- function(.x, ... ) { na.replace( .x, .na=function(x, ...) sample( na.omit(x), replace=TRUE, ...) ) } na.resample <- na.bootstrap
context("Latexify") test_that("Escaped hash", expect_true(latexify("\\ test_that("Escaped caret", expect_true(latexify("\\^") == "\\textasciicircum{}")) test_that("Escaped underscore", expect_true(latexify("_") == "\\_")) test_that("Escaped backtick", expect_true(latexify("\\`") == "\\textasciigrave{}")) test_that("Escaped tilde", expect_true(latexify("\\~") == "\\textasciitilde{}")) test_that("percent", expect_true(latexify("100%") == "100\\%")) test_that("endash", expect_true(latexify("--") == "\\textendash{}")) test_that("emdash", expect_true(latexify("---") == "\\textemdash{}")) test_that("ellipsis", expect_true(latexify("...") == "\\ldots{}")) test_that("greater", expect_true(latexify(">") == "\\textgreater{}")) test_that("less", expect_true(latexify("<") == "\\textless{}")) test_that("strikethrough", expect_true(latexify("This is ~~text~~!") == "This is \\sout{text}!")) test_that("subscript", expect_true(latexify("See footnote~123~.") == "See footnote\\textsubscript{123}.")) test_that("superscript", expect_true(latexify("See authors^123^.") == "See authors\\textsuperscript{123}.")) test_that("header 1", expect_true(latexify(" test_that("header 2", expect_true(latexify(" test_that("header 3", expect_true(latexify(" test_that("header 4", expect_true(latexify(" test_that("header 5", expect_true(latexify(" test_that("header 6", expect_true(latexify(" test_that("regex specials", expect_true(latexify(".?+()-") == ".?+()-"))
??? Try to find explanation of this -- too messy as is. L9<-40 m<-40 if (m>L9) stop("Not enough data points") lo<-c(0.0001, 0.001, 0.0001, -100, 0.0001, 0.0001) up<-c(1, 100, 100, -0.001, 1, 1) start<-c(b1=0.100, b2=2, b3=2, b4=-3, b5=-0.2, b6=2) y1<-c(0.2, 0.4, 0.8, 1, 1.6, 2, 3, 4, 0.2, 0.4, 0.8, 1, 1.6, 2, 3, 4, 0.2, 0.4, 0.8, 1, 1.6, 2, 3, 4, 0.2, 0.4, 0.8, 1, 1.6, 2, 3, 4, 0.2, 0.4, 0.8, 1, 1.6, 2, 3, 4) y2<-c(0.027, 0.052, 0.09, 0.098, 0.1, 0.099, 0.096, 0.092, 0.024, 0.045, 0.076, 0.081, 0.083, 0.082, 0.08, 0.078, 0.02, 0.038, 0.061, 0.063, 0.065, 0.065, 0.064, 0.064, 0.016, 0.029, 0.043, 0.045, 0.047, 0.047, 0.048, 0.049, 0.011, 0.019, 0.027, 0.028, 0.03, 0.031, 0.033, 0.035) y3<-c(0, 0, 0, 0, 0, 0, 0, 0, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -1, -1, -1, -1, -1, -1, -1, -1, -1.5, -1.5, -1.5, -1.5, -1.5, -1.5, -1.5, -1.5, -2, -2, -2, -2, -2, -2, -2, -2) kandat<-data.frame(y1=y1, y2=y2, y3=y3) formula <- "y 3500 LET I3=0: REM start with computable function 3510 LET Z1=Y(I,1)-Y(I,2)*(b2+b3): REM VDS-ADJUSTED 3515 LET Z2=b4+b5*Z1 3520 IF ABS(Z2)<.00001 THEN 3800: REM AVOID ZERO DIVIDE 3530 LET Z3=Y(I,3)-Y(I,2)*b2-Z2 3540 IF ABS(Z3)<0.00001 THEN 3830 3550 LET Z4=b6*(Y(I,1)-Y(I,2)*(b2+b3)) 3560 LET Z5=Z4/Z3 3565 IF ABS(Z5)>30 THEN 3860: REM AVOID LARGE EXPONENT 3570 LET Z6=EXP(Z5) 3575 LET Z7=1/Z6 3580 LET Z8=(Z6-Z7)/(Z6+Z7) 3590 LET Z9=1-(Y(I,3)-Y(I,2)*b2)/Z2 3600 LET Z0=b1*Z9*Z9*Z8 3610 LET Y(I,5)=Z0: REM SAVE MODEL VALUE 3620 LET R1=(Z0-Y(I,2))*Y(I,4) 3625 LET YEXP=Z0*Y(I,4): REM note scaling 3630 LET Y(I,6)=R1: REM SAVE RESIDUAL 3640 RETURN 3800 PRINT "Vp0 + gamma*(Vds-Id*(Rs+Rd)) near zero =";Z2; 3802 PRINT " data point ";I 3810 PRINT 3812 PRINT 3820 GOTO 3950 3830 PRINT "Denominator of tanh argument near zero = ";Z3; 3832 PRINT " data point ";I 3840 PRINT 3842 PRINT 3850 GOTO 3950 3860 PRINT "Argument of exp() too large = ";Z5;" data point ";I 3870 PRINT 3880 GOTO 3950 3950 LET I3=1: REM cannot compute the residual 3960 RETURN 4000 PRINT "DERIVATIVES NOT DEFINED" 4010 PRINT 4030 STOP 4500 PRINT "Model for small Vds" 4520 PRINT 4530 PRINT "Data","Model","Residual" 4540 PRINT 4550 FOR I=1 TO 40 STEP 8 4560 PRINT Y(I,2),Y(I,5),Y(I,6) 4570 PRINT 4580 NEXT I 4590 PRINT 4600 PRINT 4633 PRINT "number of data points available =";L9 4634 PRINT 4635 INPUT "How many points to use in fit ";M 4636 IF M>L9 THEN 3035 4637 PRINT 4640 LET N=6: REM 3 parameters 4650 RETURN
model_goodness_for_algo_crm <- function(mod, num=1){ actpred <- actual_vs_predicted_crm(mod, num) dif_vals <- apply(actpred, 1, function(x) abs(diff(x)) ) len <- 100 arr <- rep(0, len) for(i in 1:len){ k <- (i-1)/100 arr[i] <- length(which(dif_vals<=k))/length(dif_vals) } x <- seq(0, 1, length.out = (len)) y <- c(arr) auc <- pracma::trapz(x, y) mse <- mean(dif_vals^2) out <- list() out$xy <- cbind(x,y) out$auc <- auc out$mse <- mse return(out) } actual_vs_predicted_crm <- function(mod, num=1, min_item=0, max_item=1){ dat <- mod$data algo_vals <- dat[ ,num] act_prd <- matrix(0, ncol=2, nrow=length(algo_vals)) act_prd[ ,1] <- algo_vals colnames(act_prd) <- c("Actual", "Preds") paras <- mod$param alpha <- paras[num, 1] beta <- paras[num, 2] gamma <- paras[num, 3] min.item <- rep(min_item, dim(dat)[2]) max.item <- rep(max_item, dim(dat)[2]) persons <- EstCRM::EstCRMperson(dat,paras,min.item,max.item) scores <- persons$thetas[ ,2] z_vals <- log(algo_vals/(max_item - algo_vals)) theta <- seq(from = min(scores), to=max(scores), by=0.01) z <- seq(from = -6, to=6, by=0.01) theta_z <- expand.grid(theta, z) colnames(theta_z) <- c("theta", "z") pdf <- alpha*gamma/sqrt(2*pi)*exp(-alpha^2/2*(theta_z[ ,1]-beta-gamma*theta_z[ ,2])^2) pdfdf <- cbind.data.frame(theta_z, pdf) for(i in 1:length(scores)){ ind1 <- which.min(abs(pdfdf[ ,1] - scores[i])) min_val <- pdfdf[ind1, 1] inds <- which(pdfdf[ ,1] == min_val) df2 <- pdfdf[inds, ] val <- df2[which.max(df2[, 3]) ,2] act_prd[i, 2] <- max_item*exp(val)/(1 + exp(val)) } return(act_prd) } model_goodness_crm <- function(mod){ dd <- dim(mod$data)[2] mse <- acc <- matrix(0, ncol=1, nrow=dd) for(i in 1:dd){ oo <- model_goodness_for_algo_crm(mod, num=i) acc[i, 1] <- oo$auc mse[i, 1] <- oo$mse if(i==1){ curves <- matrix(0, ncol= (dd+1), nrow=dim(oo$xy)[1]) curves[ ,1] <- oo$xy[ ,1] } curves[ ,(i+1)] <- oo$xy[ ,2] } colnames(curves) <- c("x", rownames(mod$param)) rownames(acc) <-rownames(mod$param) out <- list() out$goodnessAUC <- acc out$mse <- mse out$curves <- curves return(out) }
"GetCurves" <- function (x, xnewdata, xtfnewdata, tgrid = NULL, ygrid = NULL, frail = NULL, CI = 0.95, PLOT = TRUE, ...) { if(is(x,"anovaDDP")){ estimates = plot.anovaDDP(x, xnewdata, tgrid=tgrid, CI=CI, PLOT=PLOT, ...) }else if(is(x,"spCopulaDDP")){ estimates = plot.spCopulaDDP(x, xnewdata, tgrid=tgrid, CI=CI, PLOT=PLOT, ...) }else if(is(x,"indeptCoxph")){ estimates = plot.indeptCoxph(x, xnewdata, tgrid=tgrid, CI=CI, PLOT=PLOT, ...) }else if(is(x,"spCopulaCoxph")){ estimates = plot.spCopulaCoxph(x, xnewdata, tgrid=tgrid, CI=CI, PLOT=PLOT, ...) }else if(is(x, "survregbayes")){ estimates = plot.survregbayes(x, xnewdata, tgrid=tgrid, frail=frail, CI=CI, PLOT=PLOT, ...) }else if(is(x, "frailtyGAFT")){ estimates = plot.frailtyGAFT(x, xnewdata, xtfnewdata, tgrid=tgrid, frail=frail, CI=CI, PLOT=PLOT, ...) }else if(is(x, "SuperSurvRegBayes")){ estimates = plot.SuperSurvRegBayes(x, xnewdata, tgrid=tgrid, CI=CI, PLOT=PLOT, ...) }else if(is(x, "SpatDensReg")){ estimates = plot.SpatDensReg(x, xnewdata, ygrid=ygrid, CI=CI, PLOT=PLOT, ...) } invisible(estimates) }
cpg.GC <- function(x) { if(class(x)%in% c("cpg","cpg.perm")) { holm.values<-p.adjust(x$results$gc.p.value,"holm") num.holm<-sum(holm.values<.05,na.rm=TRUE) holm.ind<-ifelse(holm.values<.05,TRUE,FALSE) if(sum(is.na(x$results[,3]))>0) { holm.ind[which(is.na(x$results[,3]))]<-FALSE } fdr.method<-x$info$FDR.method if (fdr.method=="qvalue") { if (!requireNamespace("qvalue", quietly = TRUE)) { stop("qvalue needed for this to work. Please install it.", call. = FALSE) } fdr.adj<-tryCatch(qvalue::qvalue(x$results$gc.p.value), error = function(e) NULL) if(is.null(fdr.adj)) { fdr.adj <- tryCatch(qvalue::qvalue(x$results$gc.p.value, pi0.method = "bootstrap"), error = function(e) NULL) if(is.null(fdr.adj)) { fdr.method="BH" }}} if(fdr.method!="qvalue") { fdr.adj<-p.adjust(x$results$gc.p.value,fdr.method) } num.fdr<-sum(fdr.adj<.05,na.rm=TRUE) beta.col<-nrow(x$results) levin<-is.factor(x$indep) n1<-coef(x)[1,1] gcvalue<-median(n1*ifelse(rep(levin,beta.col),x$results[,2],x$results[,2]**2),na.rm=TRUE)/qchisq(.5,n1) gcvalue<-ifelse(gcvalue<1,1,gcvalue) if(levin) { adj.test.stat<-x$results[,2]/gcvalue } else{ adj.test.stat<-sqrt(x$results[,2]**2/gcvalue)*sign(x$results[,2]) } gc.results<-data.frame(x$results[,1],adj.test.stat,x$results$gc.p.value,holm.ind,fdr.adj,stringsAsFactors=FALSE) names(gc.results)<-c("CPG.Labels","GC.Adjusted","Adjust.P.value","Adj.Holm","Adj.FDR") gc.info<-data.frame(num.holm=num.holm,FDR.method=fdr.method,num.fdr=num.fdr,gcvalue=gcvalue,stringsAsFactors=FALSE) gc.ev<-list(gc.results=gc.results,gc.info=gc.info,coefficients=coef(x)) if(class(x) %in% "cpg.perm") { perm.p.gc<-sum(x$gc.permutation.matrix[,1] <= min(gc.results[,3],na.rm=TRUE))/x$perm.p.values$nperm perm.holm.gc<-sum(x$gc.permutation.matrix[,2] >= gc.info[,1])/x$perm.p.values$nperm perm.fdr.gc<-sum(x$gc.permutation.matrix[,3] >= gc.info[,3])/x$perm.p.values$nperm gc.info<-data.frame(gc.info,perm.p.gc,perm.holm.gc,perm.fdr.gc,stringsAsFactors=FALSE) gc.ev<-list(gc.results=gc.results,gc.info=gc.info,coefficients=coef(x)) } class(gc.ev)<-ifelse(class(x)=="cpg","cpg.gc","cpg.perm.gc") gc.ev } }
NULL setMethod("initialize", "Table", function(.Object, ...) { args <- list(...) args <- .emptyDefault(args, .TableSelected, NA_character_) args <- .emptyDefault(args, .TableSearch, "") do.call(callNextMethod, c(list(.Object), args)) }) setValidity2("Table", function(object) { msg <- character(0) msg <- .singleStringError(msg, object, .TableSelected) msg <- .validStringError(msg, object, .TableSearch) if (length(msg)) { return(msg) } TRUE }) setMethod(".refineParameters", "Table", function(x, se) { x <- callNextMethod() if (is.null(x)) { return(NULL) } x }) setMethod(".multiSelectionCommands", "Table", function(x, index) { search <- slot(x, .TableSearch) searchcols <- slot(x, .TableColSearch) sprintf("selected <- rownames(contents)[iSEE::filterDT(contents, global=%s,\n column=%s)]", deparse(search), .deparse_for_viewing(searchcols, indent=2)) }) setMethod(".multiSelectionActive", "Table", function(x) { if (slot(x, .TableSearch)!="" || any(slot(x, .TableColSearch)!="")) { list(Search=slot(x, .TableSearch), ColumnSearch=slot(x, .TableColSearch)) } else { NULL } }) setMethod(".multiSelectionRestricted", "Table", function(x) TRUE) setMethod(".singleSelectionValue", "Table", function(x, contents) { slot(x, .TableSelected) }) setMethod(".defineOutput", "Table", function(x) { tagList( dataTableOutput(.getEncodedName(x)), uiOutput(paste0(.getEncodedName(x), "_", .tableExtraInfo)), hr() ) }) setMethod(".createObservers", "Table", function(x, se, input, session, pObjects, rObjects) { callNextMethod() panel_name <- .getEncodedName(x) .create_table_observers(panel_name, input=input, session=session, pObjects=pObjects, rObjects=rObjects) .createUnprotectedParameterObservers(.getEncodedName(x), .TableHidden, input, pObjects, rObjects, ignoreNULL=FALSE) }) setMethod(".renderOutput", "Table", function(x, se, ..., output, pObjects, rObjects) { .create_table_output(.getEncodedName(x), se=se, output=output, pObjects=pObjects, rObjects=rObjects) callNextMethod() }) setMethod(".generateOutput", "Table", function(x, se, ..., all_memory, all_contents) { .define_table_commands(x, se, all_memory=all_memory, all_contents=all_contents) }) setMethod(".exportOutput", "Table", function(x, se, all_memory, all_contents) { contents <- .generateOutput(x, se, all_memory=all_memory, all_contents=all_contents) newpath <- paste0(.getEncodedName(x), ".csv") write.csv(file=newpath, contents$contents) newpath }) setMethod(".defineDataInterface", "Table", function(x, se, select_info) { hidden <- slot(x, .TableHidden) .addSpecificTour(class(x), .TableHidden, function(tab_name) { data.frame( element=paste0(" intro="Here, we can hide particular columns in the table. This is helpful for hiding uninformative annotations so that we don't have to keep on scrolling left/right to see the interesting bits. Any number of column names can be specified here." ) }) c( callNextMethod(), list( .selectInput.iSEE(x, .TableHidden, choices=hidden, selected=hidden, label="Hidden columns:", multiple=TRUE) ) ) }) setMethod(".hideInterface", "Table", function(x, field) { if (field %in% c(.multiSelectHistory, .selectColRestrict, .selectRowRestrict)) { TRUE } else { callNextMethod() } }) setMethod(".definePanelTour", "Table", function(x) { mdim <- .multiSelectionDimension(x) rbind( callNextMethod(), c(paste0(" ) }) setMethod("updateObject", "Table", function(object, ..., verbose=FALSE) { if (!.is_latest_version(object)) { update.2.1 <- is(try(slot(object, .plotHoverInfo), silent=TRUE), "try-error") object <- callNextMethod() if (update.2.1){ .Deprecated(msg=sprintf("detected outdated '%s' instance, run 'updateObject(<%s>)'", class(object)[1], class(object)[1])) object[[.TableHidden]] <- character(0) } } object })
require("knitr",quietly=TRUE) opts_chunk$set(fig.path="figs/ag2-", fig.align="center", fig.width=7, fig.height=7, comment="") knit_hooks$set(output = function(x, options) { paste('\\begin{Soutput}\n', x, '\\end{Soutput}\n', sep = '') }) options(width=90) par( omi=c(0,0,0,0), mai=c(0.2,0.2,0.2,0.2) ) if(!file.exists("figs")) dir.create("figs") library( munsellinterpol ) par( omi=c(0,0,0,0), mai=c(0.5,0.5,0.1,0.1) ) plot( c(0,100), c(0,10), type='n', xlab='', ylab='', las=1, tcl=0, lab=c(10,8,7), mgp=c(3,0.25,0) ) title( xlab='Y', line=1.5 ) ; title( ylab='Value', line=1.5 ) grid( lty=1 ) ; abline( h=0, v=0 ) V = seq( 0, 10, by=0.125 ) color = unlist( list(ASTM='black',OSA='black',MgO='black',Munsell='red',Priest='blue') ) for( w in names(color) ) lines( YfromV(V,w), V, col=color[w], lty=ifelse(w=='MgO',2,1), lwd=0.75 ) lty = ifelse( names(color)=='MgO', 2, 1 ) legend( "bottomright", names(color), bty='n', lty=lty, lwd=1.5, col=color, inset=0.1 ) par( omi=c(0,0,0,0), mai=c(0.5,1,0.1,0.1) ) Y = seq( 0, 100, by=0.5 ) delta = VfromY(Y,'OSA') - VfromY(Y,'ASTM') plot( range(Y), range(delta), type='n', xlab='', ylab='', las=1, tcl=0, lab=c(10,8,7), mgp=c(3,0.25,0) ) title( xlab='Y', line=1.5 ) ; title( ylab='{OSA Value} - {ASTM Value}', line=3 ) grid( lty=1 ) ; abline( h=0, v=0 ) lines( Y, delta, lwd=0.75 ) Lightness_from_linear <- function( Y ) { ifelse( Y < (24/116)^3, (116/12)^3 * Y, 116*Y^(1/3) - 16 ) } par( omi=c(0,0,0,0), mai=c(0.5,0.75,0.1,0.1) ) Y = (0:100)/100 L = Lightness_from_linear( Y ) plot( range(Y), range(L), type='n', xlab='', ylab='', las=1, tcl=0, lab=c(10,8,7), mgp=c(3,0.25,0) ) title( xlab='Y (luminance factor)', line=1.5 ); title( ylab='Lightness', line=2 ) grid( lty=1 ) ; abline( h=0, v=0 ) lines( Y, L, lwd=0.75 ) V = VfromY( 100 * Y, 'ASTM' ) lines( Y, 10*V, lty=2 ) legend( "bottomright", c("Lightness (CIE)","10*Value (ASTM)"), lty=c(1,2), bty='n', inset=0.1 ) par( omi=c(0,0,0,0), mai=c(0.5,0.75,0.1,0.1) ) quotient = L / V plot( range(Y), range(quotient,na.rm=T), type='n', xlab='', ylab='', las=1, tcl=0, lab=c(10,8,7), mgp=c(3,0.25,0) ) title( xlab='Y (luminance factor)', line=1.5 ) title( ylab='Lightness / Value', line=3 ) grid( lty=1 ) ; abline( h=0, v=0 ) lines( Y, quotient ) knit_hooks$set(output = function(x, options) { x }) toLatex(sessionInfo(), locale=FALSE)
lslxModel$set("public", "initialize", function(model, numeric_variable, ordered_variable, weight_variable, auxiliary_variable, group_variable, reference_group, level_group, nlevel_ordered) { private$initialize_model(model = model) private$initialize_specification() private$initialize_tag( numeric_variable = numeric_variable, ordered_variable = ordered_variable, weight_variable = weight_variable, auxiliary_variable = auxiliary_variable, group_variable = group_variable, reference_group = reference_group, level_group = level_group, nlevel_ordered = nlevel_ordered ) private$organize_specification() private$expand_specification() }) lslxModel$set("private", "initialize_model", function(model) { model <- gsub(pattern = "[[:blank:]]", replacement = "", x = model) model <- gsub(pattern = "\\$|\\?|\\\\|\\^|%|&| replacement = "", x = model) model <- gsub(pattern = ";", replacement = "\n", x = model) model <- gsub(pattern = "\n{2,}", replacement = "\n", x = model) model <- unlist(x = strsplit(x = model, split = "\n"), use.names = FALSE) model <- gsub(pattern = "=~", replacement = ":=>", x = model) model <- gsub(pattern = "~~", replacement = "<=>", x = model) model <- gsub(pattern = "~\\*~", replacement = "\\*=\\*", x = model) model <- ifelse( !grepl(pattern = "\\|=|=\\||\\|~|~\\|", x = model), gsub( pattern = "\\|", replacement = "|=", x = model ), model ) model <- ifelse( !grepl(pattern = "<~|<~:|~>|:~>|<~>|\\|~|~\\|", x = model), gsub( pattern = "~", replacement = "<=", x = model ), model ) self$model <- model }) lslxModel$set("private", "initialize_specification", function() { operator <- c("|=", "=|", "|~", "~|", "*=*", "*~*", "<=:", "<~:", ":=>", ":~>", "<=", "<~", "=>", "~>", "<=>", "<~>") self$specification <- do.call(what = rbind, args = lapply( X = self$model, FUN = function(model_i) { operator_i <- operator[sapply( X = c( "\\|=", "=\\|", "\\|~", "~\\|", "\\*=\\*", "\\*~\\*", "<=:", "<~:", ":=>", ":~>", "<=[^:>]", "<~[^:>]", "[^:<]=>", "[^:<]~>", "<=>", "<~>" ), FUN = function(pattern) { grepl(pattern, model_i) } )] if (length(operator_i) > 0) { model_i_split <- strsplit(x = model_i, split = operator_i, fixed = TRUE)[[1]] if (operator_i %in% c(":=>", ":~>", "=>", "~>", "=|", "~|")) { if (operator_i %in% c(":=>", ":~>", "=>", "~>")) { operator_i <- paste0(rev(gsub( pattern = ">", replacement = "<", x = substring(operator_i, 1:nchar(operator_i), 1:nchar(operator_i)) )), collapse = "") } else { operator_i <- paste0(rev(substring( operator_i, 1:nchar(operator_i), 1:nchar(operator_i) )), collapse = "") } model_i <- c(left = model_i_split[2], operator = operator_i, right = model_i_split[1]) } else { model_i <- c(left = model_i_split[1], operator = operator_i, right = model_i_split[2]) } left_i <- unlist(strsplit(x = model_i[["left"]], split = "\\+"), use.names = FALSE) right_i <- unlist(strsplit(x = model_i[["right"]], split = "\\+"), use.names = FALSE) model_i <- expand.grid( relation = NA_character_, left = left_i, right = right_i, operator = operator_i, KEEP.OUT.ATTRS = FALSE, stringsAsFactors = FALSE ) left_i_split <- strsplit(model_i$left, split = "\\*") right_i_split <- strsplit(model_i$right, split = "\\*") model_i$left <- sapply( left_i_split, FUN = function(i) getElement(i, length(i)) ) model_i$right <- sapply( right_i_split, FUN = function(i) getElement(i, length(i)) ) if (any(model_i$right[model_i$operator %in% c("<=>", "<~>")] == "1") | any(model_i$left[model_i$operator %in% c("<=>", "<~>")] == "1")) { stop( "Intercept term '1' cannot present at any side of expression for covariance specification." ) } if (any(model_i$left[!(model_i$operator %in% c("<=>", "<~>"))] == "1")) { stop("Intercept term '1' cannot present at the arrow side of expression.") } if (any(model_i$right[model_i$operator %in% c("|=", "|~")] == "1") | any(model_i$left[model_i$operator %in% c("|=", "|~")] == "1")) { stop( "Intercept term '1' cannot present at any side of expression for threshold specification." ) } if (any(model_i$right[model_i$operator %in% c("*=*", "*~*")] == "1") | any(model_i$left[model_i$operator %in% c("*=*", "*~*")] == "1")) { stop( "Intercept term '1' cannot present at any side of expression for scale specification." ) } model_i$left_prefix <- sapply( left_i_split, FUN = function(i) { ifelse(length(i) == 1L, NA_character_, i[1]) } ) model_i$right_prefix <- sapply( right_i_split, FUN = function(i) { ifelse(length(i) == 1L, NA_character_, i[1]) } ) if (any(!(is.na(model_i$left_prefix) | is.na(model_i$right_prefix)))) { stop("Prefix before '*' cannot simultaneously present at both side of expression.") } else if (any(!is.na(model_i$left_prefix))) { model_i$prefix <- model_i$left_prefix } else if (any(!is.na(model_i$right_prefix))) { model_i$prefix <- model_i$right_prefix } else { model_i$prefix <- NA_character_ } model_i$left_prefix <- NULL model_i$right_prefix <- NULL model_i$relation <- paste0(model_i$left, ifelse( model_i$operator %in% c("<=:", "<~:", "<=", "<~"), "<-", ifelse(model_i$operator %in% c("<=>", "<~>"), "<->", ifelse(model_i$operator %in% c("|=", "|~"), "|", "**"))), model_i$right) model_i$operator <- ifelse( model_i$right == "1", ifelse( model_i$operator == "<=:", "<=", ifelse(model_i$operator == "<~:", "<~", model_i$operator) ), model_i$operator ) } else { model_i <- data.frame() } return(model_i) } )) if (any(grepl( pattern = "[[:digit:]]", x = substr( x = setdiff(x = unique( c(self$specification$left, self$specification$right) ), y = c("1")), start = 1, stop = 1 ) ))) { stop( "Names of variable(s) or factor(s) cannot start with numbers.", "\n Please check the specified 'model'." ) } }) lslxModel$set("private", "initialize_tag", function(numeric_variable, ordered_variable, weight_variable, auxiliary_variable, group_variable, reference_group, level_group, nlevel_ordered) { self$numeric_variable <- numeric_variable self$ordered_variable <- ordered_variable self$weight_variable <- weight_variable self$auxiliary_variable <- auxiliary_variable self$group_variable <- group_variable self$reference_group <- reference_group self$level_group <- level_group self$name_factor <- unique(self$specification[self$specification$operator %in% c("<=:", "<~:"), "right"]) self$name_response <- setdiff(x = unique(unlist(self$specification[!(self$specification$operator %in% c("|=", "|~")), c("left", "right")])), y = c(self$name_factor, "1")) if (!all(self$name_response %in% union(x = self$numeric_variable, y = self$ordered_variable))) { stop( "Some response variable in 'model' cannot be found in 'data' or 'sample_cov'.", "\n Response variables specified by 'model' are ", do.call(paste, as.list(self$name_response)), ".", "\n Column names of 'data' or 'sample_cov' are ", do.call(paste, as.list(union(x = self$numeric_variable, y = self$ordered_variable))), "." ) } self$numeric_variable <- intersect(x = self$name_response, y = self$numeric_variable) self$ordered_variable <- intersect(x = self$name_response, y = self$ordered_variable) if (length(self$ordered_variable) > 0) { self$nlevel_ordered <- nlevel_ordered[self$ordered_variable] self$name_threshold <- paste0("t", 1:(max(nlevel_ordered) - 1)) } else { self$nlevel_ordered <- numeric(0) self$name_threshold <- character(0) } self$auxiliary_variable <- setdiff(x = self$auxiliary_variable, y = self$name_response) self$name_eta <- c(self$name_response, self$name_factor) self$name_endogenous <- unique(self$specification[(self$specification$operator %in% c("<=:", "<~:", "<=", "<~")) & (self$specification$right != "1"), "left"]) self$name_exogenous <- unique(setdiff(x = self$name_eta, y = self$name_endogenous)) }) lslxModel$set("private", "organize_specification", function() { self$specification <- do.call(what = rbind, args = lapply( split(self$specification, 1:nrow(self$specification)), FUN = function(specification_i) { if ((specification_i[["operator"]] %in% c("<=>", "<~>")) & ( match(specification_i[["left"]], self$name_eta) < match(specification_i[["right"]], self$name_eta) )) { specification_i <- data.frame( relation = paste0(specification_i[["right"]], "<->", specification_i[["left"]]), left = specification_i[["right"]], right = specification_i[["left"]], operator = specification_i[["operator"]], prefix = specification_i[["prefix"]] ) } return(specification_i) } )) self$specification <- self$specification[!duplicated(self$specification$relation, fromLast = TRUE),] if (length(self$ordered_variable) > 0) { relation_gamma <- unlist(mapply( FUN = function(ordered_variable_i, nlevel_ordered_i) { paste0(ordered_variable_i, "|", paste0("t", 1:(nlevel_ordered_i - 1))) }, self$ordered_variable, self$nlevel_ordered), use.names = FALSE) if (!all(self$specification[(self$specification$operator %in% c("|=", "|~")), "relation"] %in% (relation_gamma))) { stop("Some specification for thresholds are not recognized.") } relation_gamma <- setdiff(x = relation_gamma, y = self$specification$relation) } else { relation_gamma <- character(0) } if (length(relation_gamma) > 0) { specification_gamma <- data.frame( relation = relation_gamma, left = substr( relation_gamma, start = 1, stop = regexpr("\\|", relation_gamma) - 1 ), right = substr( relation_gamma, start = regexpr("\\|", relation_gamma) + 1, stop = nchar(relation_gamma) ), operator = "|=", prefix = NA_character_, stringsAsFactors = FALSE ) } else { specification_gamma = data.frame() } if (length(self$ordered_variable) > 0) { relation_psi <- paste0(self$ordered_variable, "**", self$ordered_variable) if (!all(self$specification[(self$specification$operator %in% c("*=*", "*~*")), "relation"] %in% (relation_psi))) { stop("Some specification for scale are not recognized.") } relation_psi <- setdiff(x = relation_psi, y = self$specification$relation) } else { relation_psi <- character(0) } if (length(relation_psi) > 0) { specification_psi <- data.frame( relation = relation_psi, left = substr( relation_psi, start = 1, stop = regexpr("\\*\\*", relation_psi) - 1 ), right = substr( relation_psi, start = regexpr("\\*\\*", relation_psi) + 2, stop = nchar(relation_psi) ), operator = "*=*", prefix = 1, stringsAsFactors = FALSE ) } else { specification_psi = data.frame() } if (any(self$specification$right == "1")) { if (length(intersect(x = self$numeric_variable, y = self$name_exogenous)) > 0) { relation_alpha <- setdiff( x = paste( intersect( x = self$numeric_variable, y = self$name_exogenous ), "1", sep = "<-" ), y = self$specification$relation ) } else { relation_alpha <- character() } } else { if (length(self$numeric_variable) > 0) { relation_alpha <- setdiff( x = paste(self$numeric_variable, "1", sep = "<-"), y = self$specification$relation ) } else { relation_alpha <- character() } } if (length(relation_alpha) > 0) { specification_alpha <- data.frame( relation = relation_alpha, left = substr( relation_alpha, start = 1, stop = regexpr("<-", relation_alpha) - 1 ), right = "1", operator = "<=", prefix = NA_character_, stringsAsFactors = FALSE ) } else { specification_alpha = data.frame() } if (length(self$name_exogenous) > 1) { relation_phi <- setdiff(x = c( paste0(self$name_eta, "<->", self$name_eta), paste0(apply( combn(rev(self$name_exogenous), 2), 2, FUN = function(i) { paste(i[1], i[2], sep = "<->") } )) ), y = self$specification$relation) } else { relation_phi <- setdiff( x = paste0(self$name_eta, "<->", self$name_eta), y = self$specification$relation ) } if (length(relation_phi) > 0) { specification_phi <- data.frame( relation = relation_phi, left = substr( relation_phi, start = 1, stop = regexpr("<->", relation_phi) - 1 ), right = substr( relation_phi, start = regexpr("<->", relation_phi) + 3, stop = nchar(relation_phi) ), operator = "<=>", prefix = NA_character_, stringsAsFactors = FALSE ) } else { specification_phi = data.frame() } self$specification <- rbind( self$specification, specification_gamma, specification_alpha, specification_phi, specification_psi, make.row.names = FALSE, stringsAsFactors = FALSE ) }) lslxModel$set("private", "expand_specification", function() { prefix_split <- lapply(X = self$specification$prefix, FUN = function(prefix_i) { if (!is.na(prefix_i)) { if ((substr(prefix_i, start = 1, stop = 2) == "c(") & (substr(prefix_i, start = nchar(prefix_i), stop = nchar(prefix_i)) == ")")) { prefix_i <- substr(prefix_i, start = 3, stop = (nchar(prefix_i) - 1)) prefix_i_split <- character(0) while (nchar(prefix_i) > 0) { idx_left_bracket <- regexpr("\\(", prefix_i)[1] idx_right_bracket <- regexpr("\\)", prefix_i)[1] idx_comma <- regexpr(",", prefix_i)[1] if (idx_comma == -1) { prefix_i_split <- c(prefix_i_split, prefix_i) prefix_i <- "" } else { if ((idx_left_bracket == -1) & (idx_right_bracket == -1)) { prefix_i_split <- c(prefix_i_split, strsplit(prefix_i, ",")[[1]]) prefix_i <- "" } else { if ((idx_left_bracket < idx_comma) & (idx_right_bracket > idx_comma)) { prefix_i_split <- c(prefix_i_split, substr(prefix_i, start = 1, stop = idx_right_bracket)) if (idx_right_bracket < nchar(prefix_i)) { prefix_i <- substr(prefix_i, start = (idx_right_bracket + 2), stop = nchar(prefix_i)) } else { prefix_i <- "" } } else { prefix_i_split <- c(prefix_i_split, substr(prefix_i, start = 1, stop = (idx_comma - 1))) prefix_i <- substr(prefix_i, start = (idx_comma + 1), stop = nchar(prefix_i)) } } } } } else { prefix_i_split <- prefix_i } } else { prefix_i_split <- prefix_i } prefix_i_split <- ifelse(gsub(pattern = "\\(.*$", replacement = "", x = prefix_i_split) %in% c("free", "fix", "pen", "start", "lab"), prefix_i_split, ifelse(is.na(prefix_i_split), prefix_i_split, ifelse(prefix_i_split == "NA", NA, ifelse(suppressWarnings(!is.na(as.numeric(prefix_i_split))), paste0("fix", "(", prefix_i_split, ")"), paste0("lab", "(", prefix_i_split, ")"))))) return(prefix_i_split) }) if (anyNA(self$reference_group)) { if (any(sapply(X = prefix_split, FUN = function(prefix_split_i) { return(length(prefix_split_i) > 1) }))) { stop("When 'reference_group = NA', vectorized prefix cannot be used.") } if (length(self$ordered_variable) > 0) { stop("When 'reference_group = NA', response variable cannot be ordered.") } self$specification <- do.call(what = rbind, args = lapply( X = c("<NA>", self$level_group), FUN = function(level_group_i) { specification_i <- self$specification specification_i$group <- level_group_i specification_i$reference <- ifelse(level_group_i == "<NA>", TRUE, FALSE) specification_i$operator <- ifelse(specification_i$group == "<NA>", specification_i$operator, gsub(pattern = "=", replacement = "~", x = specification_i$operator)) specification_i$prefix <- sapply( X = prefix_split, FUN = function(prefix_split_j) { prefix_split_j_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix_split_j) if (prefix_split_j_verb %in% "pen") { prefix_split_j <- eval(parse(text = prefix_split_j)) } if (level_group_i != "<NA>") { if (prefix_split_j_verb %in% "fix") { prefix_split_j <- "fix(0)" } else { prefix_split_j <- NA } } return(prefix_split_j) } ) rownames(specification_i) <- paste0(specification_i$relation, "/", specification_i$group) return(specification_i) } )) } else { if (any(sapply(X = prefix_split, FUN = function(prefix_split_i) { return((length(prefix_split_i) > 1) & (length(prefix_split_i) != length(self$level_group))) }))) { stop("The length of prefix vector should be 1 or equal to to the number of groups.") } self$specification <- do.call(what = rbind, args = lapply( X = self$level_group, FUN = function(level_group_i) { specification_i <- self$specification specification_i$group <- level_group_i specification_i$reference <- ifelse( is.null(self$reference_group), FALSE, ifelse(level_group_i == self$reference_group, TRUE, FALSE) ) specification_i$prefix <- sapply( X = prefix_split, FUN = function(prefix_split_j) { if (length(prefix_split_j) == 1) { prefix_split_j_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix_split_j) if (prefix_split_j_verb %in% "pen") { prefix_split_j <- eval(parse(text = prefix_split_j)) } if (!is.null(self$reference_group)) { if (level_group_i != self$reference_group) { if (prefix_split_j_verb %in% c("free", "fix", "start")) { prefix_split_j <- paste0(prefix_split_j_verb, "(", 0, ")") } else if (prefix_split_j_verb %in% "pen") { prefix_split_j <- paste0(substr(prefix_split_j, start = 1, stop = regexpr("=", prefix_split_j)[1]), 0, substr(prefix_split_j, start = regexpr(",", prefix_split_j)[1], stop = nchar(prefix_split_j))) } else if (prefix_split_j_verb %in% c("lab")) { prefix_split_j <- "fix(0)" } else { prefix_split_j <- NA } } } } else { prefix_split_j <- prefix_split_j[level_group_i == self$level_group] prefix_split_j_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix_split_j) if (prefix_split_j_verb %in% "pen") { prefix_split_j <- eval(parse(text = prefix_split_j)) } } return(prefix_split_j) } ) rownames(specification_i) <- paste0(specification_i$relation, "/", specification_i$group) return(specification_i) } )) } self$specification$matrix <- factor( x = ifelse( self$specification$operator %in% c("|=", "|~"), "gamma", ifelse(self$specification$operator %in% c("*=*", "*~*"), "psi", ifelse( self$specification$operator %in% c("<=>", "<~>"), "phi", ifelse(self$specification$right == "1", "alpha", "beta") ))), levels = c("gamma", "alpha", "beta", "phi", "psi") ) self$specification$block <- with(self$specification, { block_left <- ifelse(left %in% self$name_response, "y", "f") block_right <- ifelse(matrix %in% "gamma", "t", ifelse( right %in% self$name_response, "y", ifelse( right %in% self$name_factor, "f", "1" ) )) block_middle <- ifelse(matrix %in% "gamma", "|", ifelse(matrix %in% "psi", "**", ifelse(matrix %in% c("alpha", "beta"), "<-", "<->"))) paste0(block_left, block_middle, block_right) }) self$specification$type <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) type <- ifelse(prefix_verb %in% "free", "free", ifelse(prefix_verb %in% "fix", "fixed", ifelse(prefix_verb %in% "pen", "pen", ifelse( operator %in% c("|=", "*=*", "<=:", "<=", "<=>"), "free", "pen")))) return(type) }) self$specification$type <- ifelse(self$specification$relation %in% c(paste0(self$ordered_variable, "<->", self$ordered_variable)), "fixed", self$specification$type) self$specification$start <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) prefix_value <- ifelse(prefix_verb %in% c("free", "fix", "start"), substr(x = prefix, start = (regexpr("\\(", prefix) + 1), stop = (nchar(prefix) - 1)), ifelse(prefix_verb %in% "pen", sapply(X = strsplit(prefix, split = "=|,|\\(|\\)"), FUN = function(x) { x[3]}, simplify = TRUE, USE.NAMES = FALSE), NA_real_)) start <- ifelse(prefix_verb %in% c("free", "fix", "pen", "start"), suppressWarnings(as.numeric(prefix_value)), NA_real_) return(start) }) self$specification$start <- ifelse(self$specification$relation %in% paste0(self$ordered_variable, "<->", self$ordered_variable), NA_real_, self$specification$start) self$specification$label <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) label <- ifelse(prefix_verb %in% "lab", substr(x = prefix, start = (regexpr("\\(", prefix) + 1), stop = (nchar(prefix) - 1)), NA_character_) return(label) }) self$specification$penalty <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) penalty <- ifelse(prefix_verb %in% "pen", sapply(X = strsplit(prefix, split = "=|,|\\(|\\)"), FUN = function(x) { x[5]}, simplify = TRUE, USE.NAMES = FALSE), ifelse(type == "pen", "default", "none")) return(penalty) }) self$specification$set <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) set <- ifelse(prefix_verb %in% "pen", sapply(X = strsplit(prefix, split = "=|,|\\(|\\)"), FUN = function(x) { as.numeric(x[7])}, simplify = TRUE, USE.NAMES = FALSE), ifelse(type == "pen", 1, 0)) return(set) }) self$specification$weight <- with(self$specification, { prefix_verb <- gsub(pattern = "\\(.*$", replacement = "", x = prefix) weight <- ifelse(prefix_verb %in% "pen", sapply(X = strsplit(prefix, split = "=|,|\\(|\\)"), FUN = function(x) { x[9]}, simplify = TRUE, USE.NAMES = FALSE), ifelse(type == "pen", 1, 0)) return(as.numeric(weight)) }) self$specification$operator <- NULL self$specification$prefix <- NULL if (length(self$ordered_variable) > 0) { specification_gamma <- self$specification[self$specification$matrix == "gamma", ] specification_non_gamma <- self$specification[self$specification$matrix != "gamma", ] specification_gamma <- specification_gamma[order( specification_gamma$reference, specification_gamma$group, specification_gamma$matrix, specification_gamma$block, match(specification_gamma$left, self$name_eta), match(specification_gamma$right, c("1", self$name_threshold, self$name_eta)), method = "radix" ),] specification_non_gamma <- specification_non_gamma[order( specification_non_gamma$reference, specification_non_gamma$group, specification_non_gamma$matrix, specification_non_gamma$block, match(specification_non_gamma$right, c("1", self$name_threshold, self$name_eta)), match(specification_non_gamma$left, self$name_eta), method = "radix" ),] self$specification <- rbind(specification_gamma, specification_non_gamma) self$specification <- self$specification[order( self$specification$reference, self$specification$group, self$specification$matrix, self$specification$block, method = "radix" ),] } else { self$specification <- self$specification[order( self$specification$reference, self$specification$group, self$specification$matrix, self$specification$block, match(self$specification$right, c("1", self$name_threshold, self$name_eta)), match(self$specification$left, self$name_eta), method = "radix" ),] } self$specification <- self$specification[order( self$specification$reference, decreasing = TRUE, method = "radix" ), ] })
loopboot <- function(j=NULL,pred.x,pred.y,xresid,yresid,ti,obs,n,m,extended.classical,cbb,joint,period){ if (is.numeric(cbb)==TRUE) { index <- sample(1:(obs+3),3,replace=FALSE) xresid2 <- c(xresid,xresid) yresid2 <- c(xresid,xresid) k <- obs/cbb xblocks <- sample(1:(obs+3),k,replace=TRUE) if (joint==FALSE) yblocks <- sample(1:(obs+3),k,replace=TRUE) else yblocks <- xblocks xressamp <- c(t(outer(xblocks,0:(cbb-1),FUN="+"))) yressamp <- c(t(outer(yblocks,0:(cbb-1),FUN="+"))) y<-yresid2[yressamp]+pred.y[-index] x<-xresid2[xressamp]+pred.x[-index] } else { index <- sample(1:(obs+3),3,replace=FALSE) if (joint==FALSE) { y<-sample(yresid,obs,replace=T)+pred.y[-index] x<-sample(xresid,obs,replace=T)+pred.x[-index] } else { resid.sampler <- sample(1:(obs+3),obs,replace=TRUE) y<-yresid[resid.sampler]+pred.y[-index] x<-xresid[resid.sampler]+pred.x[-index] } } Ta.lm<-lm.fit(cbind(rep(1,obs),sin(ti[-index]),cos(ti[-index])),x) b.x<-sqrt(coef(Ta.lm)[[2]]^2+coef(Ta.lm)[[3]]^2) phase.angle<- atan2(coef(Ta.lm)[[3]],coef(Ta.lm)[[2]])-pi/2 rad<-ti[-index]+phase.angle cx<-coef(Ta.lm)[[1]] if (extended.classical==FALSE) { Tb.lm<-lm.fit(cbind(rep(1,obs),sin(rad)^m,cos(rad)^n),y)} else { direc <- sign(cos(rad)) Tb.lm<-lm.fit(cbind(rep(1,obs),sin(rad)^m,direc*abs(cos(rad))^n),y)} b.y<-coef(Tb.lm)[[3]] retention<- coef(Tb.lm)[[2]] cy<-coef(Tb.lm)[[1]] if (n==1) beta.split.angle<-atan2(b.y,b.x)*180/pi else if (n >= 2) beta.split.angle <- 0 else beta.split.angle<-NA hysteresis.x <- 1/sqrt(1+(b.y/retention)^(2/m)) coercion <- hysteresis.x*b.x hysteresis.y <- retention/b.y lag<-abs(atan2(retention,b.y))*period/(pi*2) area <- (0.5/(beta((m+3)/2,(m+3)/2)*(m+2))+1/beta((m+1)/2,(m+1)/2)-1/beta((m+3)/2,(m-1)/2))/(2^m)*pi*abs(retention*b.x) z <- c("n"=n, "m"=m,"b.x"=b.x,"b.y"=b.y,"phase.angle"=as.vector(phase.angle),"cx"=cx,"cy"=cy,"retention"=retention, "coercion"=coercion,"area"=area,"lag"=lag, "beta.split.angle"=beta.split.angle,"hysteresis.x"=hysteresis.x, "hysteresis.y"=hysteresis.y) z }
hzeta.control <- function(save.weights = TRUE, ...) { list(save.weights = save.weights) } hzeta <- function(lshape = "logloglink", ishape = NULL, nsimEIM = 100) { stopifnot(ishape > 0) stopifnot(nsimEIM > 10, length(nsimEIM) == 1, nsimEIM == round(nsimEIM)) lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Haight's Zeta distribution f(y) = (2y-1)^(-shape) - ", "(2y+1)^(-shape),\n", " shape>0, y = 1, 2,....\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: (1-2^(-shape)) * zeta(shape) if shape>1", "\n", "Variance: (1-2^(1-shape)) * zeta(shape-1) - mean^2 if shape>2"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = FALSE, multipleResponses = FALSE, parameters.names = c("shape"), lshape = .lshape , nsimEIM = .nsimEIM ) }, list( .nsimEIM = nsimEIM, .lshape = lshape ))), initialize = eval(substitute(expression({ w.y.check(w = w, y = y, Is.integer.y = TRUE, Is.positive.y = TRUE) predictors.names <- namesof("shape", .lshape , earg = .eshape , tag = FALSE) if (!length(etastart)) { a.init <- if (length( .ishape)) .ishape else { if ((meany <- weighted.mean(y, w)) < 1.5) 3.0 else if (meany < 2.5) 1.4 else 1.1 } a.init <- rep_len(a.init, n) etastart <- theta2eta(a.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) mu <- (1-2^(-shape)) * zeta(shape) mu[shape <= 1] <- Inf mu }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$link <- c(shape = .lshape) misc$earg <- list(shape = .eshape ) misc$nsimEIM <- .nsimEIM }), list( .lshape = lshape, .eshape = eshape, .nsimEIM = nsimEIM ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dhzeta(x = y, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("hzeta"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) shape <- eta2theta(eta, .lshape , earg = .eshape ) rhzeta(nsim * length(shape), shape = shape) }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) d3 <- deriv3(~ log((2*y-1)^(-shape) - (2*y+1)^(-shape)), "shape", hessian = FALSE) eval.d3 <- eval(d3) dl.dshape <- attr(eval.d3, "gradient") c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = eval(substitute(expression({ sd3 <- deriv3(~ log((2*ysim-1)^(-shape) - (2*ysim+1)^(-shape)), "shape", hessian = FALSE) run.var <- 0 for (ii in 1:( .nsimEIM )) { ysim <- rhzeta(n, shape = shape) eval.sd3 <- eval(sd3) dl.dshape <- attr(eval.d3, "gradient") rm(ysim) temp3 <- dl.dshape run.var <- ((ii-1) * run.var + temp3^2) / ii } wz <- if (intercept.only) matrix(colMeans(cbind(run.var)), n, dimm(M), byrow = TRUE) else cbind(run.var) wz <- wz * dshape.deta^2 c(w) * wz }), list( .nsimEIM = nsimEIM )))) } dhzeta <- function(x, shape, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) if (!is.Numeric(shape, positive = TRUE)) stop("'shape' must be numeric and have positive values") nn <- max(length(x), length(shape)) if (length(x) != nn) x <- rep_len(x, nn) if (length(shape) != nn) shape <- rep_len(shape, nn) ox <- !is.finite(x) zero <- ox | round(x) != x | x < 1 ans <- rep_len(0, nn) ans[!zero] <- (2*x[!zero]-1)^(-shape[!zero]) - (2*x[!zero]+1)^(-shape[!zero]) if (log.arg) log(ans) else ans } phzeta <- function(q, shape, log.p = FALSE) { nn <- max(length(q), length(shape)) q <- rep_len(q, nn) shape <- rep_len(shape, nn) oq <- !is.finite(q) zero <- oq | q < 1 q <- floor(q) ans <- 0 * q ans[!zero] <- 1 - (2*q[!zero]+1)^(-shape[!zero]) ans[q == -Inf] <- 0 ans[q == Inf] <- 1 ans[shape <= 0] <- NaN if (log.p) log(ans) else ans } qhzeta <- function(p, shape) { if (!is.Numeric(p, positive = TRUE) || any(p >= 1)) stop("argument 'p' must have values inside the interval (0,1)") nn <- max(length(p), length(shape)) p <- rep_len(p, nn) shape <- rep_len(shape, nn) ans <- (((1 - p)^(-1/shape) - 1) / 2) ans[shape <= 0] <- NaN floor(ans + 1) } rhzeta <- function(n, shape) { use.n <- if ((length.n <- length(n)) > 1) length.n else if (!is.Numeric(n, integer.valued = TRUE, length.arg = 1, positive = TRUE)) stop("bad input for argument 'n'") else n shape <- rep_len(shape, use.n) ans <- (runif(use.n)^(-1/shape) - 1) / 2 ans[shape <= 0] <- NaN floor(ans + 1) } dkumar <- function(x, shape1, shape2, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) N <- max(length(x), length(shape1), length(shape2)) if (length(x) != N) x <- rep_len(x, N) if (length(shape1) != N) shape1 <- rep_len(shape1, N) if (length(shape2) != N) shape2 <- rep_len(shape2, N) logdensity <- rep_len(log(0), N) xok <- (0 <= x & x <= 1) logdensity[xok] <- log(shape1[xok]) + log(shape2[xok]) + (shape1[xok] - 1) * log(x[xok]) + (shape2[xok] - 1) * log1p(-x[xok]^shape1[xok]) logdensity[shape1 <= 0] <- NaN logdensity[shape2 <= 0] <- NaN if (log.arg) logdensity else exp(logdensity) } rkumar <- function(n, shape1, shape2) { ans <- (1 - (runif(n))^(1/shape2))^(1/shape1) ans[(shape1 <= 0) | (shape2 <= 0)] <- NaN ans } qkumar <- function(p, shape1, shape2, lower.tail = TRUE, log.p = FALSE) { if (!is.logical(lower.tail) || length(lower.tail) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (lower.tail) { if (log.p) { ln.p <- p ans <- (-expm1((1/shape2) * log(-expm1(ln.p))))^(1/shape1) ans[ln.p > 0] <- NaN } else { ans <- (-expm1((1/shape2) * log1p(-p)))^(1/shape1) ans[p < 0] <- NaN ans[p == 0] <- 0 ans[p == 1] <- 1 ans[p > 1] <- NaN } } else { if (log.p) { ln.p <- p ans <- (-expm1(ln.p / shape2))^(1/shape1) ans[ln.p > 0] <- NaN ans } else { ans <- (-expm1((1/shape2) * log(p)))^(1/shape1) ans[p < 0] <- NaN ans[p == 0] <- 1 ans[p == 1] <- 0 ans[p > 1] <- NaN } } ans[(shape1 <= 0) | (shape2 <= 0)] = NaN ans } pkumar <- function(q, shape1, shape2, lower.tail = TRUE, log.p = FALSE) { if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (lower.tail) { if (log.p) { ans <- log(-expm1(shape2 * log1p(-q^shape1))) ans[q <= 0 ] <- -Inf ans[q >= 1] <- 0 } else { ans <- -expm1(shape2 * log1p(-q^shape1)) ans[q <= 0] <- 0 ans[q >= 1] <- 1 } } else { if (log.p) { ans <- shape2 * log1p(-q^shape1) ans[q <= 0] <- 0 ans[q >= 1] <- -Inf } else { ans <- exp(shape2 * log1p(-q^shape1)) ans[q <= 0] <- 1 ans[q >= 1] <- 0 } } ans[(shape1 <= 0) | (shape2 <= 0)] <- NaN ans } kumar <- function(lshape1 = "loglink", lshape2 = "loglink", ishape1 = NULL, ishape2 = NULL, gshape1 = exp(2*ppoints(5) - 1), tol12 = 1.0e-4, zero = NULL) { lshape1 <- as.list(substitute(lshape1)) eshape1 <- link2list(lshape1) lshape1 <- attr(eshape1, "function.name") lshape2 <- as.list(substitute(lshape2)) eshape2 <- link2list(lshape2) lshape2 <- attr(eshape2, "function.name") if (length(ishape1) && (!is.Numeric(ishape1, length.arg = 1, positive = TRUE))) stop("bad input for argument 'ishape1'") if (length(ishape2) && !is.Numeric(ishape2)) stop("bad input for argument 'ishape2'") if (!is.Numeric(tol12, length.arg = 1, positive = TRUE)) stop("bad input for argument 'tol12'") if (!is.Numeric(gshape1, positive = TRUE)) stop("bad input for argument 'gshape1'") new("vglmff", blurb = c("Kumaraswamy distribution\n\n", "Links: ", namesof("shape1", lshape1, eshape1, tag = FALSE), ", ", namesof("shape2", lshape2, eshape2, tag = FALSE), "\n", "Mean: shape2 * beta(1 + 1 / shape1, shape2)"), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = TRUE, multipleResponses = TRUE, parameters.names = c("shape1", "shape2"), lshape1 = .lshape1 , lshape2 = .lshape2 , zero = .zero ) }, list( .zero = zero, .lshape1 = lshape1, .lshape2 = lshape2 ))), initialize = eval(substitute(expression({ checklist <- w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = Inf, ncol.y.max = Inf, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- checklist$w y <- checklist$y if (any((y <= 0) | (y >= 1))) stop("the response must be in (0, 1)") extra$ncoly <- ncoly <- ncol(y) extra$M1 <- M1 <- 2 M <- M1 * ncoly mynames1 <- param.names("shape1", ncoly, skip1 = TRUE) mynames2 <- param.names("shape2", ncoly, skip1 = TRUE) predictors.names <- c(namesof(mynames1, .lshape1 , earg = .eshape1 , tag = FALSE), namesof(mynames2, .lshape2 , earg = .eshape2 , tag = FALSE))[ interleave.VGAM(M, M1 = M1)] if (!length(etastart)) { kumar.Loglikfun <- function(shape1, y, x, w, extraargs) { mediany <- colSums(y * w) / colSums(w) shape2 <- log(0.5) / log1p(-(mediany^shape1)) sum(c(w) * dkumar(y, shape1 = shape1, shape2 = shape2, log = TRUE)) } shape1.grid <- as.vector( .gshape1 ) shape1.init <- if (length( .ishape1 )) .ishape1 else grid.search(shape1.grid, objfun = kumar.Loglikfun, y = y, x = x, w = w) shape1.init <- matrix(shape1.init, n, ncoly, byrow = TRUE) mediany <- colSums(y * w) / colSums(w) shape2.init <- if (length( .ishape2 )) .ishape2 else log(0.5) / log1p(-(mediany^shape1.init)) shape2.init <- matrix(shape2.init, n, ncoly, byrow = TRUE) etastart <- cbind(theta2eta(shape1.init, .lshape1 , earg = .eshape1 ), theta2eta(shape2.init, .lshape2 , earg = .eshape2 ))[, interleave.VGAM(M, M1 = M1)] } }), list( .lshape1 = lshape1, .lshape2 = lshape2, .ishape1 = ishape1, .ishape2 = ishape2, .eshape1 = eshape1, .eshape2 = eshape2, .gshape1 = gshape1 ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape1 <- eta2theta(eta[, c(TRUE, FALSE)], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE)], .lshape2 , earg = .eshape2 ) shape2 * (base::beta(1 + 1/shape1, shape2)) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), last = eval(substitute(expression({ misc$link <- c(rep_len( .lshape1 , ncoly), rep_len( .lshape2 , ncoly))[interleave.VGAM(M, M1 = M1)] temp.names <- c(mynames1, mynames2)[interleave.VGAM(M, M1 = M1)] names(misc$link) <- temp.names misc$earg <- vector("list", M) names(misc$earg) <- temp.names for (ii in 1:ncoly) { misc$earg[[M1*ii-1]] <- .eshape1 misc$earg[[M1*ii ]] <- .eshape2 } }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape1 <- eta2theta(eta[, c(TRUE, FALSE)], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE)], .lshape2 , earg = .eshape2 ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dkumar(x = y, shape1, shape2, log = TRUE) if (summation) sum(ll.elts) else ll.elts } }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), vfamily = c("kumar"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape1 <- eta2theta(eta[, c(TRUE, FALSE)], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE)], .lshape2 , earg = .eshape2 ) okay1 <- all(is.finite(shape1)) && all(0 < shape1) && all(is.finite(shape2)) && all(0 < shape2) okay1 }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), simslot = eval(substitute( function(object, nsim) { eta <- predict(object) shape1 <- eta2theta(eta[, c(TRUE, FALSE)], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE)], .lshape2 , earg = .eshape2 ) rkumar(nsim * length(shape1), shape1 = shape1, shape2 = shape2) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), deriv = eval(substitute(expression({ shape1 <- eta2theta(eta[, c(TRUE, FALSE)], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE)], .lshape2 , earg = .eshape2 ) dshape1.deta <- dtheta.deta(shape1, link = .lshape1 , earg = .eshape1 ) dshape2.deta <- dtheta.deta(shape2, link = .lshape2 , earg = .eshape2 ) dl.dshape1 <- 1 / shape1 + log(y) - (shape2 - 1) * log(y) * (y^shape1) / (1 - y^shape1) dl.dshape2 <- 1 / shape2 + log1p(-y^shape1) dl.deta <- c(w) * cbind(dl.dshape1 * dshape1.deta, dl.dshape2 * dshape2.deta) dl.deta[, interleave.VGAM(M, M1 = M1)] }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), weight = eval(substitute(expression({ ned2l.dshape11 <- (1 + (shape2 / (shape2 - 2)) * ((digamma(shape2) - digamma(2))^2 - (trigamma(shape2) - trigamma(2)))) / shape1^2 ned2l.dshape22 <- 1 / shape2^2 ned2l.dshape12 <- (digamma(2) - digamma(1 + shape2)) / ((shape2 - 1) * shape1) index1 <- (abs(shape2 - 1) < .tol12 ) ned2l.dshape12[index1] <- -trigamma(2) / shape1[index1] index2 <- (abs(shape2 - 2) < .tol12 ) ned2l.dshape11[index2] <- (1 - 2 * psigamma(2, deriv = 2)) / shape1[index2]^2 wz <- array(c(c(w) * ned2l.dshape11 * dshape1.deta^2, c(w) * ned2l.dshape22 * dshape2.deta^2, c(w) * ned2l.dshape12 * dshape1.deta * dshape2.deta), dim = c(n, M / M1, 3)) wz <- arwz2wz(wz, M = M, M1 = M1) wz }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2, .tol12 = tol12 )))) } drice <- function(x, sigma, vee, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) N <- max(length(x), length(vee), length(sigma)) if (length(x) != N) x <- rep_len(x, N) if (length(vee) != N) vee <- rep_len(vee , N) if (length(sigma ) != N) sigma <- rep_len(sigma , N) logdensity <- rep_len(log(0), N) xok <- (x > 0) x.abs <- abs(x[xok] * vee[xok] / sigma[xok]^2) logdensity[xok] <- log(x[xok]) - 2 * log(sigma[xok]) + (-(x[xok]^2+vee[xok]^2)/(2*sigma[xok]^2)) + log(besselI(x.abs, nu = 0, expon.scaled = TRUE)) + x.abs logdensity[sigma <= 0] <- NaN logdensity[vee < 0] <- NaN logdensity[is.infinite(x)] <- -Inf if (log.arg) logdensity else exp(logdensity) } rrice <- function(n, sigma, vee) { theta <- 1 X <- rnorm(n, mean = vee * cos(theta), sd = sigma) Y <- rnorm(n, mean = vee * sin(theta), sd = sigma) sqrt(X^2 + Y^2) } marcumQ <- function(a, b, m = 1, lower.tail = TRUE, log.p = FALSE, ... ) { pchisq(b^2, df = 2*m, ncp = a^2, lower.tail = lower.tail, log.p = log.p, ... ) } price <- function(q, sigma, vee, lower.tail = TRUE, log.p = FALSE, ...) { ans <- marcumQ(vee/sigma, q/sigma, m = 1, lower.tail = lower.tail, log.p = log.p, ... ) ans } qrice <- function(p, sigma, vee, lower.tail = TRUE, log.p = FALSE, ... ) { sqrt(qchisq(p, df = 2, ncp = (vee/sigma)^2, lower.tail = lower.tail, log.p = log.p, ... )) * sigma } riceff.control <- function(save.weights = TRUE, ...) { list(save.weights = save.weights) } riceff <- function(lsigma = "loglink", lvee = "loglink", isigma = NULL, ivee = NULL, nsimEIM = 100, zero = NULL, nowarning = FALSE) { lvee <- as.list(substitute(lvee)) evee <- link2list(lvee) lvee <- attr(evee, "function.name") lsigma <- as.list(substitute(lsigma)) esigma <- link2list(lsigma) lsigma <- attr(esigma, "function.name") if (length(ivee) && !is.Numeric(ivee, positive = TRUE)) stop("bad input for argument 'ivee'") if (length(isigma) && !is.Numeric(isigma, positive = TRUE)) stop("bad input for argument 'isigma'") if (!is.Numeric(nsimEIM, length.arg = 1, integer.valued = TRUE) || nsimEIM <= 50) stop("'nsimEIM' should be an integer greater than 50") new("vglmff", blurb = c("Rice distribution\n\n", "Links: ", namesof("sigma", lsigma, earg = esigma, tag = FALSE), ", ", namesof("vee", lvee, earg = evee, tag = FALSE), "\n", "Mean: ", "sigma*sqrt(pi/2)*exp(z/2)*((1-z)*", "besselI(-z/2, nu = 0) - z * besselI(-z/2, nu = 1)) ", "where z=-vee^2/(2*sigma^2)"), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = FALSE, multipleResponses = FALSE, parameters.names = c("sigma", "vee"), nsimEIM = .nsimEIM, lsigma = .lsigma , lvee = .lvee , zero = .zero ) }, list( .zero = zero, .lsigma = lsigma, .lvee = lvee, .nsimEIM = nsimEIM ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = 1, ncol.y.max = 1, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y predictors.names <- c(namesof("sigma", .lsigma , earg = .esigma , tag = FALSE), namesof("vee", .lvee , earg = .evee , tag = FALSE)) if (!length(etastart)) { riceff.Loglikfun <- function(vee, y, x, w, extraargs) { sigma.init <- sd(rep(y, w)) sum(c(w) * (log(y) - 2*log(sigma.init) + log(besselI(y*vee/sigma.init^2, nu = 0)) - (y^2 + vee^2) / (2*sigma.init^2))) } vee.grid <- seq(quantile(rep(y, w), probs = seq(0, 1, 0.2))["20%"], quantile(rep(y, w), probs = seq(0, 1, 0.2))["80%"], len = 11) vee.init <- if (length( .ivee )) .ivee else grid.search(vee.grid, objfun = riceff.Loglikfun, y = y, x = x, w = w) vee.init <- rep_len(vee.init, length(y)) sigma.init <- if (length( .isigma )) .isigma else sqrt(max((weighted.mean(y^2, w) - vee.init^2)/2, 0.001)) sigma.init <- rep_len(sigma.init, length(y)) etastart <- cbind(theta2eta(sigma.init, .lsigma , earg = .esigma ), theta2eta(vee.init, .lvee , earg = .evee )) } }), list( .lvee = lvee, .lsigma = lsigma, .ivee = ivee, .isigma = isigma, .evee = evee, .esigma = esigma ))), linkinv = eval(substitute(function(eta, extra = NULL) { vee <- eta2theta(eta[, 1], link = .lvee , earg = .evee ) sigma <- eta2theta(eta[, 2], link = .lsigma , earg = .esigma ) temp9 <- -vee^2 / (2*sigma^2) sigma * sqrt(pi/2) * ((1-temp9) * besselI(-temp9/2, nu = 0, expon = TRUE) - temp9 * besselI(-temp9/2, nu = 1, expon = TRUE)) }, list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma ))), last = eval(substitute(expression({ misc$link <- c("sigma" = .lsigma , "vee" = .lvee ) misc$earg <- list("sigma" = .esigma , "vee" = .evee ) misc$expected <- TRUE misc$nsimEIM <- .nsimEIM misc$multipleResponses <- FALSE }), list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma, .nsimEIM = nsimEIM ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { sigma <- eta2theta(eta[, 1], link = .lsigma , earg = .esigma ) vee <- eta2theta(eta[, 2], link = .lvee , earg = .evee ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * drice(x = y, sigma = sigma, vee = vee, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma ))), vfamily = c("riceff"), validparams = eval(substitute(function(eta, y, extra = NULL) { sigma <- eta2theta(eta[, 1], link = .lsigma , earg = .esigma ) vee <- eta2theta(eta[, 2], link = .lvee , earg = .evee ) okay1 <- all(is.finite(sigma)) && all(0 < sigma) && all(is.finite(vee )) && all(0 < vee ) okay1 }, list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) sigma <- eta2theta(eta[, 1], link = .lsigma , earg = .esigma ) vee <- eta2theta(eta[, 2], link = .lvee , earg = .evee ) rrice(nsim * length(vee), vee = vee, sigma = sigma) }, list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma ))), deriv = eval(substitute(expression({ sigma <- eta2theta(eta[, 1], link = .lsigma , earg = .esigma ) vee <- eta2theta(eta[, 2], link = .lvee , earg = .evee ) dvee.deta <- dtheta.deta(vee, link = .lvee , earg = .evee ) dsigma.deta <- dtheta.deta(sigma, link = .lsigma , earg = .esigma ) temp8 <- y * vee / sigma^2 dl.dvee <- -vee/sigma^2 + (y/sigma^2) * besselI(temp8, nu = 1) / besselI(temp8, nu = 0) dl.dsigma <- -2/sigma + (y^2 + vee^2)/(sigma^3) - (2 * temp8 / sigma) * besselI(temp8, nu = 1) / besselI(temp8, nu = 0) c(w) * cbind(dl.dsigma * dsigma.deta, dl.dvee * dvee.deta) }), list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma, .nsimEIM = nsimEIM ))), weight = eval(substitute(expression({ run.var <- run.cov <- 0 for (ii in 1:( .nsimEIM )) { ysim <- rrice(n, vee = vee, sigma = sigma) temp8 <- ysim * vee / sigma^2 dl.dvee <- -vee/sigma^2 + (ysim/sigma^2) * besselI(temp8, nu = 1) / besselI(temp8, nu = 0) dl.dsigma <- -2/sigma + (ysim^2 + vee^2)/(sigma^3) - (2 * temp8 / sigma) * besselI(temp8, nu = 1) / besselI(temp8, nu = 0) rm(ysim) temp3 <- cbind(dl.dsigma, dl.dvee) run.var <- ((ii-1) * run.var + temp3^2) / ii run.cov <- ((ii-1) * run.cov + temp3[, 1] * temp3[, 2]) / ii } wz <- if (intercept.only) matrix(colMeans(cbind(run.var, run.cov)), n, dimm(M), byrow = TRUE) else cbind(run.var, run.cov) dtheta.detas <- cbind(dsigma.deta, dvee.deta) index0 <- iam(NA_real_, NA_real_, M = M, both = TRUE, diag = TRUE) wz <- wz * dtheta.detas[, index0$row] * dtheta.detas[, index0$col] c(w) * wz }), list( .lvee = lvee, .lsigma = lsigma, .evee = evee, .esigma = esigma, .nsimEIM = nsimEIM )))) } dskellam <- function(x, mu1, mu2, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) L <- max(length(x), length(mu1), length(mu2)) if (length(x) != L) x <- rep_len(x, L) if (length(mu1) != L) mu1 <- rep_len(mu1, L) if (length(mu2) != L) mu2 <- rep_len(mu2, L) ok2 <- is.finite(mu1) & is.finite(mu2) & (mu1 >= 0) & (mu2 >= 0) ok3 <- (mu1 == 0) & (mu2 > 0) ok4 <- (mu1 > 0) & (mu2 == 0) ok5 <- (mu1 == 0) & (mu2 == 0) if (log.arg) { ans <- -mu1 - mu2 + 2 * sqrt(mu1*mu2) + 0.5 * x * log(mu1) - 0.5 * x * log(mu2) + log(besselI(2 * sqrt(mu1*mu2), nu = abs(x), expon.scaled = TRUE)) ans[ok3] <- dpois(x = -x[ok3], lambda = mu2[ok3], log = TRUE) ans[ok4] <- dpois(x = -x[ok4], lambda = mu1[ok4], log = TRUE) ans[ok5] <- dpois(x = x[ok5], lambda = 0.0, log = TRUE) ans[x != round(x)] = log(0.0) } else { ans <- (mu1/mu2)^(x/2) * exp(-mu1-mu2 + 2 * sqrt(mu1*mu2)) * besselI(2 * sqrt(mu1*mu2), nu = abs(x), expon.scaled = TRUE) ans[ok3] <- dpois(x = -x[ok3], lambda = mu2[ok3]) ans[ok4] <- dpois(x = -x[ok4], lambda = mu1[ok4]) ans[ok5] <- dpois(x = x[ok5], lambda = 0.0) ans[x != round(x)] <- 0.0 } ans[!ok2] <- NaN ans } rskellam <- function(n, mu1, mu2) { rpois(n, mu1) - rpois(n, mu2) } skellam.control <- function(save.weights = TRUE, ...) { list(save.weights = save.weights) } skellam <- function(lmu1 = "loglink", lmu2 = "loglink", imu1 = NULL, imu2 = NULL, nsimEIM = 100, parallel = FALSE, zero = NULL) { lmu1 <- as.list(substitute(lmu1)) emu1 <- link2list(lmu1) lmu1 <- attr(emu1, "function.name") lmu2 <- as.list(substitute(lmu2)) emu2 <- link2list(lmu2) lmu2 <- attr(emu2, "function.name") if (length(imu1) && !is.Numeric(imu1, positive = TRUE)) stop("bad input for argument 'imu1'") if (length(imu2) && !is.Numeric(imu2, positive = TRUE)) stop("bad input for argument 'imu2'") if (!is.Numeric(nsimEIM, length.arg = 1, integer.valued = TRUE) || nsimEIM <= 50) stop("argument 'nsimEIM' should be an integer greater than 50") new("vglmff", blurb = c("Skellam distribution\n\n", "Links: ", namesof("mu1", lmu1, earg = emu1, tag = FALSE), ", ", namesof("mu2", lmu2, earg = emu2, tag = FALSE), "\n", "Mean: mu1-mu2", "\n", "Variance: mu1+mu2"), constraints = eval(substitute(expression({ constraints <- cm.VGAM(matrix(1, M, 1), x = x, bool = .parallel , constraints = constraints, apply.int = TRUE) constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .parallel = parallel, .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = FALSE, multipleResponses = FALSE, parameters.names = c("mu1", "mu2"), nsimEIM = .nsimEIM, lmu1 = .lmu1 , lmu2 = .lmu2 , zero = .zero ) }, list( .zero = zero, .lmu1 = lmu1, .lmu2 = lmu2, .nsimEIM = nsimEIM ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, ncol.w.max = 1, ncol.y.max = 1, Is.integer.y = TRUE, out.wy = TRUE, maximize = TRUE) w <- temp5$w y <- temp5$y predictors.names <- c( namesof("mu1", .lmu1, earg = .emu1, tag = FALSE), namesof("mu2", .lmu2, earg = .emu2, tag = FALSE)) if (!length(etastart)) { junk <- lm.wfit(x = x, y = c(y), w = c(w)) var.y.est <- sum(c(w) * junk$resid^2) / junk$df.residual mean.init <- weighted.mean(y, w) mu1.init <- max((var.y.est + mean.init) / 2, 0.01) mu2.init <- max((var.y.est - mean.init) / 2, 0.01) mu1.init <- rep_len(if (length( .imu1 )) .imu1 else mu1.init, n) mu2.init <- rep_len(if (length( .imu2 )) .imu2 else mu2.init, n) etastart <- cbind(theta2eta(mu1.init, .lmu1, earg = .emu1 ), theta2eta(mu2.init, .lmu2, earg = .emu2 )) } }), list( .lmu1 = lmu1, .lmu2 = lmu2, .imu1 = imu1, .imu2 = imu2, .emu1 = emu1, .emu2 = emu2 ))), linkinv = eval(substitute(function(eta, extra = NULL) { mu1 <- eta2theta(eta[, 1], link = .lmu1, earg = .emu1 ) mu2 <- eta2theta(eta[, 2], link = .lmu2, earg = .emu2 ) mu1 - mu2 }, list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2 ))), last = eval(substitute(expression({ misc$link <- c("mu1" = .lmu1, "mu2" = .lmu2) misc$earg <- list("mu1" = .emu1, "mu2" = .emu2 ) misc$expected <- TRUE misc$nsimEIM <- .nsimEIM }), list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2, .nsimEIM = nsimEIM ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { mu1 <- eta2theta(eta[, 1], link = .lmu1, earg = .emu1 ) mu2 <- eta2theta(eta[, 2], link = .lmu2, earg = .emu2 ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- if ( is.logical( .parallel ) && length( .parallel ) == 1 && .parallel ) c(w) * log(besselI(2*mu1, nu = y, expon = TRUE)) else c(w) * (-mu1 - mu2 + 0.5 * y * log(mu1) - 0.5 * y * log(mu2) + 2 * sqrt(mu1*mu2) + log(besselI(2 * sqrt(mu1*mu2), nu = y, expon = TRUE))) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2, .parallel = parallel ))), vfamily = c("skellam"), validparams = eval(substitute(function(eta, y, extra = NULL) { mu1 <- eta2theta(eta[, 1], link = .lmu1, earg = .emu1 ) mu2 <- eta2theta(eta[, 2], link = .lmu2, earg = .emu2 ) okay1 <- all(is.finite(mu1)) && all(0 < mu1) && all(is.finite(mu2)) && all(0 < mu2) okay1 }, list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2 ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) mu1 <- eta2theta(eta[, 1], link = .lmu1, earg = .emu1 ) mu2 <- eta2theta(eta[, 2], link = .lmu2, earg = .emu2 ) rskellam(nsim * length(mu1), mu1, mu2) }, list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2, .parallel = parallel ))), deriv = eval(substitute(expression({ mu1 <- eta2theta(eta[, 1], link = .lmu1, earg = .emu1 ) mu2 <- eta2theta(eta[, 2], link = .lmu2, earg = .emu2 ) dmu1.deta <- dtheta.deta(mu1, link = .lmu1, earg = .emu1 ) dmu2.deta <- dtheta.deta(mu2, link = .lmu2, earg = .emu2 ) temp8 <- 2 * sqrt(mu1*mu2) temp9 <- besselI(temp8, nu = y , expon = TRUE) temp7 <- (besselI(temp8, nu = y-1, expon = TRUE) + besselI(temp8, nu = y+1, expon = TRUE)) / 2 temp6 <- temp7 / temp9 dl.dmu1 <- -1 + 0.5 * y / mu1 + sqrt(mu2/mu1) * temp6 dl.dmu2 <- -1 - 0.5 * y / mu2 + sqrt(mu1/mu2) * temp6 c(w) * cbind(dl.dmu1 * dmu1.deta, dl.dmu2 * dmu2.deta) }), list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2, .nsimEIM = nsimEIM ))), weight = eval(substitute(expression({ run.var <- run.cov <- 0 for (ii in 1:( .nsimEIM )) { ysim <- rskellam(n, mu1=mu1, mu2=mu2) temp9 <- besselI(temp8, nu = ysim, expon = TRUE) temp7 <- (besselI(temp8, nu = ysim-1, expon = TRUE) + besselI(temp8, nu = ysim+1, expon = TRUE)) / 2 temp6 <- temp7 / temp9 dl.dmu1 <- -1 + 0.5 * ysim/mu1 + sqrt(mu2/mu1) * temp6 dl.dmu2 <- -1 - 0.5 * ysim/mu2 + sqrt(mu1/mu2) * temp6 rm(ysim) temp3 <- cbind(dl.dmu1, dl.dmu2) run.var <- ((ii-1) * run.var + temp3^2) / ii run.cov <- ((ii-1) * run.cov + temp3[, 1] * temp3[, 2]) / ii } wz <- if (intercept.only) matrix(colMeans(cbind(run.var, run.cov)), n, dimm(M), byrow = TRUE) else cbind(run.var, run.cov) dtheta.detas <- cbind(dmu1.deta, dmu2.deta) index0 <- iam(NA_real_, NA_real_, M = M, both = TRUE, diag = TRUE) wz <- wz * dtheta.detas[, index0$row] * dtheta.detas[, index0$col] c(w) * wz }), list( .lmu1 = lmu1, .lmu2 = lmu2, .emu1 = emu1, .emu2 = emu2, .nsimEIM = nsimEIM )))) } dyules <- function(x, shape, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) LLL <- max(length(x), length(shape)) if (length(x) != LLL) x <- rep_len(x, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) bad0 <- !is.finite(shape) | shape <= 0 bad <- bad0 | !is.finite(x) | x < 1 | x != round(x) logpdf <- x + shape if (any(!bad)) { logpdf[!bad] <- log(shape[!bad]) + lbeta(x[!bad], shape[!bad] + 1) } logpdf[!bad0 & is.infinite(x)] <- log(0) logpdf[!bad0 & x < 1 ] <- log(0) logpdf[!bad0 & x != round(x) ] <- log(0) logpdf[ bad0] <- NaN if (log.arg) logpdf else exp(logpdf) } pyules <- function(q, shape, lower.tail = TRUE, log.p = FALSE) { tq <- trunc(q) if (lower.tail) { ans <- 1 - tq * beta(abs(tq), shape+1) ans[q < 1] <- 0 ans[is.infinite(q) & 0 < q] <- 1 } else { ans <- tq * beta(abs(tq), shape+1) ans[q < 1] <- 1 ans[is.infinite(q) & 0 < q] <- 0 } ans[shape <= 0] <- NaN if (log.p) log(ans) else ans ans } qyules <- function(p, shape) { LLL <- max(length(p), length(shape)) if (length(p) != LLL) p <- rep_len(p, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) ans <- p + shape bad0 <- !is.finite(shape) | shape <= 0 bad <- bad0 | !is.finite(p) | p <= 0 | 1 <= p lo <- rep_len(1, LLL) - 0.5 approx.ans <- lo hi <- 2 * lo + 10.5 dont.iterate <- bad done <- dont.iterate | p <= pyules(hi, shape) iter <- 0 max.iter <- round(log2(.Machine$double.xmax)) - 2 max.iter <- round(log2(1e300)) - 2 while (!all(done) && iter < max.iter) { lo[!done] <- hi[!done] hi[!done] <- 2 * hi[!done] + 10.5 done[!done] <- (p[!done] <= pyules(hi[!done], shape = shape[!done])) iter <- iter + 1 } foo <- function(q, shape, p) pyules(q, shape) - p lhs <- dont.iterate | (p <= dyules(1, shape)) approx.ans[!lhs] <- bisection.basic(foo, lo[!lhs], hi[!lhs], tol = 1/16, shape = shape[!lhs], p = p[!lhs]) faa <- floor(approx.ans[!lhs]) tmp <- ifelse(pyules(faa, shape = shape[!lhs]) < p[!lhs] & p[!lhs] <= pyules(faa+1, shape = shape[!lhs]), faa+1, faa) ans[!lhs] <- tmp vecTF <- !bad0 & !is.na(p) & p <= dyules(1, shape) ans[vecTF] <- 1 ans[!bad0 & !is.na(p) & p == 0] <- 1 ans[!bad0 & !is.na(p) & p == 1] <- Inf ans[!bad0 & !is.na(p) & p < 0] <- NaN ans[!bad0 & !is.na(p) & p > 1] <- NaN ans[ bad0] <- NaN ans } ryules <- function(n, shape) { rgeom(n, prob = exp(-rexp(n, rate = shape))) + 1 } yulesimon.control <- function(save.weights = TRUE, ...) { list(save.weights = save.weights) } yulesimon <- function(lshape = "loglink", ishape = NULL, nsimEIM = 200, zero = NULL) { if (length(ishape) && !is.Numeric(ishape, positive = TRUE)) stop("argument 'ishape' must be > 0") lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") if (!is.Numeric(nsimEIM, length.arg = 1, integer.valued = TRUE) || nsimEIM <= 50) stop("argument 'nsimEIM' should be an integer greater than 50") new("vglmff", blurb = c("Yule-Simon distribution ", "f(y) = shape * beta(y, shape + 1), ", "shape > 0, y = 1, 2,..\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: shape / (shape - 1), provided shape > 1\n", "Variance: shape^2 / ((shape - 1)^2 * (shape - 2)), ", "provided shape > 2"), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 1) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, multipleResponses = TRUE, nsimEIM = .nsimEIM , parameters.names = c("shape"), zero = .zero ) }, list( .zero = zero, .nsimEIM = nsimEIM ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = Inf, ncol.y.max = Inf, Is.integer.y = TRUE, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y ncoly <- ncol(y) M1 <- 1 extra$ncoly <- ncoly extra$M1 <- M1 M <- M1 * ncoly mynames1 <- param.names("shape", ncoly, skip1 = TRUE) predictors.names <- namesof(mynames1, .lshape , earg = .eshape , tag = FALSE) if (!length(etastart)) { wmeany <- colSums(y * w) / colSums(w) + 1/8 shape.init <- wmeany / (wmeany - 1) shape.init <- matrix(if (length( .ishape )) .ishape else shape.init, n, M, byrow = TRUE) etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape ))), linkinv = eval(substitute(function(eta, extra = NULL) { ans <- shape <- eta2theta(eta, .lshape , earg = .eshape ) ans[shape > 1] <- shape / (shape - 1) ans[shape <= 1] <- NA ans }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ M1 <- extra$M1 misc$link <- c(rep_len( .lshape , ncoly)) names(misc$link) <- mynames1 misc$earg <- vector("list", M) names(misc$earg) <- mynames1 for (ii in 1:ncoly) { misc$earg[[ii]] <- .eshape } misc$M1 <- M1 misc$ishape <- .ishape misc$nsimEIM <- .nsimEIM }), list( .lshape = lshape, .eshape = eshape, .nsimEIM = nsimEIM, .ishape = ishape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dyules(x = y, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("yulesimon"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) shape <- eta2theta(eta, .lshape , earg = .eshape ) ryules(nsim * length(shape), shape = shape) }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ M1 <- 1 shape <- eta2theta(eta, .lshape , earg = .eshape ) dl.dshape <- 1/shape + digamma(1+shape) - digamma(1+shape+y) dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = eval(substitute(expression({ run.var <- 0 for (ii in 1:( .nsimEIM )) { ysim <- ryules(n, shape <- shape) dl.dshape <- 1/shape + digamma(1+shape) - digamma(1+shape+ysim) rm(ysim) temp3 <- dl.dshape run.var <- ((ii-1) * run.var + temp3^2) / ii } wz <- if (intercept.only) matrix(colMeans(cbind(run.var)), n, M, byrow = TRUE) else cbind(run.var) wz <- wz * dshape.deta^2 c(w) * wz }), list( .nsimEIM = nsimEIM )))) } dlind <- function(x, theta, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) if ( log.arg ) { ans <- 2 * log(theta) + log1p(x) - theta * x - log1p(theta) ans[x < 0 | is.infinite(x)] <- log(0) } else { ans <- theta^2 * (1 + x) * exp(-theta * x) / (1 + theta) ans[x < 0 | is.infinite(x)] <- 0 } ans[theta <= 0] <- NaN ans } plind <- function(q, theta, lower.tail = TRUE, log.p = FALSE) { if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (lower.tail) { if (log.p) { ans <- log(-expm1(-theta * q + log1p(q / (1 + 1/theta)))) ans[q <= 0 ] <- -Inf ans[q == Inf] <- 0 } else { ans <- -expm1(-theta * q + log1p(q / (1 + 1/theta))) ans[q <= 0] <- 0 ans[q == Inf] <- 1 } } else { if (log.p) { ans <- -theta * q + log1p(q / (1 + 1/theta)) ans[q <= 0] <- 0 ans[q == Inf] <- -Inf } else { ans <- exp(-theta * q + log1p(q / (1 + 1/theta))) ans[q <= 0] <- 1 ans[q == Inf] <- 0 } } ans[theta <= 0] <- NaN ans } rlind <- function(n, theta) { use.n <- if ((length.n <- length(n)) > 1) length.n else if (!is.Numeric(n, integer.valued = TRUE, length.arg = 1, positive = TRUE)) stop("bad input for argument 'n'") else n ifelse(runif(use.n) < rep_len(1 / (1 + 1/theta), use.n), rexp(use.n, theta), rgamma(use.n, shape = 2, scale = 1 / theta)) } lindley <- function(link = "loglink", itheta = NULL, zero = NULL) { if (length(itheta) && !is.Numeric(itheta, positive = TRUE)) stop("argument 'itheta' must be > 0") link <- as.list(substitute(link)) earg <- link2list(link) link <- attr(earg, "function.name") new("vglmff", blurb = c("Lindley distribution f(y) = ", "theta^2 * (1 + y) * exp(-theta * y) / (1 + theta), ", "theta > 0, y > 0,\n\n", "Link: ", namesof("theta", link, earg = earg), "\n\n", "Mean: (theta + 2) / (theta * (theta + 1))\n", "Variance: (theta^2 + 4 * theta + 2) / (theta * (theta + 1))^2"), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 1) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, hadof = TRUE, multipleResponses = TRUE, parameters.names = c("theta"), zero = .zero ) }, list( .zero = zero ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = Inf, ncol.y.max = Inf, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y ncoly <- ncol(y) M1 <- 1 extra$ncoly <- ncoly extra$M1 <- M1 M <- M1 * ncoly mynames1 <- param.names("theta", ncoly, skip1 = TRUE) predictors.names <- namesof(mynames1, .link , earg = .earg , tag = FALSE) if (!length(etastart)) { wmeany <- colSums(y * w) / colSums(w) + 1/8 theta.init <- 1 / (wmeany + 1) theta.init <- matrix(if (length( .itheta )) .itheta else theta.init, n, M, byrow = TRUE) etastart <- theta2eta(theta.init, .link , earg = .earg ) } }), list( .link = link, .earg = earg, .itheta = itheta ))), linkinv = eval(substitute(function(eta, extra = NULL) { theta <- eta2theta(eta, .link , earg = .earg ) (theta + 2) / (theta * (theta + 1)) }, list( .link = link, .earg = earg ))), last = eval(substitute(expression({ M1 <- extra$M1 misc$link <- c(rep_len( .link , ncoly)) names(misc$link) <- mynames1 misc$earg <- vector("list", M) names(misc$earg) <- mynames1 for (ii in 1:ncoly) { misc$earg[[ii]] <- .earg } misc$M1 <- M1 misc$itheta <- .itheta }), list( .link = link, .earg = earg, .itheta = itheta ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { theta <- eta2theta(eta, .link , earg = .earg ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dlind(x = y, theta = theta, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .link = link, .earg = earg ))), vfamily = c("lindley"), hadof = eval(substitute( function(eta, extra = list(), deriv = 1, linpred.index = 1, w = 1, dim.wz = c(NROW(eta), NCOL(eta) * (NCOL(eta)+1)/2), ...) { theta <- eta2theta(eta, .link , earg = .earg ) numer <- theta^2 + 4 * theta + 2 denom <- (theta * (1 + theta))^2 ans <- c(w) * switch(as.character(deriv), "0" = numer / denom, "1" = (2 * theta + 4 - numer * 2 * theta * (1 + theta) * (1 + 2 * theta) / denom) / denom, "2" = NA * theta, "3" = NA * theta, stop("argument 'deriv' must be 0, 1, 2 or 3")) if (deriv == 0) ans else retain.col(ans, linpred.index) }, list( .link = link, .earg = earg ))), validparams = eval(substitute(function(eta, y, extra = NULL) { theta <- eta2theta(eta, .link , earg = .earg ) okay1 <- all(is.finite(theta)) && all(0 < theta) okay1 }, list( .link = link, .earg = earg ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) theta <- eta2theta(eta, .link , earg = .earg ) rlind(nsim * length(theta), theta = theta) }, list( .link = link, .earg = earg ))), deriv = eval(substitute(expression({ M1 <- 1 theta <- eta2theta(eta, .link , earg = .earg ) dl.dtheta <- 2 / theta - 1 / (1 + theta) - y DTHETA.DETA <- dtheta.deta(theta, .link , earg = .earg ) c(w) * dl.dtheta * DTHETA.DETA }), list( .link = link, .earg = earg ))), weight = eval(substitute(expression({ ned2l.dtheta2 <- (theta^2 + 4 * theta + 2) / (theta * (1 + theta))^2 c(w) * ned2l.dtheta2 * DTHETA.DETA^2 }), list( .zero = zero )))) } dpoislindley <- function(x, theta, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) if ( log.arg ) { ans <- 2 * log(theta) + log(theta + 2 + x) - (x+3) * log1p(theta) ans[(x != round(x)) | (x < 0)] <- log(0) } else { ans <- theta^2 * (theta + 2 + x) / (theta + 1)^(x+3) ans[(x != round(x)) | (x < 0)] <- 0 } ans[ (theta <= 0)] <- NA ans } dslash <- function(x, mu = 0, sigma = 1, log = FALSE, smallno = .Machine$double.eps * 1000) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) if (!is.Numeric(sigma) || any(sigma <= 0)) stop("argument 'sigma' must be positive") L <- max(length(x), length(mu), length(sigma)) if (length(x) != L) x <- rep_len(x, L) if (length(mu) != L) mu <- rep_len(mu, L) if (length(sigma) != L) sigma <- rep_len(sigma, L) zedd <- (x-mu)/sigma if (log.arg) { ifelse(abs(zedd) < smallno, -log(2*sigma*sqrt(2*pi)), log1p(-exp(-zedd^2/2)) - log(sqrt(2*pi)*sigma*zedd^2)) } else { ifelse(abs(zedd) < smallno, 1/(2*sigma*sqrt(2*pi)), -expm1(-zedd^2/2)/(sqrt(2*pi)*sigma*zedd^2)) } } pslash <- function(q, mu = 0, sigma = 1, very.negative = -10000, lower.tail = TRUE, log.p = FALSE) { if (anyNA(q)) stop("argument 'q' must have non-missing values") if (!is.Numeric(mu)) stop("argument 'mu' must have finite and non-missing values") if (!is.Numeric(sigma, positive = TRUE)) stop("argument 'sigma' must have positive finite non-missing values") if (!is.Numeric(very.negative, length.arg = 1) || (very.negative >= 0)) stop("argument 'very.negative' must be quite negative") if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") L <- max(length(q), length(mu), length(sigma)) if (length(q) != L) q <- rep_len(q, L) if (length(mu) != L) mu <- rep_len(mu, L) if (length(sigma) != L) sigma <- rep_len(sigma, L) zedd <- (q - mu)/sigma ans <- as.numeric(q * NA) extreme.q <- FALSE for (ii in 1:L) { use.trick <- (-abs(zedd[ii]) <= very.negative) if (use.trick) { ans[ii] <- ifelse(zedd[ii] < 0, 0.0, 1.0) extreme.q <- TRUE } else if ((zedd[ii] >= very.negative) && zedd[ii] <= 0.0) { temp2 <- integrate(dslash, lower = q[ii], upper = mu[ii], mu = mu[ii], sigma = sigma[ii]) if (temp2$message != "OK") warning("integrate() failed on 'temp2'") ans[ii] <- 0.5 - temp2$value } else { temp1 <- integrate(dslash, lower = mu[ii], upper = q[ii], mu = mu[ii], sigma = sigma[ii]) if (temp1$message != "OK") warning("integrate() failed") ans[ii] <- 0.5 + temp1$value } } if (extreme.q) warning("returning 0 or 1 values for extreme values of argument 'q'") if (lower.tail) { if (log.p) log(ans) else ans } else { if (log.p) log1p(-ans) else -expm1(log(ans)) } } rslash <- function (n, mu = 0, sigma = 1) { rnorm(n = n, mean = mu, sd = sigma) / runif(n = n) } slash.control <- function(save.weights = TRUE, ...) { list(save.weights = save.weights) } slash <- function(lmu = "identitylink", lsigma = "loglink", imu = NULL, isigma = NULL, gprobs.y = ppoints(8), nsimEIM = 250, zero = NULL, smallno = .Machine$double.eps * 1000) { lmu <- as.list(substitute(lmu)) emu <- link2list(lmu) lmu <- attr(emu, "function.name") lsigma <- as.list(substitute(lsigma)) esigma <- link2list(lsigma) lsigma <- attr(esigma, "function.name") if (length(isigma) && !is.Numeric(isigma, positive = TRUE)) stop("argument 'isigma' must be > 0") if (!is.Numeric(nsimEIM, length.arg = 1, integer.valued = TRUE) || nsimEIM <= 50) stop("argument 'nsimEIM' should be an integer greater than 50") if (!is.Numeric(gprobs.y, positive = TRUE) || max(gprobs.y) >= 1) stop("bad input for argument 'gprobs.y'") if (!is.Numeric(smallno, positive = TRUE) || smallno > 0.1) stop("bad input for argument 'smallno'") new("vglmff", blurb = c("Slash distribution\n\n", "Links: ", namesof("mu", lmu, earg = emu, tag = FALSE), ", ", namesof("sigma", lsigma, earg = esigma, tag = FALSE), "\n", paste( "1-exp(-(((y-mu)/sigma)^2)/2))/(sqrt(2*pi)*", "sigma*((y-mu)/sigma)^2)", "\ty!=mu", "\n1/(2*sigma*sqrt(2*pi))", "\t\t\t\t\t\t\ty=mu\n")), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = TRUE, multipleResponses = FALSE, parameters.names = c("mu", "sigma"), lmu = .lmu , lsigma = .lsigma , zero = .zero ) }, list( .zero = zero, .lmu = lmu, .lsigma = lsigma ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, ncol.w.max = 1, ncol.y.max = 1, out.wy = TRUE, maximize = TRUE) w <- temp5$w y <- temp5$y predictors.names <- c( namesof("mu", .lmu , earg = .emu, tag = FALSE), namesof("sigma", .lsigma , earg = .esigma, tag = FALSE)) if (!length(etastart)) { slash.Loglikfun <- function(mu, y, x, w, extraargs) { sigma <- if (is.Numeric(.isigma)) .isigma else max(0.01, ((quantile(rep(y, w), prob = 0.75)/2)-mu)/qnorm(0.75)) zedd <- (y-mu)/sigma sum(c(w) * ifelse(abs(zedd)<.smallno, -log(2*sigma*sqrt(2*pi)), log1p(-exp(-zedd^2/2)) - log(sqrt(2*pi) * sigma * zedd^2))) } gprobs.y <- .gprobs.y mu.grid <- quantile(rep(y, w), probs = gprobs.y) mu.grid <- seq(mu.grid[1], mu.grid[2], length=100) mu.init <- if (length( .imu )) .imu else grid.search(mu.grid, objfun = slash.Loglikfun, y = y, x = x, w = w) sigma.init <- if (is.Numeric(.isigma)) .isigma else max(0.01, ((quantile(rep(y, w), prob = 0.75)/2) - mu.init) / qnorm(0.75)) mu.init <- rep_len(mu.init, length(y)) etastart <- matrix(0, n, 2) etastart[, 1] <- theta2eta(mu.init, .lmu , earg = .emu ) etastart[, 2] <- theta2eta(sigma.init, .lsigma , earg = .esigma ) } }), list( .lmu = lmu, .lsigma = lsigma, .imu = imu, .isigma = isigma, .emu = emu, .esigma = esigma, .gprobs.y = gprobs.y, .smallno = smallno))), linkinv = eval(substitute(function(eta, extra = NULL) { NA * eta2theta(eta[, 1], link = .lmu , earg = .emu ) }, list( .lmu = lmu, .emu = emu ))), last = eval(substitute(expression({ misc$link <- c("mu" = .lmu , "sigma" = .lsigma ) misc$earg <- list("mu" = .emu , "sigma" = .esigma ) misc$expected <- TRUE misc$nsimEIM <- .nsimEIM }), list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma, .nsimEIM = nsimEIM ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { mu <- eta2theta(eta[, 1], link = .lmu , earg = .emu ) sigma <- eta2theta(eta[, 2], link = .lsigma , earg = .esigma ) zedd <- (y - mu) / sigma if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dslash(x = y, mu = mu, sigma = sigma, log = TRUE, smallno = .smallno) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma, .smallno = smallno ))), vfamily = c("slash"), validparams = eval(substitute(function(eta, y, extra = NULL) { mu <- eta2theta(eta[, 1], link = .lmu , earg = .emu ) sigma <- eta2theta(eta[, 2], link = .lsigma , earg = .esigma ) okay1 <- all(is.finite(mu)) && all(is.finite(sigma)) && all(0 < sigma) okay1 }, list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) mu <- eta2theta(eta[, 1], link = .lmu , earg = .emu ) sigma <- eta2theta(eta[, 2], link = .lsigma , earg = .esigma ) rslash(nsim * length(sigma), mu = mu, sigma = sigma) }, list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma, .smallno = smallno ))), deriv = eval(substitute(expression({ mu <- eta2theta(eta[, 1], link = .lmu , earg = .emu ) sigma <- eta2theta(eta[, 2], link = .lsigma , earg = .esigma ) dmu.deta <- dtheta.deta(mu, link = .lmu , earg = .emu ) dsigma.deta <- dtheta.deta(sigma, link = .lsigma , earg = .esigma ) zedd <- (y - mu) / sigma d3 <- deriv3(~ w * log(1 - exp(-(((y - mu) / sigma)^2) / 2)) - log(sqrt(2 * pi) * sigma * ((y - mu) / sigma)^2), c("mu", "sigma")) eval.d3 <- eval(d3) dl.dthetas <- attr(eval.d3, "gradient") dl.dmu <- dl.dthetas[, 1] dl.dsigma <- dl.dthetas[, 2] ind0 <- (abs(zedd) < .smallno) dl.dmu[ind0] <- 0 dl.dsigma[ind0] <- -1 / sigma[ind0] c(w) * cbind(dl.dmu * dmu.deta, dl.dsigma * dsigma.deta) }), list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma, .smallno = smallno ))), weight = eval(substitute(expression({ run.varcov <- 0 ind1 <- iam(NA_real_, NA_real_, M = M, both = TRUE, diag = TRUE) sd3 <- deriv3(~ w * log(1 - exp(-(((ysim - mu) / sigma)^2) / 2))- log(sqrt(2 * pi) * sigma * ((ysim - mu) / sigma)^2), c("mu", "sigma")) for (ii in 1:( .nsimEIM )) { ysim <- rslash(n, mu = mu, sigma = sigma) seval.d3 <- eval(sd3) dl.dthetas <- attr(seval.d3, "gradient") dl.dmu <- dl.dthetas[, 1] dl.dsigma <- dl.dthetas[, 2] temp3 <- cbind(dl.dmu, dl.dsigma) run.varcov <- run.varcov + temp3[, ind1$row] * temp3[, ind1$col] } run.varcov <- run.varcov / .nsimEIM wz <- if (intercept.only) matrix(colMeans(run.varcov, na.rm = FALSE), n, ncol(run.varcov), byrow = TRUE) else run.varcov dthetas.detas <- cbind(dmu.deta, dsigma.deta) wz <- wz * dthetas.detas[, ind1$row] * dthetas.detas[, ind1$col] c(w) * wz }), list( .lmu = lmu, .lsigma = lsigma, .emu = emu, .esigma = esigma, .nsimEIM = nsimEIM, .smallno = smallno )))) } dnefghs <- function(x, tau, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) N <- max(length(x), length(tau)) if (length(x) != N) x <- rep_len(x, N) if (length(tau) != N) tau <- rep_len(tau, N) logdensity <- log(sin(pi*tau)) + (1-tau)*x - log(pi) - log1pexp(x) logdensity[tau < 0] <- NaN logdensity[tau > 1] <- NaN if (log.arg) logdensity else exp(logdensity) } nefghs <- function(link = "logitlink", itau = NULL, imethod = 1) { if (length(itau) && !is.Numeric(itau, positive = TRUE) || any(itau >= 1)) stop("argument 'itau' must be in (0, 1)") link <- as.list(substitute(link)) earg <- link2list(link) link <- attr(earg, "function.name") if (!is.Numeric(imethod, length.arg = 1, integer.valued = TRUE, positive = TRUE) || imethod > 2) stop("argument 'imethod' must be 1 or 2") new("vglmff", blurb = c("Natural exponential family generalized hyperbolic ", "secant distribution\n", "f(y) = sin(pi*tau)*exp((1-tau)*y)/(pi*(1+exp(y))\n\n", "Link: ", namesof("tau", link, earg = earg), "\n\n", "Mean: pi / tan(pi * tau)\n"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, multipleResponses = FALSE, parameters.names = c("tau"), ltau = .link ) }, list( .link = link ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, ncol.w.max = 1, ncol.y.max = 1, out.wy = TRUE, maximize = TRUE) w <- temp5$w y <- temp5$y predictors.names <- namesof("tau", .link , earg = .earg , tag = FALSE) if (!length(etastart)) { wmeany <- if ( .imethod == 1) weighted.mean(y, w) else median(rep(y, w)) if (abs(wmeany) < 0.01) wmeany <- 0.01 tau.init <- atan(pi / wmeany) / pi + 0.5 tau.init[tau.init < 0.03] <- 0.03 tau.init[tau.init > 0.97] <- 0.97 tau.init <- rep_len(if (length( .itau )) .itau else tau.init, n) etastart <- theta2eta(tau.init, .link , earg = .earg ) } }), list( .link = link, .earg = earg, .itau = itau, .imethod = imethod ))), linkinv = eval(substitute(function(eta, extra = NULL) { tau <- eta2theta(eta, .link , earg = .earg ) pi / tan(pi * tau) }, list( .link = link, .earg = earg ))), last = eval(substitute(expression({ misc$link <- c(tau = .link ) misc$earg <- list(tau = .earg ) misc$expected <- TRUE misc$imethod <- .imethod }), list( .link = link, .earg = earg, .imethod = imethod ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { tau <- eta2theta(eta, .link , earg = .earg ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dnefghs(x = y, tau = tau, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .link = link, .earg = earg ))), vfamily = c("nefghs"), validparams = eval(substitute(function(eta, y, extra = NULL) { tau <- eta2theta(eta, .link , earg = .earg ) okay1 <- all(is.finite(tau)) && all(0 < tau) okay1 }, list( .link = link, .earg = earg ))), deriv = eval(substitute(expression({ tau <- eta2theta(eta, .link , earg = .earg ) dl.dtau <- pi / tan(pi * tau) - y dtau.deta <- dtheta.deta(tau, .link , earg = .earg ) w * dl.dtau * dtau.deta }), list( .link = link, .earg = earg ))), weight = eval(substitute(expression({ ned2l.dtau2 <- (pi / sin(pi * tau))^2 wz <- ned2l.dtau2 * dtau.deta^2 c(w) * wz }), list( .link = link )))) } dlogF <- function(x, shape1, shape2, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) logdensity <- shape1*x - lbeta(shape1, shape2) - (shape1 + shape2) * log1pexp(x) logdensity[is.infinite(x)] <- -Inf if (log.arg) logdensity else exp(logdensity) } logF <- function(lshape1 = "loglink", lshape2 = "loglink", ishape1 = NULL, ishape2 = 1, imethod = 1) { if (length(ishape1) && !is.Numeric(ishape1, positive = TRUE)) stop("argument 'ishape1' must be positive") if ( !is.Numeric(ishape2, positive = TRUE)) stop("argument 'ishape2' must be positive") lshape1 <- as.list(substitute(lshape1)) eshape1 <- link2list(lshape1) lshape1 <- attr(eshape1, "function.name") lshape2 <- as.list(substitute(lshape2)) eshape2 <- link2list(lshape2) lshape2 <- attr(eshape2, "function.name") if (!is.Numeric(imethod, length.arg = 1, integer.valued = TRUE, positive = TRUE) || imethod > 2) stop("argument 'imethod' must be 1 or 2") new("vglmff", blurb = c("log F distribution\n", "f(y) = exp(-shape2 * y) / (beta(shape1, shape2) * ", "(1 + exp(-y))^(shape1 + shape2))\n\n", "Link: ", namesof("shape1", lshape1, earg = eshape1), ", ", namesof("shape2", lshape2, earg = eshape2), "\n\n", "Mean: digamma(shape1) - digamma(shape2)"), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = TRUE, multipleResponses = FALSE, parameters.names = c("shape1", "shape2"), lshape1 = .lshape1 , lshape2 = .lshape2 , imethod = .imethod ) }, list( .lshape1 = lshape1, .imethod = imethod, .lshape2 = lshape2 ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, ncol.w.max = 1, ncol.y.max = 1, out.wy = TRUE, maximize = TRUE) w <- temp5$w y <- temp5$y predictors.names <- c( namesof("shape1", .lshape1 , earg = .eshape1 , tag = FALSE), namesof("shape2", .lshape2 , earg = .eshape2 , tag = FALSE)) if (!length(etastart)) { wmeany <- if ( .imethod == 1) weighted.mean(y, w) else median(rep(y, w)) shape1.init <- shape2.init <- rep_len( .ishape2 , n) shape1.init <- if (length( .ishape1)) rep_len( .ishape1, n) else { index1 <- (y > wmeany) shape1.init[ index1] <- shape2.init[ index1] + 1/1 shape1.init[!index1] <- shape2.init[!index1] - 1/1 shape1.init <- pmax(shape1.init, 1/8) shape1.init } etastart <- cbind(theta2eta(shape1.init, .lshape1 , earg = .eshape1 ), theta2eta(shape2.init, .lshape2 , earg = .eshape2 )) } }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2, .ishape1 = ishape1, .ishape2 = ishape2, .imethod = imethod ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape1 <- eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, 2], .lshape2 , earg = .eshape2 ) digamma(shape1) - digamma(shape2) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), last = eval(substitute(expression({ misc$link <- c(shape1 = .lshape1 , shape2 = .lshape2 ) misc$earg <- list(shape1 = .eshape1 , shape2 = .eshape2 ) extra$percentile <- numeric(ncol(y)) locat <- cbind(digamma(shape1) - digamma(shape2)) for (ii in 1:ncol(y)) { y.use <- if (ncol(y) > 1) y[, ii] else y extra$percentile[ii] <- 100 * weighted.mean(y.use <= locat[, ii], w[, min(ii, ncol(w))]) } misc$expected <- TRUE misc$imethod <- .imethod }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2, .imethod = imethod ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape1 <- eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, 2], .lshape2 , earg = .eshape2 ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dlogF(x = y, shape1 = shape1, shape2 = shape2, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), vfamily = c("logF"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape1 <- eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, 2], .lshape2 , earg = .eshape2 ) okay1 <- all(is.finite(shape1)) && all(0 < shape1) && all(is.finite(shape2)) && all(0 < shape2) okay1 }, list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), deriv = eval(substitute(expression({ shape1 <- eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, 2], .lshape2 , earg = .eshape2 ) tmp888 <- digamma(shape1 + shape2) - log1pexp(-y) dl.dshape1 <- tmp888 - digamma(shape1) dl.dshape2 <- tmp888 - digamma(shape2) - y dshape1.deta <- dtheta.deta(shape1, .lshape1 , earg = .eshape1 ) dshape2.deta <- dtheta.deta(shape2, .lshape2 , earg = .eshape2 ) c(w) * cbind(dl.dshape1 * dshape1.deta, dl.dshape2 * dshape2.deta) }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 ))), weight = eval(substitute(expression({ tmp888 <- trigamma(shape1 + shape2) ned2l.dshape12 <- trigamma(shape1) - tmp888 ned2l.dshape22 <- trigamma(shape2) - tmp888 ned2l.dshape1shape2 <- -tmp888 wz <- matrix(0, n, dimm(M)) wz[, iam(1, 1, M = M)] <- ned2l.dshape12 * dshape1.deta^2 wz[, iam(2, 2, M = M)] <- ned2l.dshape22 * dshape2.deta^2 wz[, iam(1, 2, M = M)] <- ned2l.dshape1shape2 * dshape1.deta * dshape2.deta c(w) * wz }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2 )))) } dbenf <- function(x, ndigits = 1, log = FALSE) { if (!is.Numeric(ndigits, length.arg = 1, positive = TRUE, integer.valued = TRUE) || ndigits > 2) stop("argument 'ndigits' must be 1 or 2") lowerlimit <- ifelse(ndigits == 1, 1, 10) upperlimit <- ifelse(ndigits == 1, 9, 99) if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) ans <- x * NA indexTF <- is.finite(x) & (x >= lowerlimit) ans[indexTF] <- log10(1 + 1/x[indexTF]) ans[!is.na(x) & !is.nan(x) & ((x < lowerlimit) | (x > upperlimit) | (x != round(x)))] <- 0.0 if (log.arg) log(ans) else ans } rbenf <- function(n, ndigits = 1) { if (!is.Numeric(ndigits, length.arg = 1, positive = TRUE, integer.valued = TRUE) || ndigits > 2) stop("argument 'ndigits' must be 1 or 2") lowerlimit <- ifelse(ndigits == 1, 1, 10) upperlimit <- ifelse(ndigits == 1, 9, 99) use.n <- if ((length.n <- length(n)) > 1) length.n else if (!is.Numeric(n, integer.valued = TRUE, length.arg = 1, positive = TRUE)) stop("bad input for argument 'n'") else n myrunif <- runif(use.n) ans <- rep_len(lowerlimit, use.n) for (ii in (lowerlimit+1):upperlimit) { indexTF <- (pbenf(ii-1, ndigits = ndigits) < myrunif) & (myrunif <= pbenf(ii, ndigits = ndigits)) ans[indexTF] <- ii } ans } pbenf <- function(q, ndigits = 1, lower.tail = TRUE, log.p = FALSE) { if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (!is.Numeric(ndigits, length.arg = 1, positive = TRUE, integer.valued = TRUE) || ndigits > 2) stop("argument 'ndigits' must be 1 or 2") lowerlimit <- ifelse(ndigits == 1, 1, 10) upperlimit <- ifelse(ndigits == 1, 9, 99) ans <- q * NA floorq <- floor(q) indexTF <- is.finite(q) & (floorq >= lowerlimit) if (ndigits == 1) { if (lower.tail) { if (log.p) { ans[indexTF] <- log(log10(1 + floorq[indexTF])) ans[q < lowerlimit ] <- -Inf ans[q >= upperlimit] <- 0 } else { ans[indexTF] <- log10(1 + floorq[indexTF]) ans[q < lowerlimit] <- 0 ans[q >= upperlimit] <- 1 } } else { if (log.p) { ans[indexTF] <- log1p(-log10(1 + floorq[indexTF])) ans[q < lowerlimit] <- 0 ans[q >= upperlimit] <- -Inf } else { ans[indexTF] <- log10(10 / (1 + floorq[indexTF])) ans[q < lowerlimit] <- 1 ans[q >= upperlimit] <- 0 } } } else { if (lower.tail) { if (log.p) { ans[indexTF] <- log(log10((1 + floorq[indexTF])/10)) ans[q < lowerlimit ] <- -Inf ans[q >= upperlimit] <- 0 } else { ans[indexTF] <- log10((1 + floorq[indexTF])/10) ans[q < lowerlimit] <- 0 ans[q >= upperlimit] <- 1 } } else { if (log.p) { ans[indexTF] <- log(log10(100/(1 + floorq[indexTF]))) ans[q < lowerlimit] <- 0 ans[q >= upperlimit] <- -Inf } else { ans[indexTF] <- log10(100/(1 + floorq[indexTF])) ans[q < lowerlimit] <- 1 ans[q >= upperlimit] <- 0 } } } ans } if (FALSE) qbenf <- function(p, ndigits = 1) { if (!is.Numeric(ndigits, length.arg = 1, positive = TRUE, integer.valued = TRUE) || ndigits > 2) stop("argument 'ndigits' must be 1 or 2") lowerlimit <- ifelse(ndigits == 1, 1, 10) upperlimit <- ifelse(ndigits == 1, 9, 99) bad <- !is.na(p) & !is.nan(p) & ((p < 0) | (p > 1)) if (any(bad)) stop("bad input for argument 'p'") ans <- rep_len(lowerlimit, length(p)) for (ii in (lowerlimit+1):upperlimit) { indexTF <- is.finite(p) & (pbenf(ii-1, ndigits = ndigits) < p) & (p <= pbenf(ii, ndigits = ndigits)) ans[indexTF] <- ii } ans[ is.na(p) | is.nan(p)] <- NA ans[!is.na(p) & !is.nan(p) & (p == 0)] <- lowerlimit ans[!is.na(p) & !is.nan(p) & (p == 1)] <- upperlimit ans } qbenf <- function(p, ndigits = 1, lower.tail = TRUE, log.p = FALSE) { if (!is.Numeric(ndigits, length.arg = 1, positive = TRUE, integer.valued = TRUE) || ndigits > 2) stop("argument 'ndigits' must be 1 or 2") if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (log.p) { bad <- ((p > 0) | is.na(p) | is.nan(p)) } else { bad <- ((p < 0) | (p > 1) | is.na(p) | is.nan(p)) } if (any(bad)) stop("bad input for argument 'p'") lowerlimit <- ifelse(ndigits == 1, 1, 10) upperlimit <- ifelse(ndigits == 1, 9, 99) ans <- rep_len(lowerlimit, length(p)) if (lower.tail) { for (ii in (lowerlimit+1):upperlimit) { indexTF <- is.finite(p) & (pbenf(ii-1, ndigits = ndigits, lower.tail = lower.tail, log.p = log.p) < p) & (p <= pbenf(ii, ndigits = ndigits, lower.tail = lower.tail, log.p = log.p)) ans[indexTF] <- ii } } else { for (ii in (lowerlimit+1):upperlimit) { indexTF <- is.finite(p) & (pbenf(ii-1, ndigits = ndigits, lower.tail = lower.tail, log.p = log.p) >= p) & (p > pbenf(ii, ndigits = ndigits, lower.tail = lower.tail, log.p = log.p)) ans[indexTF] <- ii } } if (lower.tail) { if (log.p) { ans[p > 0] <- NaN ans[p == -Inf] <- lowerlimit } else { ans[p < 0] <- NaN ans[p == 0] <- lowerlimit ans[p == 1] <- upperlimit ans[p > 1] <- NaN } } else { if (log.p) { ans[p > 0] <- NaN ans[p == -Inf] <- upperlimit } else { ans[p < 0] <- NaN ans[p == 0] <- upperlimit ans[p == 1] <- lowerlimit ans[p > 1] <- NaN } } ans } truncgeometric <- function(upper.limit = Inf, link = "logitlink", expected = TRUE, imethod = 1, iprob = NULL, zero = NULL) { if (is.finite(upper.limit) && !is.Numeric(upper.limit, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'upper.limit'") if (any(upper.limit < 0)) stop("bad input for argument 'upper.limit'") if (!is.logical(expected) || length(expected) != 1) stop("bad input for argument 'expected'") link <- as.list(substitute(link)) earg <- link2list(link) link <- attr(earg, "function.name") if (!is.Numeric(imethod, length.arg = 1, integer.valued = TRUE, positive = TRUE) || imethod > 3) stop("argument 'imethod' must be 1 or 2 or 3") uu.ll <- min(upper.limit) new("vglmff", blurb = c("Truncated geometric distribution ", "(P[Y=y] =\n", " ", "prob * (1 - prob)^y / [1-(1-prob)^", uu.ll+1, "], y = 0,1,...,", uu.ll, ")\n", "Link: ", namesof("prob", link, earg = earg), "\n", "Mean: mu = 1 / prob - 1 ", ifelse(is.finite(upper.limit), paste("- (", upper.limit+1, ") * (1 - prob)^", upper.limit+1, " / (1 - ", "(1 - prob)^", upper.limit+1, ")", sep = ""), "")), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 1) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = .expected , imethod = .imethod , multipleResponses = TRUE, parameters.names = c("prob"), upper.limit = .upper.limit , zero = .zero ) }, list( .zero = zero, .expected = expected, .imethod = imethod, .upper.limit = upper.limit ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, Is.nonnegative.y = TRUE, Is.integer.y = TRUE, ncol.w.max = Inf, ncol.y.max = Inf, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y ncoly <- ncol(y) M1 <- 1 extra$ncoly <- ncoly extra$M1 <- M1 M <- M1 * ncoly extra$upper.limit <- matrix( .upper.limit , n, ncoly, byrow = TRUE) if (any(y > extra$upper.limit)) stop("some response values greater than argument 'upper.limit'") mynames1 <- param.names("prob", ncoly, skip1 = TRUE) predictors.names <- namesof(mynames1, .link , earg = .earg , tag = FALSE) if (!length(etastart)) { prob.init <- if ( .imethod == 2) 1 / (1 + y + 1/16) else if ( .imethod == 3) 1 / (1 + apply(y, 2, median) + 1/16) else 1 / (1 + colSums(y * w) / colSums(w) + 1/16) if (!is.matrix(prob.init)) prob.init <- matrix(prob.init, n, M, byrow = TRUE) if (length( .iprob )) prob.init <- matrix( .iprob , n, M, byrow = TRUE) etastart <- theta2eta(prob.init, .link , earg = .earg ) } }), list( .link = link, .earg = earg, .upper.limit = upper.limit, .imethod = imethod, .iprob = iprob ))), linkinv = eval(substitute(function(eta, extra = NULL) { prob <- eta2theta(eta, .link , earg = .earg ) QQQ <- 1 - prob upper.limit <- extra$upper.limit tmp1 <- QQQ^(upper.limit+1) answer <- 1 / prob - 1 - (upper.limit+1) * tmp1 / (1 - tmp1) answer[!is.finite(answer)] <- 1 / prob[!is.finite(answer)] - 1 answer }, list( .link = link, .earg = earg ))), last = eval(substitute(expression({ M1 <- extra$M1 misc$link <- c(rep_len( .link , ncoly)) names(misc$link) <- mynames1 misc$earg <- vector("list", M) names(misc$earg) <- mynames1 for (ii in 1:ncoly) { misc$earg[[ii]] <- .earg } misc$M1 <- M1 misc$multipleResponses <- TRUE misc$expected <- .expected misc$imethod <- .imethod misc$iprob <- .iprob }), list( .link = link, .earg = earg, .iprob = iprob, .upper.limit = upper.limit, .expected = expected, .imethod = imethod ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { prob <- eta2theta(eta, .link , earg = .earg ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { upper.limit <- extra$upper.limit ll.elts <- c(w) * (dgeom(x = y, prob = prob, log = TRUE) - log1p(-(1.0 - prob)^(1 + upper.limit))) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .link = link, .earg = earg ))), vfamily = c("truncgeometric"), validparams = eval(substitute(function(eta, y, extra = NULL) { prob <- eta2theta(eta, .link , earg = .earg ) okay1 <- all(is.finite(prob)) && all(0 < prob & prob < 1) okay1 }, list( .link = link, .earg = earg ))), deriv = eval(substitute(expression({ prob <- eta2theta(eta, .link , earg = .earg ) sss <- upper.limit <- extra$upper.limit QQQ <- 1 - prob tmp1 <- QQQ^(upper.limit + 1) dl.dprob <- 1 / prob + (0 - y) / (1 - prob) - (1+upper.limit) * QQQ^(upper.limit - 0) / (1 - tmp1) dl.dprob[!is.finite(upper.limit)] <- 1 / prob[!is.finite(upper.limit)] + (0 - y[!is.finite(upper.limit)]) / (1 - prob[!is.finite(upper.limit)]) dprobdeta <- dtheta.deta(prob, .link , earg = .earg ) c(w) * cbind(dl.dprob * dprobdeta) }), list( .link = link, .earg = earg, .upper.limit = upper.limit, .expected = expected ))), weight = eval(substitute(expression({ eim.oim.fun <- function(mu.y, sss) ifelse(is.finite(sss), 1/prob^2 + (0 + mu.y) / QQQ^2 - (1+sss) * ((sss-0) * QQQ^(sss-1) / (1 - tmp1) + (1+sss) * QQQ^(2*sss) / (1 - tmp1)^2), 1 / (prob^2 * (1 - prob))) ned2l.dprob2 <- if ( .expected ) { eim.oim.fun(mu, sss) } else { eim.oim.fun(y, sss) } wz <- ned2l.dprob2 * dprobdeta^2 if ( !( .expected )) wz <- wz - dl.dprob * d2theta.deta2(prob, .link , earg = .earg ) c(w) * wz }), list( .link = link, .earg = earg, .expected = expected )))) } betaff <- function(A = 0, B = 1, lmu = "logitlink", lphi = "loglink", imu = NULL, iphi = NULL, gprobs.y = ppoints(8), gphi = exp(-3:5)/4, zero = NULL) { if (!is.Numeric(A, length.arg = 1) || !is.Numeric(B, length.arg = 1) || A >= B) stop("A must be < B, and both must be of length one") stdbeta <- (A == 0 && B == 1) lmu <- as.list(substitute(lmu)) emu <- link2list(lmu) lmu <- attr(emu, "function.name") lphi <- as.list(substitute(lphi)) ephi <- link2list(lphi) lphi <- attr(ephi, "function.name") if (length(imu) && (!is.Numeric(imu, positive = TRUE) || any(imu <= A) || any(imu >= B))) stop("bad input for argument 'imu'") if (length(iphi) && !is.Numeric(iphi, positive = TRUE)) stop("bad input for argument 'iphi'") new("vglmff", blurb = c("Beta distribution parameterized by mu and a ", "precision parameter\n", if (stdbeta) paste("f(y) = y^(mu*phi-1) * (1-y)^((1-mu)*phi-1)", "/ beta(mu*phi,(1-mu)*phi),\n", " 0<y<1, 0<mu<1, phi>0\n\n") else paste("f(y) = (y-",A,")^(mu1*phi-1) * (",B, "-y)^(((1-mu1)*phi)-1) / \n(beta(mu1*phi,(1-mu1)*phi) * (", B, "-", A, ")^(phi-1)),\n", A," < y < ",B, ", ", A," < mu < ",B, ", mu = ", A, " + ", (B-A), " * mu1", ", phi > 0\n\n", sep = ""), "Links: ", namesof("mu", lmu, earg = emu), ", ", namesof("phi", lphi, earg = ephi)), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = TRUE, multipleResponses = FALSE, parameters.names = c("mu", "phi"), A = .A , B = .B , zero = .zero ) }, list( .zero = zero, .A = A, .B = B ))), initialize = eval(substitute(expression({ if (min(y) <= .A || max(y) >= .B) stop("data not within (A, B)") temp5 <- w.y.check(w = w, y = y, out.wy = TRUE, maximize = TRUE) w <- temp5$w y <- temp5$y extra$A <- .A extra$B <- .B predictors.names <- c(namesof("mu", .lmu , .emu , short = TRUE), namesof("phi", .lphi , .ephi, short = TRUE)) if (!length(etastart)) { NOS <- 1 muu.init <- phi.init <- matrix(NA_real_, n, NOS) gprobs.y <- .gprobs.y gphi <- if (length( .iphi )) .iphi else .gphi betaff.Loglikfun <- function(muu, phi, y, x, w, extraargs) { zedd <- (y - extraargs$A) / ( extraargs$B - extraargs$A) m1u <- (muu - extraargs$A) / ( extraargs$B - extraargs$A) shape1 <- phi * m1u shape2 <- (1 - m1u) * phi sum(c(w) * (dbeta(x = zedd, shape1, shape2, log = TRUE) - log(abs( extraargs$B - extraargs$A )))) } for (jay in 1:NOS) { gmuu <- if (length( .imu )) .imu else quantile(y[, jay], probs = gprobs.y) try.this <- grid.search2(gmuu, gphi, objfun = betaff.Loglikfun, y = y[, jay], w = w[, jay], extraargs = list(A = .A , B = .B ), ret.objfun = TRUE) muu.init[, jay] <- try.this["Value1"] phi.init[, jay] <- try.this["Value2"] } if (FALSE) { mu.init <- if (is.Numeric( .imu )) .imu else { if ( .imethod == 1) weighted.mean(y, w) else (y + weighted.mean(y, w)) / 2 } mu1.init <- (mu.init - .A ) / ( .B - .A ) phi.init <- if (is.Numeric( .iphi )) .iphi else max(0.01, -1 + ( .B - .A )^2 * mu1.init*(1-mu1.init)/var(y)) } etastart <- matrix(0, n, 2) etastart[, 1] <- theta2eta(muu.init, .lmu , earg = .emu ) etastart[, 2] <- theta2eta(phi.init, .lphi , earg = .ephi ) } }), list( .lmu = lmu, .lphi = lphi, .imu = imu, .iphi = iphi, .A = A, .B = B, .emu = emu, .ephi = ephi, .gprobs.y = gprobs.y, .gphi = gphi ))), linkinv = eval(substitute(function(eta, extra = NULL) { mu <- eta2theta(eta[, 1], .lmu , .emu ) mu }, list( .lmu = lmu, .emu = emu, .A = A, .B = B))), last = eval(substitute(expression({ misc$link <- c(mu = .lmu , phi = .lphi ) misc$earg <- list(mu = .emu , phi = .ephi ) misc$limits <- c( .A , .B ) misc$stdbeta <- .stdbeta }), list( .lmu = lmu, .lphi = lphi, .A = A, .B = B, .emu = emu, .ephi = ephi, .stdbeta = stdbeta ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { mu <- eta2theta(eta[, 1], .lmu , earg = .emu ) phi <- eta2theta(eta[, 2], .lphi , earg = .ephi ) m1u <- if ( .stdbeta ) mu else (mu - .A ) / ( .B - .A ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { shape1 <- phi * m1u shape2 <- (1 - m1u) * phi zedd <- (y - .A) / ( .B - .A) ll.elts <- c(w) * (dbeta(x = zedd, shape1 = shape1, shape2 = shape2, log = TRUE) - log( abs( .B - .A ))) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lmu = lmu, .lphi = lphi, .A = A, .B = B, .emu = emu, .ephi = ephi, .stdbeta = stdbeta ))), vfamily = "betaff", validparams = eval(substitute(function(eta, y, extra = NULL) { mu <- eta2theta(eta[, 1], .lmu , .emu ) phi <- eta2theta(eta[, 2], .lphi , .ephi ) okay1 <- all(is.finite(mu )) && all(extra$A < mu & mu < extra$B) && all(is.finite(phi)) && all(0 < phi) okay1 }, list( .lmu = lmu, .lphi = lphi, .A = A, .B = B, .emu = emu, .ephi = ephi ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) mu <- eta2theta(eta[, 1], .lmu , earg = .emu ) phi <- eta2theta(eta[, 2], .lphi , earg = .ephi ) m1u <- if ( .stdbeta ) mu else (mu - .A ) / ( .B - .A ) shape1 <- phi * m1u shape2 <- (1 - m1u) * phi .A + ( .B - .A ) * rbeta(nsim * length(shape1), shape1 = shape1, shape2 = shape2) }, list( .lmu = lmu, .lphi = lphi, .A = A, .B = B, .emu = emu, .ephi = ephi, .stdbeta = stdbeta ))), deriv = eval(substitute(expression({ mu <- eta2theta(eta[, 1], .lmu , .emu ) phi <- eta2theta(eta[, 2], .lphi , .ephi ) m1u <- if ( .stdbeta ) mu else (mu - .A) / ( .B - .A) dmu.deta <- dtheta.deta(mu, .lmu , .emu ) dmu1.dmu <- 1 / ( .B - .A ) dphi.deta <- dtheta.deta(phi, .lphi , .ephi ) temp1 <- m1u*phi temp2 <- (1-m1u)*phi if ( .stdbeta ) { dl.dmu1 <- phi * (digamma(temp2) - digamma(temp1) + log(y) - log1p(-y)) dl.dphi <- digamma(phi) - mu*digamma(temp1) - (1-mu)*digamma(temp2) + mu*log(y) + (1-mu)*log1p(-y) } else { dl.dmu1 <- phi*(digamma(temp2) - digamma(temp1) + log(y-.A) - log( .B-y)) dl.dphi <- digamma(phi) - m1u*digamma(temp1) - (1-m1u)*digamma(temp2) + m1u*log(y-.A) + (1-m1u)*log( .B-y) - log( .B -.A) } c(w) * cbind(dl.dmu1 * dmu1.dmu * dmu.deta, dl.dphi * dphi.deta) }), list( .lmu = lmu, .lphi = lphi, .emu = emu, .ephi = ephi, .A = A, .B = B, .stdbeta = stdbeta ))), weight = eval(substitute(expression({ ned2l.dmu12 <- (trigamma(temp1) + trigamma(temp2)) * phi^2 ned2l.dphi2 <- -trigamma(phi) + trigamma(temp1) * m1u^2 + trigamma(temp2) * (1-m1u)^2 ned2l.dmu1phi <- temp1 * trigamma(temp1) - temp2 * trigamma(temp2) wz <- matrix(NA_real_, n, dimm(M)) wz[, iam(1, 1, M)] <- ned2l.dmu12 * dmu1.dmu^2 * dmu.deta^2 wz[, iam(2, 2, M)] <- ned2l.dphi2 * dphi.deta^2 wz[, iam(1, 2, M)] <- ned2l.dmu1phi * dmu1.dmu * dmu.deta * dphi.deta c(w) * wz }), list( .A = A, .B = B )))) } betaR <- function(lshape1 = "loglink", lshape2 = "loglink", i1 = NULL, i2 = NULL, trim = 0.05, A = 0, B = 1, parallel = FALSE, zero = NULL) { lshape1 <- as.list(substitute(lshape1)) eshape1 <- link2list(lshape1) lshape1 <- attr(eshape1, "function.name") lshape2 <- as.list(substitute(lshape2)) eshape2 <- link2list(lshape2) lshape2 <- attr(eshape2, "function.name") if (length( i1 ) && !is.Numeric( i1, positive = TRUE)) stop("bad input for argument 'i1'") if (length( i2 ) && !is.Numeric( i2, positive = TRUE)) stop("bad input for argument 'i2'") if (!is.Numeric(A, length.arg = 1) || !is.Numeric(B, length.arg = 1) || A >= B) stop("A must be < B, and both must be of length one") stdbeta <- (A == 0 && B == 1) new("vglmff", blurb = c("Two-parameter Beta distribution ", "(shape parameters parameterization)\n", if (stdbeta) paste("y^(shape1-1) * (1-y)^(shape2-1) / B(shape1,shape2),", "0 <= y <= 1, shape1>0, shape2>0\n\n") else paste("(y-",A,")^(shape1-1) * (",B, "-y)^(shape2-1) / [B(shape1,shape2) * (", B, "-", A, ")^(shape1+shape2-1)], ", A," <= y <= ",B," shape1>0, shape2>0\n\n", sep = ""), "Links: ", namesof("shape1", lshape1, earg = eshape1), ", ", namesof("shape2", lshape2, earg = eshape2)), constraints = eval(substitute(expression({ constraints <- cm.VGAM(matrix(1, M, 1), x = x, bool = .parallel , constraints, apply.int = TRUE) constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .parallel = parallel, .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, A = .A, B = .B, multipleResponses = FALSE, zero = .zero ) }, list( .A = A, .B = B, .zero = zero ))), initialize = eval(substitute(expression({ if (min(y) <= .A || max(y) >= .B) stop("data not within (A, B)") if (NCOL(y) != 1) stop("response must be a vector or a one-column matrix") w.y.check(w = w, y = y) predictors.names <- c(namesof("shape1", .lshape1 , earg = .eshape1 , short = TRUE), namesof("shape2", .lshape2 , earg = .eshape2 , short = TRUE)) if (!length(etastart)) { mu1d <- mean(y, trim = .trim ) uu <- (mu1d - .A) / ( .B - .A) DD <- ( .B - .A)^2 pinit <- max(0.01, uu^2 * (1 - uu) * DD / var(y) - uu) qinit <- max(0.01, pinit * (1 - uu) / uu) etastart <- matrix(0, n, 2) etastart[, 1] <- theta2eta( pinit, .lshape1 , earg = .eshape1 ) etastart[, 2] <- theta2eta( qinit, .lshape2 , earg = .eshape2 ) } if (is.Numeric( .i1 )) etastart[, 1] <- theta2eta( .i1 , .lshape1 , earg = .eshape1 ) if (is.Numeric( .i2 )) etastart[, 2] <- theta2eta( .i2 , .lshape2 , earg = .eshape2 ) }), list( .lshape1 = lshape1, .lshape2 = lshape2, .i1 = i1, .i2 = i2, .trim = trim, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), linkinv = eval(substitute(function(eta, extra = NULL) { shapes <- cbind(eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ), eta2theta(eta[, 2], .lshape2 , earg = .eshape2 )) .A + ( .B - .A ) * shapes[, 1] / (shapes[, 1] + shapes[, 2]) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), last = eval(substitute(expression({ misc$link <- c(shape1 = .lshape1 , shape2 = .lshape2 ) misc$earg <- list(shape1 = .eshape1 , shape2 = .eshape2 ) misc$limits <- c( .A , .B ) }), list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shapes <- cbind(eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ), eta2theta(eta[, 2], .lshape2 , earg = .eshape2 )) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { zedd <- (y - .A ) / ( .B - .A ) ll.elts <- c(w) * (dbeta(x = zedd, shape1 = shapes[, 1], shape2 = shapes[, 2], log = TRUE) - log( abs( .B - .A ))) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), vfamily = "betaR", validparams = eval(substitute(function(eta, y, extra = NULL) { shapes <- cbind(eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ), eta2theta(eta[, 2], .lshape2 , earg = .eshape2 )) okay1 <- all(is.finite(shapes)) && all(0 < shapes) okay1 }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) shapes <- cbind(eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ), eta2theta(eta[, 2], .lshape2 , earg = .eshape2 )) .A + ( .B - .A ) * rbeta(nsim * length(shapes[, 1]), shape1 = shapes[, 1], shape2 = shapes[, 2]) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), deriv = eval(substitute(expression({ shapes <- cbind(eta2theta(eta[, 1], .lshape1 , earg = .eshape1 ), eta2theta(eta[, 2], .lshape2 , earg = .eshape2 )) dshapes.deta <- cbind(dtheta.deta(shapes[, 1], .lshape1 , earg = .eshape1), dtheta.deta(shapes[, 2], .lshape2 , earg = .eshape2)) dl.dshapes <- cbind(log(y - .A ), log( .B - y)) - digamma(shapes) + digamma(shapes[, 1] + shapes[, 2]) - log( .B - .A ) c(w) * dl.dshapes * dshapes.deta }), list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2 ))), weight = expression({ trig.sum <- trigamma(shapes[, 1] + shapes[, 2]) ned2l.dshape12 <- trigamma(shapes[, 1]) - trig.sum ned2l.dshape22 <- trigamma(shapes[, 2]) - trig.sum ned2l.dshape1shape2 <- -trig.sum wz <- matrix(NA_real_, n, dimm(M)) wz[, iam(1, 1, M)] <- ned2l.dshape12 * dshapes.deta[, 1]^2 wz[, iam(2, 2, M)] <- ned2l.dshape22 * dshapes.deta[, 2]^2 wz[, iam(1, 2, M)] <- ned2l.dshape1shape2 * dshapes.deta[, 1] * dshapes.deta[, 2] c(w) * wz })) } betaprime <- function(lshape = "loglink", ishape1 = 2, ishape2 = NULL, zero = NULL) { lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Beta-prime distribution\n", "y^(shape1-1) * (1+y)^(-shape1-shape2) / Beta(shape1,shape2),", " y>0, shape1>0, shape2>0\n\n", "Links: ", namesof("shape1", lshape, earg = eshape), ", ", namesof("shape2", lshape, earg = eshape), "\n", "Mean: shape1/(shape2-1) provided shape2>1"), constraints = eval(substitute(expression({ constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 2) }), list( .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 2, Q1 = 1, expected = TRUE, multipleResponses = FALSE, parameters.names = c("shape1", "shape2"), lshape1 = .lshape , lshape2 = .lshape , zero = .zero ) }, list( .zero = zero, .lshape = lshape ))), initialize = eval(substitute(expression({ w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = 1, ncol.y.max = 1) predictors.names <- c(namesof("shape1", .lshape , earg = .eshape , short = TRUE), namesof("shape2", .lshape , earg = .eshape , short = TRUE)) if (is.numeric( .ishape1) && is.numeric( .ishape2 )) { vec <- c( .ishape1, .ishape2 ) vec <- c(theta2eta(vec[1], .lshape , earg = .eshape ), theta2eta(vec[2], .lshape , earg = .eshape )) etastart <- matrix(vec, n, 2, byrow = TRUE) } if (!length(etastart)) { init1 <- if (length( .ishape1 )) rep_len( .ishape1 , n) else rep_len(1, n) init2 <- if (length( .ishape2 )) rep_len( .ishape2 , n) else 1 + init1 / (y + 0.1) etastart <- matrix(theta2eta(c(init1, init2), .lshape , earg = .eshape ), n, 2, byrow = TRUE) } }), list( .lshape = lshape, .eshape = eshape, .ishape1 = ishape1, .ishape2 = ishape2 ))), linkinv = eval(substitute(function(eta, extra = NULL) { shapes <- eta2theta(eta, .lshape , earg = .eshape ) ifelse(shapes[, 2] > 1, shapes[, 1] / (shapes[, 2] - 1), NA) }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$link <- c(shape1 = .lshape , shape2 = .lshape ) misc$earg <- list(shape1 = .eshape , shape2 = .eshape ) }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shapes <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * ((shapes[, 1]-1) * log(y) - lbeta(shapes[, 1], shapes[, 2]) - (shapes[, 2] + shapes[, 1]) * log1p(y)) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = "betaprime", validparams = eval(substitute(function(eta, y, extra = NULL) { shapes <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shapes)) && all(0 < shapes) okay1 }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shapes <- eta2theta(eta, .lshape , earg = .eshape ) dshapes.deta <- dtheta.deta(shapes, .lshape , earg = .eshape ) dl.dshapes <- cbind(log(y) - log1p(y) - digamma(shapes[, 1]) + digamma(shapes[, 1] + shapes[, 2]), - log1p(y) - digamma(shapes[, 2]) + digamma(shapes[, 1] + shapes[, 2])) c(w) * dl.dshapes * dshapes.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = expression({ temp2 <- trigamma(shapes[, 1] + shapes[, 2]) ned2l.dshape12 <- trigamma(shapes[, 1]) - temp2 ned2l.dshape22 <- trigamma(shapes[, 2]) - temp2 ned2l.dshape1shape2 <- -temp2 wz <- matrix(NA_real_, n, dimm(M)) wz[, iam(1, 1, M)] <- ned2l.dshape12 * dshapes.deta[, 1]^2 wz[, iam(2, 2, M)] <- ned2l.dshape22 * dshapes.deta[, 2]^2 wz[, iam(1, 2, M)] <- ned2l.dshape1shape2 * dshapes.deta[, 1] * dshapes.deta[, 2] c(w) * wz })) } zoabetaR <- function(lshape1 = "loglink", lshape2 = "loglink", lpobs0 = "logitlink", lpobs1 = "logitlink", ishape1 = NULL, ishape2 = NULL, trim = 0.05, type.fitted = c("mean", "pobs0", "pobs1", "beta.mean"), parallel.shape = FALSE, parallel.pobs = FALSE, zero = NULL) { A <- 0 B <- 1 lshape1 <- as.list(substitute(lshape1)) eshape1 <- link2list(lshape1) lshape1 <- attr(eshape1, "function.name") lshape2 <- as.list(substitute(lshape2)) eshape2 <- link2list(lshape2) lshape2 <- attr(eshape2, "function.name") lprobb0 <- as.list(substitute(lpobs0)) eprobb0 <- link2list(lprobb0) lprobb0 <- attr(eprobb0, "function.name") lprobb1 <- as.list(substitute(lpobs1)) eprobb1 <- link2list(lprobb1) lprobb1 <- attr(eprobb1, "function.name") if (length( ishape1 ) && !is.Numeric( ishape1, positive = TRUE)) stop("bad input for argument 'ishape1'") if (length( ishape2 ) && !is.Numeric( ishape2, positive = TRUE)) stop("bad input for argument 'ishape2'") if (!is.Numeric(A, length.arg = 1) || !is.Numeric(B, length.arg = 1) || A >= B) stop("A must be < B, and both must be of length one") stdbeta <- (A == 0 && B == 1) type.fitted <- match.arg(type.fitted, c("mean", "pobs0", "pobs1", "beta.mean"))[1] new("vglmff", blurb = c("Standard Beta distribution with 0- and \n", "1-inflation ", "(shape parameters parameterization)\n", if (stdbeta) paste("y^(shape1-1) * (1-y)^(shape2-1) / beta(shape1,shape2),", "0 <= y <= 1, shape1>0, shape2>0\n\n") else paste("(y-",A,")^(shape1-1) * (",B, "-y)^(shape2-1) / [beta(shape1,shape2) * (", B, "-", A, ")^(shape1+shape2-1)], ", A," <= y <= ",B," shape1>0, shape2>0, ", "0 < pobs0 < 1, 0 < pobs1 < 1 \n\n", sep = ""), "Links: ", namesof("shape1", lshape1, earg = eshape1), ", ", namesof("shape2", lshape2, earg = eshape2), ", ", namesof("pobs0", lprobb0, earg = eprobb0), ", ", namesof("pobs1", lprobb1, earg = eshape1)), constraints = eval(substitute(expression({ constraints.orig <- constraints if (is.logical( .parallel.probb ) && .parallel.probb && (cind0[1] + cind1[1] <= 1)) warning("argument 'parallel.pobs' specified when there is only ", "one of 'pobs0' and 'pobs1'") cmk.s <- kronecker(matrix(1, NOS, 1), rbind(1, 1, 0, 0)) cmk.S <- kronecker(diag(NOS), rbind(diag(2), 0*diag(2))) con.s <- cm.VGAM(cmk.s, x = x, bool = .parallel.shape , constraints = constraints.orig, apply.int = TRUE, cm.default = cmk.S, cm.intercept.default = cmk.S) print("con.s") print( con.s ) cmk.p <- kronecker(matrix(1, NOS, 1), rbind(0, 0, 1, 1)) cmk.P <- kronecker(diag(NOS), rbind(0*diag(2), diag(2))) con.p <- cm.VGAM(cmk.p, x = x, bool = .parallel.probb , constraints = constraints.orig, apply.int = TRUE, cm.default = cmk.P, cm.intercept.default = cmk.P) print("con.p") print( con.p ) con.use <- con.s for (klocal in seq_along(con.s)) { print("klocal") print( klocal ) con.use[[klocal]] <- cbind(con.s[[klocal]], con.p[[klocal]]) print("con.use") print( con.use ) if (!cind0[1]) { print("hi1a") vec.use <- rep_len(c(TRUE, TRUE, FALSE, TRUE), nrow(con.use[[klocal]])) con.use[[klocal]] <- (con.use[[klocal]])[vec.use, ] } if (!cind1[1]) { print("hi1b") vec.use <- rep_len(c(TRUE, TRUE, TRUE, FALSE), nrow(con.use[[klocal]])) con.use[[klocal]] <- (con.use[[klocal]])[vec.use, ] } col.delete <- apply(con.use[[klocal]], 2, function(HkCol) all(HkCol == 0)) print("col.delete") print( col.delete ) con.use[[klocal]] <- (con.use[[klocal]])[, !col.delete] } print("con.use1") print( con.use ) constraints <- con.use constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = M1) }), list( .parallel.shape = parallel.shape, .parallel.probb = parallel.pobs, .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = NA, Q1 = 1, A = .A , B = .B , expected = TRUE, multipleResponses = TRUE, type.fitted = .type.fitted , zero = .zero ) }, list( .A = A, .B = B, .type.fitted = type.fitted, .zero = zero ))), initialize = eval(substitute(expression({ if (min(y) < .A || max(y) > .B) stop("data not within [A, B]") temp5 <- w.y.check(w = w, y = y, ncol.w.max = Inf, ncol.y.max = Inf, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y ncoly <- NOS <- ncol(y) if (ncoly > 1 && !( .stdbeta )) stop("can only input multiple responses with the standard beta") cind0 <- colSums(ind0 <- y == 0) > 0 cind1 <- colSums(ind1 <- y == 1) > 0 if (!any(cind0 | cind1)) stop("no 0s or 1s in the responses to perform 0- and/or ", "1-inflation! ", "Try using betaff() or betaR() instead.") if (ncoly > 1 && !all(cind0 == cind0[1]) && !all(cind0 == cind0[1])) stop("with multiple responses, cannot have 0-inflation in ", "some responses and 1-inflation in other responses") M1 <- 2 + cind0[1] + cind1[1] M <- M1 * NOS print("c(cind0, cind1)") print( c(cind0, cind1) ) mynames1 <- param.names("shape1", ncoly, skip1 = TRUE) mynames2 <- param.names("shape2", ncoly, skip1 = TRUE) mynames3 <- param.names("pobs0", ncoly, skip1 = TRUE) mynames4 <- param.names("pobs1", ncoly, skip1 = TRUE) predictors.names <- c(namesof(mynames1, .lshape1 , earg = .eshape1 , short = TRUE), namesof(mynames2, .lshape2 , earg = .eshape2 , short = TRUE), if (cind0[1]) namesof(mynames3, .lprobb0 , earg = .eprobb0 , short = TRUE) else NULL, if (cind1[1]) namesof(mynames4, .lprobb1 , earg = .eprobb1 , short = TRUE) else NULL)[interleave.VGAM(M, M1 = M1)] extra$type.fitted <- .type.fitted extra$colnames.y <- colnames(y) extra$M1 <- M1 extra$cind0 <- cind0 extra$cind1 <- cind1 if (!length(etastart)) { p0init <- matrix(colMeans(ind0), n, ncoly, byrow = TRUE) p1init <- matrix(colMeans(ind1), n, ncoly, byrow = TRUE) mu1d <- matrix(NA_real_, n, NOS) for (jay in 1:ncoly) { yy <- y[, jay] yy <- yy[ .A < yy & yy < .B ] mu1d[, jay] <- weighted.mean(yy, trim = .trim ) } uu <- (mu1d - .A ) / ( .B - .A ) DD <- ( .B - .A )^2 p.init <- if (is.Numeric( .ishape1 )) matrix( .ishape1 , n, ncoly, byrow = TRUE) else uu^2 * (1 - uu) * DD / var(yy) - uu p.init[p.init < 0.01] <- 0.01 q.init <- if (is.Numeric( .ishape2 )) matrix( .ishape2 , n, ncoly, byrow = TRUE) else p.init * (1 - uu) / uu q.init[q.init < 0.01] <- 0.01 etastart <- cbind( theta2eta(p.init, .lshape1 , earg = .eshape1 ), theta2eta(q.init, .lshape2 , earg = .eshape2 ), if (cind0[1]) theta2eta(p0init, .lprobb0 , earg = .eprobb0 ) else NULL, if (cind1[1]) theta2eta(p1init, .lprobb1 , earg = .eprobb1 ) else NULL)[, interleave.VGAM(M, M1 = M1)] } }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1, .ishape1 = ishape1, .ishape2 = ishape2, .trim = trim, .A = A, .B = B, .type.fitted = type.fitted, .stdbeta = stdbeta ))), linkinv = eval(substitute(function(eta, extra = NULL) { M1 <- extra$M1 cind0 <- extra$cind0 cind1 <- extra$cind1 NOS <- ncol(eta) / M1 shape1 <- eta2theta(eta[, c(TRUE, rep(FALSE, M1 - 1)), drop = FALSE], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE, rep(FALSE, M1 - 2)), drop = FALSE], .lshape2 , earg = .eshape2 ) probb0 <- if (cind0[1]) eta2theta(eta[, c(FALSE, FALSE, TRUE, if (cind1[1]) FALSE else NULL), drop = FALSE], .lprobb0 , earg = .eprobb0 ) else 0 probb1 <- if (cind1[1]) eta2theta(eta[, c(FALSE, FALSE, if (cind0[1]) FALSE else NULL, TRUE), drop = FALSE], .lprobb1 , earg = .eprobb1 ) else 0 type.fitted <- match.arg(extra$type.fitted, c("mean", "pobs0", "pobs1", "beta.mean"))[1] ans <- switch(type.fitted, "mean" = (1 - probb0) * shape1 / (shape1 + shape2) + probb1 * shape2 / (shape1 + shape2), "beta.mean" = shape1/(shape1+shape2), "pobs0" = probb0, "pobs1" = probb1) label.cols.y(ans, colnames.y = extra$colnames.y, NOS = NOS) }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1 ))), last = eval(substitute(expression({ misc$link <- rep_len( c( .lshape1 , .lshape2 , if (cind0[1]) .lprobb0 else NULL, if (cind1[1]) .lprobb1 else NULL), M) names(misc$link) <- c(mynames1, mynames2, if (cind0[1]) mynames3 else NULL, if (cind1[1]) mynames4 else NULL)[ interleave.VGAM(M, M1 = M1)] misc$earg <- vector("list", M) names(misc$earg) <- names(misc$link) jay <- 1 while (jay <= M) { misc$earg[[jay]] <- .eshape1 jay <- jay + 1 misc$earg[[jay]] <- .eshape2 jay <- jay + 1 if (cind0[1]) { misc$earg[[jay]] <- .eprobb0 jay <- jay + 1 } if (cind1[1]) { misc$earg[[jay]] <- .eprobb1 jay <- jay + 1 } } misc$supportlimits <- c( .A , .B ) }), list( .lshape1 = lshape1, .lshape2 = lshape2, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1, .A = A, .B = B ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { M1 <- 4 M1 <- extra$M1 cind0 <- extra$cind0 cind1 <- extra$cind1 NOS <- ncol(eta) / M1 shape1 <- eta2theta(eta[, c(TRUE, rep(FALSE, M1 - 1)), drop = FALSE], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE, rep(FALSE, M1 - 2)), drop = FALSE], .lshape2 , earg = .eshape2 ) probb0 <- if (cind0[1]) eta2theta(eta[, c(FALSE, FALSE, TRUE, if (cind1[1]) FALSE else NULL), drop = FALSE], .lprobb0 , earg = .eprobb0 ) else 0 probb1 <- if (cind1[1]) eta2theta(eta[, c(FALSE, FALSE, if (cind0[1]) FALSE else NULL, TRUE), drop = FALSE], .lprobb1 , earg = .eprobb1 ) else 0 if (residuals) { stop("loglikelihood residuals not implemented yet") } else { zedd <- (y - .A ) / ( .B - .A ) ll.elts <- c(w) * (dzoabeta(x = zedd, shape1 = shape1, shape2 = shape2, pobs0 = probb0, pobs1 = probb1, log = TRUE) - log( abs( .B - .A ))) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1 ))), vfamily = "zoabetaR", validparams = eval(substitute(function(eta, y, extra = NULL) { M1 <- 4 M1 <- extra$M1 cind0 <- extra$cind0 cind1 <- extra$cind1 NOS <- ncol(eta) / M1 shape1 <- eta2theta(eta[, c(TRUE, rep(FALSE, M1 - 1)), drop = FALSE], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE, rep(FALSE, M1 - 2)), drop = FALSE], .lshape2 , earg = .eshape2 ) probb0 <- if (cind0[1]) eta2theta(eta[, c(FALSE, FALSE, TRUE, if (cind1[1]) FALSE else NULL), drop = FALSE], .lprobb0 , earg = .eprobb0 ) else 0.5 probb1 <- if (cind1[1]) eta2theta(eta[, c(FALSE, FALSE, if (cind0[1]) FALSE else NULL, TRUE), drop = FALSE], .lprobb1 , earg = .eprobb1 ) else 0.5 okay1 <- all(is.finite(shape1)) && all(0 < shape1) && all(is.finite(shape2)) && all(0 < shape2) && all(is.finite(probb0)) && all(0 < probb0 & probb0 < 1) && all(is.finite(probb1)) && all(0 < probb1 & probb1 < 1) okay1 }, list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1 ))), deriv = eval(substitute(expression({ M1 <- 4 M1 <- extra$M1 cind0 <- extra$cind0 cind1 <- extra$cind1 NOS <- ncol(eta) / M1 shape1 <- eta2theta(eta[, c(TRUE, rep(FALSE, M1 - 1)), drop = FALSE], .lshape1 , earg = .eshape1 ) shape2 <- eta2theta(eta[, c(FALSE, TRUE, rep(FALSE, M1 - 2)), drop = FALSE], .lshape2 , earg = .eshape2 ) probb0 <- if (cind0[1]) eta2theta(eta[, c(FALSE, FALSE, TRUE, if (cind1[1]) FALSE else NULL), drop = FALSE], .lprobb0 , earg = .eprobb0 ) else 0 probb1 <- if (cind1[1]) eta2theta(eta[, c(FALSE, FALSE, if (cind0[1]) FALSE else NULL, TRUE), drop = FALSE], .lprobb1 , earg = .eprobb1 ) else 0 dshape1.deta <- dtheta.deta(shape1, .lshape1 , earg = .eshape1 ) dshape2.deta <- dtheta.deta(shape2, .lshape2 , earg = .eshape2 ) dprobb0.deta <- dtheta.deta(probb0, .lprobb0 , earg = .eprobb0 ) dprobb1.deta <- dtheta.deta(probb1, .lprobb1 , earg = .eprobb1 ) index0 <- y == 0 index1 <- y == 1 indexi <- !index0 & !index1 dig.sum <- digamma(shape1 + shape2) QQ <- 1 - probb0 - probb1 if (cind0[1]) { dl.dprobb0 <- -1 / QQ dl.dprobb0[index0] <- 1 / probb0[index0] dl.dprobb0[index1] <- 0 } if (cind1[1]) { dl.dprobb1 <- -1 / QQ dl.dprobb1[index0] <- 0 dl.dprobb1[index1] <- 1 / probb1[index1] } dl.dshape1 <- log(y) - digamma(shape1) + dig.sum dl.dshape2 <- log1p(-y) - digamma(shape2) + dig.sum dl.dshape1[!indexi] <- 0 dl.dshape2[!indexi] <- 0 myderiv <- c(w) * cbind(dl.dshape1 * dshape1.deta, dl.dshape2 * dshape2.deta, if (cind0[1]) dl.dprobb0 * dprobb0.deta else NULL, if (cind1[1]) dl.dprobb1 * dprobb1.deta else NULL) colnames(myderiv) <- NULL myderiv[, interleave.VGAM(M, M1 = M1)] }), list( .lshape1 = lshape1, .lshape2 = lshape2, .A = A, .B = B, .eshape1 = eshape1, .eshape2 = eshape2, .lprobb0 = lprobb0, .lprobb1 = lprobb1, .eprobb0 = eprobb0, .eprobb1 = eprobb1 ))), weight = expression({ trig.sum <- trigamma(shape1 + shape2) ned2l.dshape12 <- (trigamma(shape1) - trig.sum) * QQ ned2l.dshape22 <- (trigamma(shape2) - trig.sum) * QQ ned2l.dprobb02 <- (1 - probb1) / (probb0 * QQ) ned2l.dprobb12 <- (1 - probb0) / (probb1 * QQ) ned2l.dshape1shape2 <- -trig.sum * QQ ned2l.dshape2probb0 <- 0 ned2l.dprobb0probb1 <- 1 / QQ ned2l.dshape1probb0 <- 0 ned2l.dshape2probb1 <- 0 ned2l.dshape1probb1 <- 0 ned2l.dshape1probb0 <- 0 wz <- array(c(c(w) * ned2l.dshape12 * dshape1.deta^2, c(w) * ned2l.dshape22 * dshape2.deta^2, if (cind0[1]) c(w) * ned2l.dprobb02 * dprobb0.deta^2 else NULL, if (cind1[1]) c(w) * ned2l.dprobb12 * dprobb1.deta^2 else NULL, c(w) * ned2l.dshape1shape2 * dshape1.deta * dshape2.deta, if (cind0[1]) c(w) * ned2l.dshape2probb0 * dshape2.deta * dprobb0.deta, c(w) * ned2l.dprobb0probb1 * dprobb0.deta * dprobb1.deta, if (cind0[1]) c(w) * ned2l.dshape1probb0 * dshape1.deta * dprobb0.deta, if (cind1[1]) c(w) * ned2l.dshape2probb1 * dshape2.deta * dprobb1.deta, if (cind1[1]) c(w) * ned2l.dshape1probb1 * dshape1.deta * dprobb1.deta), dim = c(n, M / M1, M1*(M1+1)/2)) wz <- arwz2wz(wz, M = M, M1 = M1) wz })) } dtopple <- function(x, shape, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) L <- max(length(x), length(shape)) if (length(x) != L) x <- rep_len(x, L) if (length(shape) != L) shape <- rep_len(shape, L) logdensity <- rep_len(log(0), L) xok <- (0 <= x) & (x <= 1) logdensity[xok] <- log(2) + log(shape[xok]) + log1p(-x[xok]) + (shape[xok] - 1) * (log(x[xok]) + log(2) + log1p(-x[xok]/2)) logdensity[shape >= 1] <- NaN if (log.arg) logdensity else exp(logdensity) } ptopple <- function(q, shape, lower.tail = TRUE, log.p = FALSE) { if (!is.logical(lower.tail) || length(lower.tail ) != 1) stop("bad input for argument 'lower.tail'") if (!is.logical(log.p) || length(log.p) != 1) stop("bad input for argument 'log.p'") if (lower.tail) { if (log.p) { ans <- shape * (log(q) + log(2) + log1p(-q/2)) ans[q <= 0 ] <- -Inf ans[q >= 1] <- 0 } else { ans <- (q * (2 - q))^shape ans[q <= 0] <- 0 ans[q >= 1] <- 1 } } else { if (log.p) { ans <- log1p(-(q * (2 - q))^shape) ans[q <= 0] <- 0 ans[q >= 1] <- -Inf } else { ans <- exp(log1p(-(q * (2 - q))^shape)) ans[q <= 0] <- 1 ans[q >= 1] <- 0 } } ans[shape <= 0] <- NaN ans[shape >= 1] <- NaN ans } qtopple <- function(p, shape) { ans <- -expm1(0.5 * log1p(-p^(1/shape))) ans[shape <= 0] <- NaN ans[shape >= 1] <- NaN ans } rtopple <- function(n, shape) { qtopple(runif(n), shape) } topple <- function(lshape = "logitlink", zero = NULL, gshape = ppoints(8), parallel = FALSE, type.fitted = c("mean", "percentiles", "Qlink"), percentiles = 50) { type.fitted <- match.arg(type.fitted, c("mean", "percentiles", "Qlink"))[1] lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Topp-Leone distribution ", "F(y; shape) = (y * (2 - y))^shape, ", "0 < y < 1, 0 < shape < 1\n", "Link: ", namesof("shape", lshape, earg = eshape)), constraints = eval(substitute(expression({ constraints <- cm.VGAM(matrix(1, M, 1), x = x, bool = .parallel , constraints, apply.int = FALSE) constraints <- cm.zero.VGAM(constraints, x = x, .zero , M = M, predictors.names = predictors.names, M1 = 1) }), list( .parallel = parallel, .zero = zero ))), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, hadof = TRUE, multipleResponses = TRUE, parallel = .parallel , parameters.names = "shape", percentiles = .percentiles , type.fitted = .type.fitted , zero = .zero ) }, list( .parallel = parallel, .percentiles = percentiles , .type.fitted = type.fitted, .zero = zero ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, Is.positive.y = TRUE, ncol.w.max = Inf, ncol.y.max = Inf, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y if (any(y >= 1)) stop("response must be in (0, 1)") ncoly <- ncol(y) M1 <- 1 M <- M1 * ncoly extra$ncoly <- ncoly extra$type.fitted <- .type.fitted extra$colnames.y <- colnames(y) extra$percentiles <- .percentiles extra$M1 <- M1 if ((NOS <- M / M1) > 1 && length( .percentiles ) > 1) stop("can only have one response when 'percentiles' is a ", "vector longer than unity") mynames1 <- param.names("shape", ncoly, skip1 = TRUE) predictors.names <- namesof(mynames1, .lshape , earg = .eshape , tag = FALSE) if (!length(etastart)) { shape.init <- matrix(0, nrow(x), ncoly) gshape <- .gshape topple.Loglikfun <- function(shape, y, x = NULL, w, extraargs = NULL) { sum(c(w) * dtopple(x = y, shape = shape, log = TRUE)) } for (jay in 1:ncoly) { shape.init[, jay] <- grid.search(gshape, objfun = topple.Loglikfun, y = y[, jay], w = w[, jay]) } etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .gshape = gshape, .eshape = eshape, .percentiles = percentiles, .type.fitted = type.fitted ))), linkinv = eval(substitute(function(eta, extra = NULL) { type.fitted <- if (length(extra$type.fitted)) { extra$type.fitted } else { warning("cannot find 'type.fitted'. Returning the 'mean'.") "mean" } type.fitted <- match.arg(type.fitted, c("mean", "percentiles", "Qlink"))[1] if (type.fitted == "Qlink") { eta2theta(eta, link = "logitlink") } else { shape <- eta2theta(eta, .lshape , earg = .eshape ) pcent <- extra$percentiles perc.mat <- matrix(pcent, NROW(eta), length(pcent), byrow = TRUE) / 100 fv <- switch(type.fitted, "mean" = 1 - (gamma(1 + shape))^2 * 4^shape / gamma(2 * (1 + shape)), "percentiles" = qtopple(perc.mat, shape = matrix(shape, nrow(perc.mat), ncol(perc.mat)))) if (type.fitted == "percentiles") fv <- label.cols.y(fv, colnames.y = extra$colnames.y, NOS = NCOL(eta), percentiles = pcent, one.on.one = FALSE) fv } }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$earg <- vector("list", M) names(misc$earg) <- mynames1 for (ilocal in 1:ncoly) { misc$earg[[ilocal]] <- .eshape } misc$link <- rep_len( .lshape , ncoly) names(misc$link) <- mynames1 }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dtopple(x = y, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("topple"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape & shape < 1) okay1 }, list( .lshape = lshape, .eshape = eshape ))), hadof = eval(substitute( function(eta, extra = list(), deriv = 1, linpred.index = 1, w = 1, dim.wz = c(NROW(eta), NCOL(eta) * (NCOL(eta)+1)/2), ...) { shape <- eta2theta(eta, .lshape , earg = .eshape ) ans <- c(w) * switch(as.character(deriv), "0" = 1 / shape^2, "1" = -2 / shape^3, "2" = 6 / shape^4, "3" = -24 / shape^5, stop("argument 'deriv' must be 0, 1, 2 or 3")) if (deriv == 0) ans else retain.col(ans, linpred.index) }, list( .lshape = lshape, .eshape = eshape ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) shape <- eta2theta(eta, .lshape , earg = .eshape ) rtopple(nsim * length(shape), shape = c(shape)) }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) dl.dshape <- 1 / shape + log(y) + log(2) + log1p(-y/2) dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = eval(substitute(expression({ ned2l.dshape2 <- 1 / shape^2 wz <- c(w) * ned2l.dshape2 * dshape.deta^2 wz }), list( .lshape = lshape, .eshape = eshape )))) } dzeta <- function(x, shape, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) LLL <- max(length(shape), length(x)) if (length(x) != LLL) x <- rep_len(x, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) ox <- !is.finite(x) zero <- ox | round(x) != x | x < 1 ans <- rep_len(if (log.arg) log(0) else 0, LLL) if (any(!zero)) { if (log.arg) { ans[!zero] <- (-shape[!zero]-1) * log(x[!zero]) - log(zeta(shape[!zero] + 1)) } else { ans[!zero] <- x[!zero]^(-shape[!zero]-1) / zeta(shape[!zero]+1) } } if (any(ox)) ans[ox] <- if (log.arg) log(0) else 0 ans[shape <= 0] <- NaN ans } pzeta <- function(q, shape, lower.tail = TRUE) { LLL <- max(lenq <- length(q), lens <- length(shape)) if (length(q) != LLL) q <- rep_len(q, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) ans <- rep_len(0, LLL) aa <- 12 qfloor <- floor(q) for (nn in 1:(aa-1)) ans <- ans + as.numeric(nn <= qfloor) / nn^(shape+1) vecTF <- (aa-1 <= qfloor) if (lower.tail) { if (any(vecTF)) ans[vecTF] <- zeta(shape[vecTF]+1) - Zeta.aux(shape[vecTF]+1, qfloor[vecTF] ) } else { ans <- zeta(shape+1) - ans if (any(vecTF)) ans[vecTF] <- Zeta.aux(shape[vecTF]+1, qfloor[vecTF] ) } ans / zeta(shape+1) } qzeta <- function(p, shape) { LLL <- max(lenp <- length(p), lens <- length(shape)) if (length(p) != LLL) p <- rep_len(p, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) ans <- rep_len(0, LLL) lowsup <- 1 lo <- rep_len(lowsup - 0.5, LLL) approx.ans <- lo hi <- 2 * lo + 10.5 dont.iterate <- p == 1 | shape <= 0 done <- p <= pzeta(hi, shape) | dont.iterate while (!all(done)) { lo[!done] <- hi[!done] hi[!done] <- 2 * hi[!done] + 10.5 done[!done] <- (p[!done] <= pzeta(hi[!done], shape[!done])) } foo <- function(q, shape, p) pzeta(q, shape) - p lhs <- (p <= dzeta(1, shape)) | dont.iterate approx.ans[!lhs] <- bisection.basic(foo, lo[!lhs], hi[!lhs], tol = 1/16, shape = shape[!lhs], p = p[!lhs]) faa <- floor(approx.ans) ans <- ifelse(pzeta(faa, shape) < p & p <= pzeta(faa+1, shape), faa+1, faa) ans[p == 1] <- Inf ans[shape <= 0] <- NaN ans } rzeta <- function(n, shape) { qzeta(runif(n), shape) } zetaff <- function(lshape = "loglink", ishape = NULL, gshape = 1 + exp(-seq(7)), zero = NULL) { if (length(ishape) && !is.Numeric(ishape, positive = TRUE)) stop("argument 'ishape' must be > 0") lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Zeta distribution ", "f(y; shape) = 1/(y^(shape+1) zeta(shape+1)), ", "shape>0, y = 1, 2,..\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: zeta(shape) / zeta(shape+1), provided shape>1\n", "Variance: zeta(shape-1) / zeta(shape+1) - mean^2, if shape>2"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, multipleResponses = TRUE, parameters.names = "shape", zero = .zero , lshape = .lshape ) }, list( .lshape = lshape, .zero = zero ))), initialize = eval(substitute(expression({ temp5 <- w.y.check(w = w, y = y, ncol.w.max = Inf, ncol.y.max = Inf, Is.integer.y = TRUE, Is.positive.y = TRUE, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y ncoly <- ncol(y) mynames1 <- param.names("shape", ncoly, skip1 = TRUE) predictors.names <- namesof(mynames1, .lshape , earg = .eshape , tag = FALSE) M1 <- 1 extra$ncoly <- ncoly extra$M1 <- M1 M <- M1 * ncoly if (!length(etastart)) { zetaff.Loglikfun <- function(shape, y, x, w, extraargs) { sum(c(w) * dzeta(x = y, shape, log = TRUE)) } gshape <- .gshape if (!length( .ishape )) { shape.init <- matrix(NA_real_, n, M, byrow = TRUE) for (jay in 1:ncoly) { shape.init[, jay] <- grid.search(gshape, objfun = zetaff.Loglikfun, y = y[, jay], x = x, w = w[, jay]) } } else { shape.init <- matrix( .ishape , n, M, byrow = TRUE) } etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape, .gshape = gshape ))), linkinv = eval(substitute(function(eta, extra = NULL) { ans <- pp <- eta2theta(eta, .lshape , earg = .eshape ) ans[pp > 1] <- zeta(pp[pp > 1]) / zeta(pp[pp > 1] + 1) ans[pp <= 1] <- NA ans }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$link <- rep_len( .lshape , ncoly) names(misc$link) <- mynames1 misc$earg <- vector("list", M) names(misc$earg) <- mynames1 for (jay in 1:ncoly) { misc$earg[[jay]] <- .eshape } }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dzeta(x = y, shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("zetaff"), hadof = eval(substitute( function(eta, extra = list(), deriv = 1, linpred.index = 1, w = 1, dim.wz = c(NROW(eta), NCOL(eta) * (NCOL(eta)+1)/2), ...) { shape <- eta2theta(eta, .lshape , earg = .eshape ) fred0 <- zeta(shape+1) fred1 <- zeta(shape+1, deriv = 1) fred2 <- zeta(shape+1, deriv = 2) ans <- c(w) * switch(as.character(deriv), "0" = fred2 / fred0 - (fred1/fred0)^2, "1" = (zeta(shape + 1, deriv = 3) - fred2 * fred1 / fred0) / fred0 - 2 * (fred1 / fred0) * ( fred2 /fred0 - (fred1/fred0)^2), "2" = NA * theta, "3" = NA * theta, stop("argument 'deriv' must be 0, 1, 2 or 3")) if (deriv == 0) ans else retain.col(ans, linpred.index) }, list( .lshape = lshape, .eshape = eshape ))), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) fred0 <- zeta(shape + 1) fred1 <- zeta(shape + 1, deriv = 1) dl.dshape <- -log(y) - fred1 / fred0 dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = expression({ NOS <- NCOL(y) ned2l.dshape2 <- zeta(shape + 1, deriv = 2) / fred0 - (fred1 / fred0)^2 wz <- ned2l.dshape2 * dshape.deta^2 w.wz.merge(w = w, wz = wz, n = n, M = M, ndepy = NOS) })) } gharmonic2 <- function(n, shape = 1) { if (!is.Numeric(n, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'n'") LLL <- max(length(n), length(shape)) if (length(n) != LLL) n <- rep_len(n, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) aa <- 12 ans <- rep_len(0, LLL) for (ii in 1:aa) ans <- ans + as.numeric(ii <= n) / ii^shape vecTF <- (aa < n) if (any(vecTF)) ans[vecTF] <- zeta(shape[vecTF]) - Zeta.aux(shape[vecTF], 1 + n[vecTF]) ans } gharmonic <- function(n, shape = 1, deriv = 0) { if (!is.Numeric(n, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'n'") if (!is.Numeric(deriv, length.arg = 1, integer.valued = TRUE) || deriv < 0) stop("bad input for argument 'deriv'") lognexponent <- deriv sign <- ifelse(deriv %% 2 == 0, 1, -1) ans <- if (length(n) == 1 && length(shape) == 1) { if (lognexponent != 0) sum(log(1:n)^lognexponent * (1:n)^(-shape)) else sum((1:n)^(-shape)) } else { LEN <- max(length(n), length(shape)) n <- rep_len(n, LEN) ans <- shape <- rep_len(shape, LEN) if (lognexponent != 0) { for (ii in 1:LEN) ans[ii] <- sum(log(1:n[ii])^lognexponent * (1:n[ii])^(-shape[ii])) } else { for (ii in 1:LEN) ans[ii] <- sum((1:n[ii])^(-shape[ii])) } ans } sign * ans } dzipf <- function(x, N, shape, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) if (!is.Numeric(x)) stop("bad input for argument 'x'") if (!is.Numeric(N, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'N'") if (!is.Numeric(shape, positive = TRUE)) stop("bad input for argument 'shape'") nn <- max(length(x), length(N), length(shape)) if (length(x) != nn) x <- rep_len(x, nn) if (length(N) != nn) N <- rep_len(N, nn) if (length(shape) != nn) shape <- rep_len(shape, nn) ox <- !is.finite(x) zero <- ox | round(x) != x | x < 1 | x > N ans <- (if (log.arg) log(0) else 0) * x if (any(!zero)) if (log.arg) { ans[!zero] <- (-shape[!zero]) * log(x[!zero]) - log(gharmonic2(N[!zero], shape[!zero])) } else { ans[!zero] <- x[!zero]^(-shape[!zero]) / gharmonic2(N[!zero], shape[!zero]) } ans } pzipf <- function(q, N, shape, log.p = FALSE) { if (!is.Numeric(N, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'N'") nn <- max(length(q), length(N), length(shape)) if (length(q) != nn) q <- rep_len(q, nn) if (length(N) != nn) N <- rep_len(N, nn) if (length(shape) != nn) shape <- rep_len(shape, nn) oq <- !is.finite(q) dont.iterate <- shape <= 0 zeroOR1 <- oq | q < 1 | N <= q | dont.iterate floorq <- floor(q) ans <- 0 * floorq ans[oq | q >= N] <- 1 if (any(!zeroOR1)) ans[!zeroOR1] <- gharmonic2(floorq[!zeroOR1], shape[!zeroOR1]) / gharmonic2( N[!zeroOR1], shape[!zeroOR1]) ans[shape <= 0] <- NaN if (log.p) log(ans) else ans } qzipf <- function(p, N, shape) { if (!is.Numeric(p)) stop("bad input for argument 'p'") if (!is.Numeric(N, integer.valued = TRUE, positive = TRUE)) stop("bad input for argument 'N'") if (!is.Numeric(shape, positive = TRUE)) stop("bad input for argument 'shape'") nn <- max(length(p), length(N), length(shape)) if (length(p) != nn) p <- rep_len(p, nn) if (length(N) != nn) N <- rep_len(N, nn) if (length(shape) != nn) shape <- rep_len(shape, nn) a <- rep_len(1, nn) b <- rep_len(N, nn) approx.ans <- a foo <- function(q, N, shape, p) pzipf(q, N, shape) - p dont.iterate <- p == 1 | shape <= 0 lhs <- (p <= dzipf(1, N, shape)) | dont.iterate approx.ans[!lhs] <- bisection.basic(foo, a[!lhs], b[!lhs], shape = shape[!lhs], tol = 1/16, p = p[!lhs], N = N[!lhs]) faa <- floor(approx.ans) ans <- ifelse(pzipf(faa, N, shape) < p & p <= pzipf(faa+1, N, shape), faa+1, faa) ans[shape <= 0] <- NaN ans[p == 1] <- N ans } rzipf <- function(n, N, shape) { qzipf(runif(n), N, shape) } zipf <- function(N = NULL, lshape = "loglink", ishape = NULL) { if (length(N) && (!is.Numeric(N, positive = TRUE, integer.valued = TRUE, length.arg = 1) || N <= 1)) stop("bad input for argument 'N'") enteredN <- length(N) if (length(ishape) && !is.Numeric(ishape, positive = TRUE)) stop("argument 'ishape' must be > 0") lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Zipf distribution f(y;s) = y^(-s) / sum((1:N)^(-s)),", " s > 0, y = 1, 2,...,N", ifelse(enteredN, paste(" = ", N, sep = ""), ""), "\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: gharmonic(N, shape-1) / gharmonic(N, shape)"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, multipleResponses = FALSE, parameters.names = "shape", N = enteredN, lshape = .lshape ) }, list( .lshape = lshape, .enteredN = enteredN ))), initialize = eval(substitute(expression({ w.y.check(w = w, y = y, Is.integer.y = TRUE) predictors.names <- namesof("shape", .lshape , earg = .eshape , tag = FALSE) NN <- .N if (!is.Numeric(NN, length.arg = 1, positive = TRUE, integer.valued = TRUE)) NN <- max(y) if (max(y) > NN) stop("maximum of the response is greater than argument 'N'") if (any(y < 1)) stop("all response values must be in 1, 2, 3,...,N( = ", NN,")") extra$N <- NN if (!length(etastart)) { llfun <- function(shape, y, N, w) { sum(c(w) * dzipf(x = y, N = extra$N, shape = shape, log = TRUE)) } shape.init <- if (length( .ishape )) .ishape else getInitVals(gvals = seq(0.1, 3, length.out = 19), llfun = llfun, y = y, N = extra$N, w = w) shape.init <- rep_len(shape.init, length(y)) if ( .lshape == "logloglink") shape.init[shape.init <= 1] <- 1.2 etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape, .N = N ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) gharmonic2(extra$N, shape = shape - 1) / gharmonic2(extra$N, shape = shape) }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$expected <- FALSE misc$link <- c(shape = .lshape) misc$earg <- list(shape = .eshape ) misc$N <- extra$N }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * dzipf(x = y, N = extra$N, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("zipf"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), simslot = eval(substitute( function(object, nsim) { pwts <- if (length(pwts <- [email protected]) > 0) pwts else weights(object, type = "prior") if (any(pwts != 1)) warning("ignoring prior weights") eta <- predict(object) extra <- object@extra shape <- eta2theta(eta, .lshape , earg = .eshape ) rzipf(nsim * length(shape), N = extra$N, shape = shape) }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) fred1 <- gharmonic(extra$N, shape, deriv = 1) fred0 <- gharmonic2(extra$N, shape) dl.dshape <- -log(y) - fred1 / fred0 dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) d2shape.deta2 <- d2theta.deta2(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = expression({ d2l.dshape <- gharmonic(extra$N, shape, deriv = 2) / fred0 - (fred1/fred0)^2 wz <- c(w) * (dshape.deta^2 * d2l.dshape - d2shape.deta2 * dl.dshape) wz })) } ddiffzeta <- function(x, shape, start = 1, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) LLL <- max(length(shape), length(x), length(start)) if (length(x) != LLL) x <- rep_len(x, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) ox <- !is.finite(x) zero <- ox | round(x) != x | x < start ans <- rep_len(if (log.arg) log(0) else 0, LLL) if (any(!zero)) { ans[!zero] <- (start[!zero] / x[!zero]) ^(shape[!zero]) - (start[!zero] / (1 + x[!zero]))^(shape[!zero]) if (log.arg) ans[!zero] <- log(ans[!zero]) } if (any(ox)) ans[ox] <- if (log.arg) log(0) else 0 ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } pdiffzeta <- function(q, shape, start = 1, lower.tail = TRUE) { LLL <- max(length(shape), length(q), length(start)) if (length(q) != LLL) q <- rep_len(q, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) if (lower.tail) { ans <- 1 - (start / floor(1 + q))^shape } else { ans <- (start / floor(1 + q))^shape } ans[q < start] <- if (lower.tail) 0 else 1 ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } qdiffzeta <- function(p, shape, start = 1) { LLL <- max(length(p), length(shape), length(start)) if (length(p) != LLL) p <- rep_len(p, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) lo <- rep_len(start, LLL) approx.ans <- lo hi <- 2 * lo + 10.5 dont.iterate <- p == 1 | shape <= 0 | start != round(start) | start < 1 done <- p <= pdiffzeta(hi, shape, start = start) | dont.iterate max.iter <- 100 iter <- 0 while (!all(done) && iter < max.iter) { lo[!done] <- hi[!done] hi[!done] <- 2 * hi[!done] + 10.5 done[!done] <- is.infinite(hi[!done]) | (p[!done] <= pdiffzeta(hi[!done], shape[!done], start[!done])) iter <- iter + 1 } foo <- function(q, shape, start, p) pdiffzeta(q, shape, start) - p lhs <- (p <= ddiffzeta(start, shape, start = start)) | dont.iterate approx.ans[!lhs] <- bisection.basic(foo, lo[!lhs], hi[!lhs], tol = 1/16, shape = shape[!lhs], start = start[!lhs], p = p[!lhs]) faa <- floor(approx.ans) ans <- ifelse(pdiffzeta(faa , shape, start = start) < p & p <= pdiffzeta(faa+1, shape, start = start), faa+1, faa) ans[p == 1] <- Inf ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } rdiffzeta <- function(n, shape, start = 1) { rr <- runif(n) qdiffzeta(rr, shape, start = start) } diffzeta <- function(start = 1, lshape = "loglink", ishape = NULL) { if (!is.Numeric(start, positive = TRUE, integer.valued = TRUE, length.arg = 1)) stop("bad input for argument 'start'") enteredstart <- length(start) if (length(ishape) && !is.Numeric(ishape, positive = TRUE)) stop("argument 'ishape' must be > 0") lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Difference in 2 Zipf distributions ", "f(y; shape) = y^(-shape) / sum((1:start)^(-shape)), ", "shape > 0, start, start+1,...", ifelse(enteredstart, paste("start = ", start, sep = ""), ""), "\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: gharmonic(start, shape-1) / gharmonic(start, shape)"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, multipleResponses = TRUE, start = .start , parameters.names = "shape") }, list( .start = start ))), initialize = eval(substitute(expression({ start <- .start temp5 <- w.y.check(w = w, y = y, ncol.w.max = Inf, ncol.y.max = Inf, Is.integer.y = TRUE, Is.positive.y = TRUE, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y if (any(y < start)) stop("some response values less than 'start'") predictors.names <- namesof("shape", .lshape , earg = .eshape , tag = FALSE) extra$start <- start if (!length(etastart)) { llfun <- function(shape, y, start, w) { sum(c(w) * ddiffzeta(x = y, start = extra$start, shape = shape, log = TRUE)) } shape.init <- if (length( .ishape )) .ishape else getInitVals(gvals = seq(0.1, 3.0, length.out = 19), llfun = llfun, y = y, start = extra$start, w = w) shape.init <- rep_len(shape.init, length(y)) if ( .lshape == "logloglink") shape.init[shape.init <= 1] <- 1.2 etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape, .start = start ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) aa <- extra$start if (length(aa) != 1 || aa < 1 || round(aa) != aa) stop("the 'start' variable must be of unit length") if (aa == 1) return(zeta(shape)) mymat <- matrix(1:aa, NROW(eta), aa, byrow = TRUE) temp1 <- rowSums(1 / mymat^shape) (aa^shape) * (zeta(shape) - temp1 + 1 / aa^(shape-1)) }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$expected <- FALSE misc$link <- c(shape = .lshape ) misc$earg <- list(shape = .eshape ) misc$start <- extra$start }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * ddiffzeta(x = y, start = extra$start, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("diffzeta"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) temp1 <- extra$start / y temp2 <- extra$start / (y+1) AA <- temp1^shape - temp2^shape Aprime <- log(temp1) * temp1^shape - log(temp2) * temp2^shape dl.dshape <- Aprime / AA dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = expression({ ned2l.dshape <- (Aprime / AA)^2 wz <- c(w) * ned2l.dshape * dshape.deta^2 wz })) } ddiffzeta <- function(x, shape, start = 1, log = FALSE) { if (!is.logical(log.arg <- log) || length(log) != 1) stop("bad input for argument 'log'") rm(log) LLL <- max(length(shape), length(x), length(start)) if (length(x) != LLL) x <- rep_len(x, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) ox <- !is.finite(x) zero <- ox | round(x) != x | x < start ans <- rep_len(if (log.arg) log(0) else 0, LLL) if (any(!zero)) { ans[!zero] <- (start[!zero] / x[!zero]) ^(shape[!zero]) - (start[!zero] / (1 + x[!zero]))^(shape[!zero]) if (log.arg) ans[!zero] <- log(ans[!zero]) } if (any(ox)) ans[ox] <- if (log.arg) log(0) else 0 ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } pdiffzeta <- function(q, shape, start = 1, lower.tail = TRUE) { LLL <- max(length(shape), length(q), length(start)) if (length(q) != LLL) q <- rep_len(q, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) if (lower.tail) { ans <- 1 - (start / floor(1 + q))^shape } else { ans <- (start / floor(1 + q))^shape } ans[q < start] <- if (lower.tail) 0 else 1 ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } qdiffzeta <- function(p, shape, start = 1) { LLL <- max(length(p), length(shape), length(start)) if (length(p) != LLL) p <- rep_len(p, LLL) if (length(shape) != LLL) shape <- rep_len(shape, LLL) if (length(start) != LLL) start <- rep_len(start, LLL) lo <- rep_len(start, LLL) approx.ans <- lo hi <- 2 * lo + 10.5 dont.iterate <- p == 1 | shape <= 0 | start != round(start) | start < 1 done <- p <= pdiffzeta(hi, shape, start = start) | dont.iterate max.iter <- 100 iter <- 0 while (!all(done) && iter < max.iter) { lo[!done] <- hi[!done] hi[!done] <- 2 * hi[!done] + 10.5 done[!done] <- is.infinite(hi[!done]) | (p[!done] <= pdiffzeta(hi[!done], shape[!done], start[!done])) iter <- iter + 1 } foo <- function(q, shape, start, p) pdiffzeta(q, shape, start) - p lhs <- (p <= ddiffzeta(start, shape, start = start)) | dont.iterate approx.ans[!lhs] <- bisection.basic(foo, lo[!lhs], hi[!lhs], tol = 1/16, shape = shape[!lhs], start = start[!lhs], p = p[!lhs]) faa <- floor(approx.ans) ans <- ifelse(pdiffzeta(faa , shape, start = start) < p & p <= pdiffzeta(faa+1, shape, start = start), faa+1, faa) ans[p == 1] <- Inf ans[shape <= 0] <- NaN ans[start != round(start) | start < 1] <- NaN ans } rdiffzeta <- function(n, shape, start = 1) { rr <- runif(n) qdiffzeta(rr, shape, start = start) } diffzeta <- function(start = 1, lshape = "loglink", ishape = NULL) { if (!is.Numeric(start, positive = TRUE, integer.valued = TRUE, length.arg = 1)) stop("bad input for argument 'start'") enteredstart <- length(start) if (length(ishape) && !is.Numeric(ishape, positive = TRUE)) stop("argument 'ishape' must be > 0") lshape <- as.list(substitute(lshape)) eshape <- link2list(lshape) lshape <- attr(eshape, "function.name") new("vglmff", blurb = c("Difference in 2 Zipf distributions ", "f(y; shape) = y^(-shape) / sum((1:start)^(-shape)), ", "shape > 0, start, start+1,...", ifelse(enteredstart, paste("start = ", start, sep = ""), ""), "\n\n", "Link: ", namesof("shape", lshape, earg = eshape), "\n\n", "Mean: gharmonic(start, shape-1) / gharmonic(start, shape)"), infos = eval(substitute(function(...) { list(M1 = 1, Q1 = 1, expected = TRUE, multipleResponses = TRUE, start = .start , parameters.names = "shape") }, list( .start = start ))), initialize = eval(substitute(expression({ start <- .start temp5 <- w.y.check(w = w, y = y, ncol.w.max = Inf, ncol.y.max = Inf, Is.integer.y = TRUE, Is.positive.y = TRUE, out.wy = TRUE, colsyperw = 1, maximize = TRUE) w <- temp5$w y <- temp5$y if (any(y < start)) stop("some response values less than 'start'") predictors.names <- namesof("shape", .lshape , earg = .eshape , tag = FALSE) extra$start <- start if (!length(etastart)) { llfun <- function(shape, y, start, w) { sum(c(w) * ddiffzeta(x = y, start = extra$start, shape = shape, log = TRUE)) } shape.init <- if (length( .ishape )) .ishape else getInitVals(gvals = seq(0.1, 3.0, length.out = 19), llfun = llfun, y = y, start = extra$start, w = w) shape.init <- rep_len(shape.init, length(y)) if ( .lshape == "logloglink") shape.init[shape.init <= 1] <- 1.2 etastart <- theta2eta(shape.init, .lshape , earg = .eshape ) } }), list( .lshape = lshape, .eshape = eshape, .ishape = ishape, .start = start ))), linkinv = eval(substitute(function(eta, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) aa <- extra$start if (length(aa) != 1 || aa < 1 || round(aa) != aa) stop("the 'start' variable must be of unit length") if (aa == 1) return(zeta(shape)) mymat <- matrix(1:aa, NROW(eta), aa, byrow = TRUE) temp1 <- rowSums(1 / mymat^shape) (aa^shape) * (zeta(shape) - temp1 + 1 / aa^(shape-1)) }, list( .lshape = lshape, .eshape = eshape ))), last = eval(substitute(expression({ misc$expected <- FALSE misc$link <- c(shape = .lshape ) misc$earg <- list(shape = .eshape ) misc$start <- extra$start }), list( .lshape = lshape, .eshape = eshape ))), loglikelihood = eval(substitute( function(mu, y, w, residuals = FALSE, eta, extra = NULL, summation = TRUE) { shape <- eta2theta(eta, .lshape , earg = .eshape ) if (residuals) { stop("loglikelihood residuals not implemented yet") } else { ll.elts <- c(w) * ddiffzeta(x = y, start = extra$start, shape = shape, log = TRUE) if (summation) { sum(ll.elts) } else { ll.elts } } }, list( .lshape = lshape, .eshape = eshape ))), vfamily = c("diffzeta"), validparams = eval(substitute(function(eta, y, extra = NULL) { shape <- eta2theta(eta, .lshape , earg = .eshape ) okay1 <- all(is.finite(shape)) && all(0 < shape) okay1 }, list( .lshape = lshape, .eshape = eshape ))), deriv = eval(substitute(expression({ shape <- eta2theta(eta, .lshape , earg = .eshape ) temp1 <- extra$start / y temp2 <- extra$start / (y+1) AA <- temp1^shape - temp2^shape Aprime <- log(temp1) * temp1^shape - log(temp2) * temp2^shape dl.dshape <- Aprime / AA dshape.deta <- dtheta.deta(shape, .lshape , earg = .eshape ) c(w) * dl.dshape * dshape.deta }), list( .lshape = lshape, .eshape = eshape ))), weight = expression({ ned2l.dshape <- (Aprime / AA)^2 wz <- c(w) * ned2l.dshape * dshape.deta^2 wz })) }
smallFilter <- function(dat, threshold = 1000L) { dat[dat$size >= threshold, ] }
f.star.test<-function(means,variances,ns){ MSB.s=sum(ns*(means-mean(means))^2) MSW.s=sum((1-ns/sum(ns))*variances) F.s=MSB.s/MSW.s gs=((1-ns/sum(ns))*variances)/MSW.s f=1/(sum(gs^2/(ns-1))) p.value=1-pf(F.s,length(means)-1,f) f.squared=(length(means)-1)*F.s/sum(ns) return(list("statistic"=F.s,"p.value"=p.value,"est.f.squared"=f.squared)) }
.make_file_resource <- function(path = "/data/CNSIM1.csv", format = "csv") { newResource( name = "test", url = paste0("file://", path), format = format ) } test_that("file resource resolver works", { res <- .make_file_resource() resolver <- TidyFileResourceResolver$new() expect_true(resolver$isFor(res)) res <- newResource( name = "CNSIM1", url = "app+https://app.example.org/files/data/CNSIM1.csv", secret = "DSDFrezerFgbgBC", format = "csv" ) expect_false(resolver$isFor(res)) }) test_that("file resource resolver is loaded", { res <- .make_file_resource() registerResourceResolver(TidyFileResourceResolver$new()) resolver <- resolveResource(res) expect_false(is.null(resolver)) client <- newResourceClient(res) expect_false(is.null(client)) }) test_that("file resource client factory, file not found", { res <- .make_file_resource() resolver <- TidyFileResourceResolver$new() client <- resolver$newClient(res) expect_equal(class(client), c("TidyFileResourceClient", "FileResourceClient", "ResourceClient", "R6")) expect_equal(client$downloadFile(), "/data/CNSIM1.csv") expect_error(client$asDataFrame()) }) test_that("file resource client factory, csv file", { res <- .make_file_resource("./data/dataset.csv") resolver <- TidyFileResourceResolver$new() client <- resolver$newClient(res) expect_equal(class(client), c("TidyFileResourceClient", "FileResourceClient", "ResourceClient", "R6")) expect_equal(client$downloadFile(), "data/dataset.csv") df <- client$asDataFrame() expect_false(is.null(df)) expect_true("data.frame" %in% class(df)) expect_true("tbl" %in% class(df)) client$close() }) test_that("file resource client factory, spss file", { res <- .make_file_resource("./data/dataset.sav", format = "spss") resolver <- TidyFileResourceResolver$new() client <- resolver$newClient(res) expect_equal(class(client), c("TidyFileResourceClient", "FileResourceClient", "ResourceClient", "R6")) expect_equal(client$downloadFile(), "data/dataset.sav") df <- client$asDataFrame() expect_false(is.null(df)) expect_true("data.frame" %in% class(df)) expect_true("tbl" %in% class(df)) client$close() }) test_that("csv file resource coercing to data.frame", { res <- .make_file_resource("./data/dataset.csv") registerResourceResolver(TidyFileResourceResolver$new()) df <- as.data.frame(res) expect_false(is.null(df)) expect_true("data.frame" %in% class(df)) expect_true("tbl" %in% class(df)) }) test_that("csv file resource client coercing to data.frame", { res <- .make_file_resource("./data/dataset.csv") registerResourceResolver(TidyFileResourceResolver$new()) client <- newResourceClient(res) df <- as.data.frame(client) expect_false(is.null(df)) expect_true("data.frame" %in% class(df)) expect_true("tbl" %in% class(df)) })
setGeneric("existsSheet", function(object, name) standardGeneric("existsSheet")) setMethod("existsSheet", signature(object = "workbook"), function(object, name) { xlcCall(object, "existsSheet", name) } )
context("class level lsm_c_core_cv metric") landscapemetrics_class_landscape_value <- lsm_c_core_cv(landscape) test_that("lsm_c_core_cv is typestable", { expect_is(lsm_c_core_cv(landscape), "tbl_df") expect_is(lsm_c_core_cv(landscape_stack), "tbl_df") expect_is(lsm_c_core_cv(landscape_brick), "tbl_df") expect_is(lsm_c_core_cv(landscape_list), "tbl_df") }) test_that("lsm_c_core_cv returns the desired number of columns", { expect_equal(ncol(landscapemetrics_class_landscape_value), 6) }) test_that("lsm_c_core_cv returns in every column the correct type", { expect_type(landscapemetrics_class_landscape_value$layer, "integer") expect_type(landscapemetrics_class_landscape_value$level, "character") expect_type(landscapemetrics_class_landscape_value$class, "integer") expect_type(landscapemetrics_class_landscape_value$id, "integer") expect_type(landscapemetrics_class_landscape_value$metric, "character") expect_type(landscapemetrics_class_landscape_value$value, "double") })
flamingo <- structure(list(LOS = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 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"DCM", "ND", "ND", "DEXF", "DEX", "DC", "NSU", "ND", "ND", "ND", "ND", "NSU", "DEX", "DC", "DCM", "NT", "DEX", "NSU", "ND", "DC", "DS", "DC", "ND", "NTH", "DS", "NDH", "DC", "NDH", "NTH", "NDH", "DS", "DC", "DC", "DEXF", "NDH", "NDH", "NDH", "DC", "DS", "DC", "FM", "NDH", "NSUH", "DC", "DC", "DCM", "DC", "DC", "DC", "DC", "DS", "DC", "FC", "NDH", "FS", "DCM", "DEX", "FM", "DC", "DC", "DC", "DCM", "FC", "DS", "DCM", "FC", "DEX", "DS", "DC", "ND", "DEX", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "NSU", "NSU", "DC", "DCM", "DS", "DEXF", "DC", "DC", "DS", "DS", "DEX", "DEX", "DC", "DC", "DC", "DS", "DCM", "DC", "DEX", "DC", "DC", "DS", "FC", "DC", "DC", "DC", "DS", "DC", "DC", "DC", "DC", "DEX", "DEX", "DC", "DEX", "FC", "DC", "FC", "DC", "DC", "DC", "DC", "DC", "DS", "FC", "DS", "DS", "DC", "DC", "DC", "DC", "DEX", "DEX", "DC", "DC", "DC", "DC", "FC", "NSU", "DS", "DC", "NSU", "DC", "DCM", "DC", "DC", "DC", "DC", "DC", "NSU", "NT", "NSU", "ND", "NSU", "NT", "FC", "DC", "NSU", "NSU", "NT", "DEX", "DS", "NT", "DCM", "DC", "DEX", "NT", "NSU", "DEX", "DEX", "FC", "ND", "NSU", "NSU", "DC", "ND", "DC", "DC", "DC", "ND", "DEX", "DC", "DC", "DS", "DC", "DC", "FC", "NT", "NT", "DC", "DEXF", "ND", "NSU", "DEX", "DC", "DC", "DC", "DC", "DC", "NDH", "NDH", "NDH", "DC", "DC", "DS", "DCM", "DC", "DC", "ND", "ND", "DS", "DC", "DC", "DS", "DC", "ND", "DC", "DC", "DEX", "ND", "ND", "DS", "ND", "DC", "NT", "FC", "DS", "NSU", "DC", "DCM", "DC", "DCM", "DC", "ND", "DC", "DC", "DC", "NT", "DC", "FC", "DS", "DCM", "DS", "DEX", "DC", "ND", "DC", "DS", "DS", "DCM", "ND", "ND", "DC", "DS", "DC", "DC", "FC", "FC", "DC", "DC", "DEXF", "DCM", "DS", "FC", "FC", "ND", "ND", "DS", "DEXF", "FC", "DC", "FC", "DC", "DC", "DC", "FC", "DC", "FC", "FC", "DC", "FC", "DC", "DC", "DC", "DCM", "DCM", "DC", "DC", "FC", "FC", "FC", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "FC", "DC", "DEXF", "DCM", "DC", "DCM", "DC", "DCM", "FC", "DC", "DC", "DC", "DC", "ND", "DC", "DC", "FC", "DC", "FC", "DC", "ND", "DC", "DC", "DEXF", "ND", "DC", "DC", "FC", "DEX", "S", "S", "NT", "DEX", "NT", "NSU", "NSU", "NSU", "DC", "DEXF", "DEXF", "ND", "ND", "DEX", "NSU", "DC", "NSU", "NSU", "NSU", "NSU", "DEX", "DEXF", "DEX", "DEX", "ND", "NSU", "DEXF", "DC", "DEXF", "DC", "DCM", "NSU", "ND", "DC", "DEXF", "DS", "DC", "NT", "ND", "NDH", "DC", "DEXF", "DEXF", "DS", "DEXF", "DC", "NDH", "DC", "DC", "DC", "DC", "NSU", "DEX", "DS", "DEX", "NSU", "DEX", "NDH", "NTH", "DC", "DC", "FC", "DC", "DC", "DC", "DCM", "DC", "DC", "DC", "DC", "DC", "DC", "DEX", "DEX", "DC", "DC", "NSU", "ND", "ND", "DC", "DEX", "ND", "DEX", "DC", "DC", "DC", "NSU", "DCM", "DC", "DC", "DC", "DC", "DEX", "DC", "DEX", "DEXF", "DC", "DC", "DC", "ND", "FM", "DS", "DS", "DS", "DC", "DS", "DC", "ND", "DC", "DC", "DC", "DC", "DS", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "DEX", "NSU", "NSU", "DC", "DEX", "DEX", "DEX", "DEX", "DEX", "NSU", "NSU", "DC", "NSU", "NSU", "DEX", "DC", "DC", "FC", "DC", "DC", "NDH", "DC", "ND", "NSU", "DC", "DC", "DC", "DC", "DC", "DC", "DC", "DEX", "DEX", "DEX", "NSU", "DCM", "DC", "DCM", "DCM", "DEX", "NT", "S", "DC", "NSU", "ND", "DEX", "DC", "FC", "DS", "DC", "DC", "DC", "ND", "DEX", "DC", "DC", "FC", "ND", "FM", "DC", "DC", "DC", "NT", "DC", "DCM", "DC", "DC", "DS", "DCM", "DC", "S", "S", "S", "NSU", "DC", "NSU", "DC", "FM", "DC", "DC", "NSU", "DC", "DC", "NTH", "DC", "DC", "DS", "NDH", "NDH", "NDH", "NTH", "NTH", "DCM", "DC", "DC", "DS", "DC", "DS", "DC", "DC", "DC", "DC", "DC", "FC", "NSU", "DC", "DC", "FM", "FC", "DEX", "DC", "DEX", "DC", "DC", "DC", "DC", "DS", "DC", "S", "S", "S", "NSU", "DEX", "NSU", "ND", "ND", "DC", "FC", "DC", "DC", "DEX", "DC", "DS", "DC", "DC", "DS", "FC", "DC", "DC", "DC", "DC", "DC", "DC", "DEX", "DS", "NSU", "DEX", "DC", "DCM", "DC", "DC", "DEX", "DCM", "NSU", "DS", "DS", "DEX", "FC", "DCM", "DC", "NT", "DC", "DC", "DCM", "DEX", "DEX", "DEXF", "DC", "DC", "DC", "DEXF", "DC", "DC", "DS", "DC", "DC", "ND", "ND", "ND", "ND", "DC", "FC", "NT", "NSU", "ND", "DEX", "DS", "DC", "DC", "DS", "FC", "SUM", "FC", "DS", "DC", "DCM", "DC", "DC", "DC", "DS", "DC", "DS", "DEX", "DC", "DC", "DS", "DS", "DC", "DEX", "DCM", "DCM", "DS", "DS", "DS", "DS", "DCM", "DCM", "DS", "DC", "DC", "DS", "DC", "DC", "DC", "DEX", "DC", "DCM", "DC", "NSU", "NSU", "ND", "NSU", "DC", "S", "SUM", "NSU", "NSU", "NSU", "FC", "DEX", "NSU", "NSU", "DEX", "DC", "DEX", "DC", "ND", "NSU", "ND", "ND", "NSU", "DC", "DC", "DC", "DC", "DC", "DCM", "DCM", "DC", "DC", "DEXF", "FC", "DC", "DC", "ND", "DC", "DEX", "NTH", "NSU", "ND", "NDH", "DEXF", "NDH", "DC", "DS", "NSUH", "NDH", "DC", "NDH", "NTH", "NTH", "NDH", "NTH", "DC", "DS", "NTH", "NTH", "DC", "DC", "NDH", "DC", "DC", "DEX", "DEX", "DC", "DC", "NSU", "DC", "DS", "DC", "S", "FM", "DC", "ND", "DC", "DC", "DEX", "DS", "DC", "DC", "DC", "DCM", "DEXF", "ND", "ND", "ND", "ND", "DC", "DC", "NSU", "DC", "ND", "DC", "NSU", "NSU", "ND", "DC", "NT", "ND", "DS", "DCM", "DC", "DEX", "DEX", "DEX", "NSU", "NSU", "DS", "NSU", "NSU", "DC", "DEX", "DC", "NSUH", "DS", "ND", "ND", "NSU", "DC", "DC", "DEXF", "DC", "DC", "NSU", "DEXF", "DS", "DC", "DC", "DC", "NT", "DC"), rmtype3 = structure(c(1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 3L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 3L, 3L, 3L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 3L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 3L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 2L, 1L, 3L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 1L, 1L, 2L, 2L, 3L, 3L, 1L, 1L, 1L, 3L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 3L, 3L, 3L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 1L, 3L, 3L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 1L, 2L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 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3, 1, 2, 2, 4, 4, 3, 4, 2, 2, 3, 2, 2, 2, 2, 2, 2, 2, 4, 3, 2, 3, 2, 2, 4, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 1, 2, 2, 1, 2, 2, 2, 2, 2, 2, 1, 2, 1, 1, 5, 2, 2, 1, 1, 1, 2, 2, 2, 4, 3, 2, 2, 2, 4, 2, 3, 2, 2, 2, 2, 2, 3, 3, 2, 2, 3, 2, 2, 2, 2, 3, 2, 2, 2, 1, 2, 2, 2, 2, 2, 1, 2, 1, 2, 4, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 2, 1, 4, 3, 1, 1, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 2, 2, 3, 1, 2, 2, 2, 3, 2, 4, 2, 2, 3, 2, 2, 2, 2, 2, 4, 2, 4, 2, 3, 1, 3, 2, 2, 2, 2, 2, 2, 1, 1, 1, 1, 3, 2, 4, 3, 4, 2, 2, 2, 2, 2, 3, 2, 2, 2, 2, 2, 2, 3, 3, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 3, 4, 3, 1, 1, 4, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 1, 4, 3, 3, 2, 2, 1, 4, 2, 2, 2, 1, 2, 1, 2, 2, 4, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 4, 3, 2, 3, 2, 1, 1, 1, 1, 3, 3, 1, 2, 4, 2, 2, 3, 3, 2, 2, 2, 1, 2, 3, 4, 3, 4, 2, 1, 2, 2, 2, 2, 4, 2, 4, 2, 1, 2, 2, 2, 1, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 1, 1, 2, 2, 2, 1, 2, 2, 1, 2, 1, 2, 2, 2, 2, 5, 2, 2, 2, 2, 1, 2, 4, 2, 2, 4, 3, 4, 2, 2, 2, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 3, 2, 3, 2, 2, 1, 4, 3, 3, 1, 2, 1, 2, 3, 2, 1, 2, 4, 2, 3, 2, 4, 2, 2, 2, 3, 3, 2, 3, 2, 3, 3, 3, 1, 2, 2, 2, 2, 2, 2, 1, 2, 2, 2, 2, 2, 1, 2, 2, 1, 3, 1, 1, 2, 2, 3, 1, 2, 4, 2, 2, 1, 2, 3, 2, 2, 2, 2, 3, 2, 2, 2, 3, 3, 2, 2, 2, 2, 1, 2, 1, 4, 3, 3, 4, 4, 1, 1, 2, 2, 2, 2, 2, 2, 1, 3, 3, 2, 1, 2, 4, 3, 1, 2, 1, 3, 1), arrangement = structure(c(1L, 3L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 1L, 2L, 3L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 3L, 1L, 1L, 2L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 3L, 1L, 2L, 2L, 2L, 3L, 3L, 1L, 3L, 1L, 2L, 2L, 1L, 1L, 2L, 1L, 2L, 1L, 2L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 2L, 2L, 2L, 2L, 1L, 2L, 1L, 1L, 2L, 2L, 3L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 3L, 1L, 1L, 2L, 1L, 1L, 2L, 1L, 2L, 3L, 1L, 2L, 1L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 2L, 2L, 1L, 2L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 2L, 1L, 1L, 1L, 2L, 2L, 1L, 2L, 2L, 1L, 1L, 1L, 1L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 1L, 1L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 3L, 3L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 1L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 3L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 2L, 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4681L, 4682L, 4683L, 4684L, 4685L, 4686L, 4687L, 4688L, 4689L, 4690L, 4691L, 4692L, 4693L, 4694L, 4695L, 4696L, 4697L, 4698L, 4699L, 4700L, 4701L, 4702L, 4703L, 4704L, 4705L, 4706L, 4707L, 4708L, 4709L, 4710L, 4711L, 4712L, 4713L, 4714L, 4715L, 4716L, 4717L, 4718L, 4719L, 4720L, 4721L, 4722L, 4724L, 4725L, 4726L, 4727L, 4728L, 4729L, 4730L, 4731L, 4732L, 4733L, 4734L, 4735L, 4736L, 4737L, 4738L, 4739L, 4740L, 4741L, 4742L, 4743L, 4744L, 4745L, 4746L, 4747L, 4748L, 4749L, 4750L, 4751L, 4752L, 4753L, 4754L, 4755L, 4756L, 4757L, 4758L, 4759L, 4760L, 4761L, 4762L, 4763L, 4764L, 4765L, 4766L, 4767L, 4768L, 4769L, 4770L, 4771L, 4772L, 4773L, 4774L, 4775L, 4776L, 4777L, 4779L, 4780L, 4781L, 4782L, 4783L, 4784L, 4785L, 4786L, 4787L, 4788L, 4789L, 4790L, 4791L, 4792L, 4793L, 4794L, 4795L, 4796L, 4797L, 4798L, 4799L, 4800L, 4801L, 4802L, 4803L, 4804L, 4805L, 4806L, 4807L, 4808L, 4809L, 4810L, 4811L, 4812L, 4813L, 4814L, 4815L, 4816L, 4817L, 4818L, 4819L, 4820L, 4821L, 4822L, 4823L, 4824L, 4825L, 4826L, 4827L, 4828L, 4829L, 4830L, 4831L, 4832L, 4833L, 4834L, 4835L, 4836L, 4837L, 4838L, 4839L, 4840L, 4841L, 4842L, 4843L, 4844L, 4845L, 4846L, 4847L, 4848L, 4849L, 4850L, 4851L, 4852L, 4853L, 4854L, 4855L, 4856L, 4857L, 4858L, 4859L, 4860L, 4861L, 4862L, 4863L, 4864L, 4865L, 4866L, 4867L, 4868L, 4869L, 4870L, 4871L, 4872L, 4873L, 4874L, 4875L, 4876L, 4877L, 4878L, 4879L, 4880L, 4881L, 4882L, 4883L, 4884L, 4885L, 4886L, 4887L, 4888L, 4889L, 4890L, 4891L, 4892L, 4893L, 4894L, 4895L, 4896L, 4897L, 4898L, 4899L, 4900L, 4901L, 4902L, 4903L, 4904L, 4905L, 4906L, 4907L, 4908L, 4909L, 4910L, 4911L, 4912L, 4913L, 4914L, 4915L, 4916L, 4917L, 4918L, 4919L, 4920L, 4921L, 4922L, 4923L, 4924L, 4925L, 4926L, 4927L, 4928L, 4929L, 4930L, 4931L, 4932L, 4933L, 4934L, 4935L, 4936L, 4937L, 4938L, 4939L, 4940L, 4941L, 4942L, 4943L, 4944L, 4945L, 4946L, 4947L, 4948L, 4949L, 4950L, 4951L, 4952L, 4953L, 4954L, 4955L, 4956L, 4957L, 4958L, 4959L, 4960L, 4961L, 4962L, 4963L, 4964L, 4965L, 4966L, 4967L, 4968L, 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labkey.webdav.get <- function(baseUrl=NULL, folderPath, remoteFilePath, localFilePath, overwrite=TRUE, fileSet="@files") { baseUrl=labkey.getBaseUrl(baseUrl); if (missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(remoteFilePath) || missing(localFilePath)){ stop (paste("A value must be specified for each of baseUrl, folderPath, fileSet, remoteFilePath, and localFilePath")); } if (labkey.webdav.isDirectory(baseUrl = baseUrl, folderPath = folderPath, remoteFilePath = remoteFilePath, fileSet = fileSet, haltOnError = T)){ stop('The requested file is a directory. Please see labkey.webdav.downloadFolder()') } folderPath <- encodeFolderPath(folderPath); remoteFilePath <- encodeRemotePath(remoteFilePath) url <- paste(baseUrl, "_webdav", folderPath, fileSet, "/", remoteFilePath, sep=""); ret <- labkey.webdav.getByUrl(url, localFilePath, overwrite) if (!is.null(ret) && !is.na(ret) && ret == FALSE) { return(FALSE) } return(file.exists(localFilePath)) } labkey.webdav.getByUrl <- function(url, localFilePath, overwrite=TRUE) { if (!overwrite & file.exists(localFilePath)) { return(FALSE) } if (dir.exists(localFilePath)) { stop(paste0("The local filepath exists and is a directory: ", localFilePath)) } localDownloadDir <- dirname(localFilePath) if (!file.exists(localDownloadDir)) { dir.create(localDownloadDir, recursive=TRUE) } options <- labkey.getRequestOptions(method="GET") if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE){ print(paste0("URL: ", url)) response <- GET(url=url, write_disk(localFilePath, overwrite=overwrite), config=options, verbose(data_in=TRUE, info=TRUE, ssl=TRUE)) } else { response <- GET(url=url, write_disk(localFilePath, overwrite=overwrite), config=options) } processResponse(response) } labkey.webdav.put <- function(localFile, baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files", description=NULL) { if (missing(localFile)) { stop (paste("A value must be specified for localFile")) } if (!file.exists(localFile)){ stop (paste0("File does not exist: ", localFile)); } url <- labkey.webdav.validateAndBuildRemoteUrl(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath) options <- labkey.getRequestOptions(method="POST") pbody <- upload_file(localFile) if (!is.null(description)) { url <- paste0(url, "?description=", URLencode(description)) } if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE) { print(paste0("URL: ", url)) response <- PUT(url=url, config=options, body=pbody, verbose(data_in=TRUE, info=TRUE, ssl=TRUE)) } else { response <- PUT(url=url, config=options, body=pbody) } processResponse(response, responseType="text/plain; charset=utf-8") return(TRUE) } labkey.webdav.mkDir <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files") { url <- labkey.webdav.validateAndBuildRemoteUrl(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath) options <- labkey.getRequestOptions(method="POST") if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE) { print(paste0("URL: ", url)) response <- VERB("MKCOL", url=url, config=options, verbose(data_in=TRUE, info=TRUE, ssl=TRUE)) } else { response <- VERB("MKCOL", url=url, config=options) } processResponse(response, responseType="text/plain; charset=utf-8") return(TRUE) } labkey.webdav.validateAndBuildRemoteUrl <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files") { baseUrl=labkey.getBaseUrl(baseUrl); if (missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(fileSet) || missing(remoteFilePath)){ stop (paste("A value must be specified for each of baseUrl, folderPath, fileSet, and remoteFilePath")); } folderPath <- encodeFolderPath(folderPath); remoteFilePath <- encodeRemotePath(remoteFilePath) return(paste(baseUrl, "_webdav", folderPath, fileSet, "/", remoteFilePath, sep="")) } encodeRemotePath <- function(path, splitSlash = TRUE) { if (splitSlash) { path <- strsplit(path, "/")[[1]] } return(paste0(sapply(path, URLencode, reserved = T), collapse = '/')) } labkey.webdav.pathExists <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files") { baseUrl=labkey.getBaseUrl(baseUrl); if (missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(remoteFilePath)) { stop (paste("A value must be specified for each of baseUrl, folderPath, fileSet, and remoteFilePath")); } ret <- labkey.webdav.listDir(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath, haltOnError=F) return(is.null(ret$exception)) } labkey.webdav.isDirectory <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files", haltOnError = TRUE) { json <- labkey.webdav.listDir(baseUrl = baseUrl, folderPath = folderPath, remoteFilePath = remoteFilePath, fileSet = fileSet, haltOnError = haltOnError) return(!is.null(json[['fileCount']])) } labkey.webdav.listDir <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files", haltOnError = TRUE) { baseUrl=labkey.getBaseUrl(baseUrl); url <- labkey.webdav.validateAndBuildRemoteUrl(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath) url <- paste0(url, "?method=JSON") logMessage(paste0("URL: ", url)) content <- labkey.post(url, pbody="", responseType="text/plain; charset=utf-8", haltOnError = haltOnError) ret <- fromJSON(content, simplifyVector=FALSE, simplifyDataFrame=FALSE) colNames <- c("id", "href", "text", "creationdate", "createdby", "lastmodified", "contentlength", "size", "isdirectory") ret[["files"]] <- lapply(ret[["files"]], function(l){ idx <- match("collection", names(l)) if (!is.na(idx)){ names(l)[idx] <- "isdirectory" } else { l$isdirectory <- FALSE } l <- l[colNames] names(l) <- colNames return(l) }) return(ret) } labkey.webdav.delete <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files") { baseUrl=labkey.getBaseUrl(baseUrl); url <- labkey.webdav.validateAndBuildRemoteUrl(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath) url <- paste0(url, "?method=DELETE") if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE) { print(paste0("URL: ", url)) } labkey.post(url, pbody="", responseType="text/plain; charset=utf-8") return(T) } labkey.webdav.mkDirs <- function(baseUrl=NULL, folderPath, remoteFilePath, fileSet="@files") { baseUrl=labkey.getBaseUrl(baseUrl); if (missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(remoteFilePath)){ stop (paste("A value must be specified for each of baseUrl, folderPath, fileSet, and remoteFilePath")) } remoteFilePaths <- strsplit(remoteFilePath, "/")[[1]] toCreate <- "" for (folderName in remoteFilePaths) { toCreate <- paste0(toCreate, folderName, "/") if (!labkey.webdav.pathExists(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=toCreate)) { if (!labkey.webdav.mkDir(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=toCreate)){ stop(paste0("Failed to create folder: ", toCreate)) } } } return(TRUE) } labkey.webdav.downloadFolder <- function(localBaseDir, baseUrl=NULL, folderPath, remoteFilePath, overwriteFiles=TRUE, mergeFolders=TRUE, fileSet="@files") { if (missing(localBaseDir) || missing(baseUrl) || is.null(baseUrl) || missing(folderPath) || missing(remoteFilePath)){ stop (paste("A value must be specified for each of localBaseDir, baseUrl, folderPath, fileSet, and remoteFilePath")) } if (file.exists(localBaseDir) && !dir.exists(localBaseDir)) { stop(paste0("Download folder exists, but is not a directory: ", localBaseDir)) } if (!dir.exists(localBaseDir)) { stop(paste0("Download folder does not exist: ", localBaseDir)) } remoteFilePath <- normalizeSlash(remoteFilePath, leading = F) subfolder <- basename(remoteFilePath) if (subfolder != ''){ localBaseDir <- normalizeFolder(localBaseDir) localBaseDir <- file.path(localBaseDir, subfolder) logMessage(paste0('target local folder: ', localBaseDir)) } if (!labkey.webdav.isDirectory(baseUrl = baseUrl, folderPath = folderPath, remoteFilePath = remoteFilePath, fileSet = fileSet, haltOnError = T)){ stop('The requested file is not a directory.') } if (!prepareDirectory(localPath = localBaseDir, overwriteFiles = overwriteFiles, mergeFolders = mergeFolders)){ return(F) } labkey.webdav.doDownloadFolder(localDir = localBaseDir, baseUrl = baseUrl, folderPath = folderPath, remoteFilePath = remoteFilePath, overwriteFiles = overwriteFiles, mergeFolders = mergeFolders, fileSet = fileSet) } normalizeFolder <- function(localDir){ localDir <- gsub("[\\]", "/", localDir) localDir <- gsub("[/]+", "/", localDir) if (substr(localDir, nchar(localDir), nchar(localDir))=="/") { localDir <- substr(localDir,1, nchar(localDir)-1) } return(localDir) } logMessage <- function(msg) { if (!is.null(.lkdefaults[["debug"]]) && .lkdefaults[["debug"]] == TRUE) { print(msg) } } labkey.webdav.doDownloadFolder <- function(localDir, baseUrl=NULL, folderPath, remoteFilePath, depth, overwriteFiles=TRUE, mergeFolders=TRUE, fileSet="@files") { baseUrl <- normalizeSlash(baseUrl, leading = F, trailing = F) folderPath <- normalizeSlash(folderPath, leading = F) fileSet <- normalizeSlash(fileSet, leading = F, trailing = F) remoteFilePath <- normalizeSlash(remoteFilePath, leading = F) localDir <- normalizeFolder(localDir) prefix <- paste0("/_webdav/", folderPath, fileSet, '/') files <- labkey.webdav.listDir(baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=remoteFilePath) for (file in files[["files"]]) { relativeToRemoteRoot <- sub(prefix, "", file[["id"]]) relativeToDownloadStart <- sub(paste0(prefix, remoteFilePath), "", file[["id"]]) localPath <- file.path(localDir, relativeToDownloadStart) if (file[["isdirectory"]]) { logMessage(paste0("Downloading folder: ", relativeToRemoteRoot)) logMessage(paste0("to: ", localPath)) if (file.exists(localPath) && !dir.exists(localPath)) { if (overwriteFiles) { unlink((localPath)) } else { stop(paste0('Target of folder download already exists, but is a file, not a folder: ', localPath)) } } if (!prepareDirectory(localPath, overwriteFiles, mergeFolders)) { next } labkey.webdav.doDownloadFolder(localDir=localPath, baseUrl=baseUrl, folderPath=folderPath, fileSet=fileSet, remoteFilePath=relativeToRemoteRoot, overwriteFiles=overwriteFiles, mergeFolders=mergeFolders) } else { url <- paste0(baseUrl, trimLeadingPath(file[["href"]])) logMessage(paste0("Downloading file: ", relativeToRemoteRoot)) logMessage(paste0("to: ", localPath)) labkey.webdav.getByUrl(url, localPath, overwriteFiles) } } return(TRUE) } trimLeadingPath <- function(url){ pos <- regexpr('/_webdav', tolower(url)) if (pos == -1) { return(url) } return(substr(url, pos, nchar(url))) } prepareDirectory <- function(localPath, overwriteFiles, mergeFolders) { if (dir.exists(localPath)) { logMessage(paste0('existing folder found: ', localPath)) if (!mergeFolders && overwriteFiles) { logMessage('deleting existing folder') unlink(localPath, recursive = T) } else if (!mergeFolders && !overwriteFiles) { logMessage('skipping existing folder') return(F) } else if (mergeFolders) { logMessage('existing folder will be left alone and contents downloaded') } } else { dir.create(localPath, recursive=TRUE) } return(T) }
test_that("gs4_fodder() works", { dat <- gs4_fodder(3, 5) expect_named(dat, LETTERS[1:5]) ltrs <- rep(LETTERS[1:5], each = 3) nbrs <- rep(1:3, 5) + 1 expect_equal( as.vector(as.matrix(dat)), paste0(ltrs, nbrs) ) })
checkPathForOutput = function(x, overwrite = FALSE, extension = NULL) { if (!qtest(x, "S+")) return("No path provided") qassert(overwrite, "B1") x = normalizePath(x, mustWork = FALSE) dn = dirname(x) w = wf(!dir.exists(dn)) if (length(w) > 0L) return(sprintf("Path to file (dirname) does not exist: '%s' of '%s'", dn[w], x[w])) w = which(file.exists(x)) if (length(w) > 0L) { if (overwrite) return(checkAccess(dn, "w") %and% checkAccess(x[w], "rw")) return(sprintf("File at path already exists: '%s'", x[w])) } if (!is.null(extension)) { qassert(extension, "S1") if (!endsWith(x, paste0(".", extension))) return(sprintf("File must have extension '.%s'", extension)) } return(checkAccess(dn, "w")) } check_path_for_output = checkPathForOutput assertPathForOutput = makeAssertionFunction(checkPathForOutput, use.namespace = FALSE) assert_path_for_output = assertPathForOutput testPathForOutput = makeTestFunction(checkPathForOutput) test_path_for_output = testPathForOutput expect_path_for_output = makeExpectationFunction(checkPathForOutput, use.namespace = FALSE)
data(met) Obs = Obs[order(Obs$ID),] Gen = data.matrix(Gen) chr = data.frame(table(as.numeric(substring(colnames(Gen),3,4))))[,2] fam = as.numeric(substring(rownames(Gen),6,7)) Y = matrix(NA,nrow(Gen),3) rownames(Y) = rownames(Gen) colnames(Y) = 2013:2015 y13 = Obs[which(Obs$Year==2013),'DTM'] names(y13) = as.character(Obs[which(Obs$Year==2013),'ID']) Y[,1] = y13[rownames(Y)] y14 = Obs[which(Obs$Year==2014),'DTM'] names(y14) = as.character(Obs[which(Obs$Year==2014),'ID']) Y[,2] = y14[rownames(Y)] y15 = Obs[which(Obs$Year==2015),'DTM'] names(y15) = as.character(Obs[which(Obs$Year==2015),'ID']) Y[,3] = y15[rownames(Y)] chr = round(chr/5) subsample = seq(1,nrow(Y),5) Gen = Gen[subsample,seq(1,ncol(Gen),5)] Y = Y[subsample,]; fam = fam[subsample] GxE_GWA = gwasGE(Y,Gen,fam,chr) par(mfrow=c(1,1)) plot(GxE_GWA,main="GWAS",pch=20) par(mfrow=c(2,2)) plot(GxE_GWA$PolyTest$vi,main="Allele Effect",pch=20,ylab="Mu") plot(GxE_GWA$PolyTest$vi,main="GxE variance",pch=20,ylab="Var (GE)") plot(GxE_GWA$PolyTest$vg,main="Genetic variance",pch=20,ylab="Var (G)") plot(GxE_GWA$PolyTest$vg,main="Environmental variance",pch=20,ylab="Var (E)")
backprop_r = function(model,a,c,j,...){ if(model$network_type == "rnn"){ backprop_rnn(model,a,c,j,...) } else if (model$network_type == "lstm"){ backprop_lstm(model,a,c,j,...) } else if (model$network_type == "gru"){ backprop_gru(model,a,c,j,...) }else{ stop("network_type_unknown for the backprop") } } backprop_rnn = function(model,a,c,j,...){ model$last_layer_error[j,,] = c - model$store[[length(model$store)]][j,,,drop=F] model$last_layer_delta[j,,] = model$last_layer_error[j,,,drop = F] * sigmoid_output_to_derivative(model$store[[length(model$store)]][j,,,drop=F]) if(model$seq_to_seq_unsync){ model$last_layer_error[j,1:(model$time_dim_input - 1),] = 0 model$last_layer_delta[j,1:(model$time_dim_input - 1),] = 0 } model$error[j,model$current_epoch] <- apply(model$last_layer_error[j,,,drop=F],1,function(x){sum(abs(x))}) future_layer_delta = list() for(i in seq(length(model$hidden_dim))){ future_layer_delta[[i]] <- matrix(0,nrow=length(j), ncol = model$hidden_dim[i]) } for (position in model$time_dim:1) { x = array(a[,position,],dim=c(length(j),model$input_dim)) layer_up_delta = array(model$last_layer_delta[j,position,],dim=c(length(j),model$output_dim)) for(i in (length(model$store)):1){ if(i != 1){ layer_current = array(model$store[[i-1]][j,position,],dim=c(length(j),model$hidden_dim[i-1])) if(position != 1){ prev_layer_current = array(model$store[[i-1]][j,position - 1,],dim=c(length(j),model$hidden_dim[i-1])) }else{ prev_layer_current = array(0,dim=c(length(j),model$hidden_dim[i-1])) } layer_current_delta = (future_layer_delta[[i-1]] %*% t(model$recurrent_synapse[[i-1]]) + layer_up_delta %*% t(model$time_synapse[[i]])) * sigmoid_output_to_derivative(layer_current) model$time_synapse_update[[i]] = model$time_synapse_update[[i]] + t(layer_current) %*% layer_up_delta model$bias_synapse_update[[i]] = model$bias_synapse_update[[i]] + colMeans(layer_up_delta) model$recurrent_synapse_update[[i-1]] = model$recurrent_synapse_update[[i-1]] + t(prev_layer_current) %*% layer_current_delta layer_up_delta = layer_current_delta future_layer_delta[[i-1]] = layer_current_delta }else{ model$time_synapse_update[[i]] = model$time_synapse_update[[i]] + t(x) %*% layer_up_delta } } } return(model) } backprop_lstm = function(model,a,c,j,...){ model$last_layer_error[j,,] = c - model$store[[length(model$store)]][j,,,drop=F] model$last_layer_delta[j,,] = model$last_layer_error[j,,,drop = F] * sigmoid_output_to_derivative(model$store[[length(model$store)]][j,,,drop=F]) if(model$seq_to_seq_unsync){ model$last_layer_error[j,1:(model$time_dim_input - 1),] = 0 model$last_layer_delta[j,1:(model$time_dim_input - 1),] = 0 } model$error[j,model$current_epoch] <- apply(model$last_layer_error[j,,,drop=F],1,function(x){sum(abs(x))}) future_layer_cell_delta = list() future_layer_hidden_delta = list() for(i in seq(length(model$hidden_dim))){ future_layer_cell_delta[[i]] = matrix(0, nrow = length(j), ncol = model$hidden_dim[i]) future_layer_hidden_delta[[i]] = matrix(0, nrow = length(j), ncol = model$hidden_dim[i]) } for (position in model$time_dim:1) { layer_up_delta = array(model$last_layer_delta[j,position,],dim=c(length(j),model$output_dim)) i = length(model$hidden_dim) layer_hidden = array(model$store[[i]][j,position,,1],dim=c(length(j),model$hidden_dim[i])) model$time_synapse_update[[i+1]] = model$time_synapse_update[[i+1]] + (t(layer_hidden) %*% layer_up_delta) model$bias_synapse_update[[i+1]] = model$bias_synapse_update[[i+1]] + colMeans(layer_up_delta) layer_up_delta = (layer_up_delta %*% t(model$time_synapse_update[[i+1]])) * sigmoid_output_to_derivative(layer_hidden) + future_layer_hidden_delta[[i]] for(i in length(model$hidden_dim):1){ if(i == 1){ x = array(a[,position,],dim=c(length(j),model$input_dim)) }else{ x = array(model$store[[i - 1]][j,position,,1],dim=c(length(j),model$synapse_dim[i])) } layer_hidden = array(model$store[[i]][j,position,,1],dim=c(length(j),model$hidden_dim[i])) layer_cell = array(model$store[[i]][j,position,,2],dim=c(length(j), model$hidden_dim[i])) if(position != 1){ prev_layer_hidden =array(model$store[[i]][j,position-1,,1],dim=c(length(j),model$hidden_dim[i])) preview_layer_cell = array(model$store[[i]][j,position-1,,2],dim=c(length(j), model$hidden_dim[i])) }else{ prev_layer_hidden =array(0,dim=c(length(j),model$hidden_dim[i])) preview_layer_cell = array(0,dim=c(length(j), model$hidden_dim[i])) } layer_f = array(model$store[[i]][j,position,,3],dim=c(length(j), model$hidden_dim[i])) layer_i = array(model$store[[i]][j,position,,4],dim=c(length(j), model$hidden_dim[i])) layer_c = array(model$store[[i]][j,position,,5],dim=c(length(j), model$hidden_dim[i])) layer_o = array(model$store[[i]][j,position,,6],dim=c(length(j), model$hidden_dim[i])) layer_cell_delta = (layer_up_delta * layer_o)* tanh_output_to_derivative(layer_cell) + future_layer_cell_delta[[i]] layer_o_delta_post_activation = layer_up_delta * tanh(layer_cell) layer_c_delta_post_activation = layer_cell_delta * layer_i layer_i_delta_post_activation = layer_cell_delta * layer_c layer_f_delta_post_activation = layer_cell_delta * preview_layer_cell future_layer_cell_delta[[i]] = layer_cell_delta * layer_f layer_o_delta_pre_activation = layer_o_delta_post_activation * sigmoid_output_to_derivative(layer_o) layer_c_delta_pre_activation = layer_c_delta_post_activation * tanh_output_to_derivative(layer_c) layer_i_delta_pre_activation = layer_i_delta_post_activation * sigmoid_output_to_derivative(layer_i) layer_f_delta_pre_activation = layer_f_delta_post_activation * sigmoid_output_to_derivative(layer_f) model$recurrent_synapse_update[[i]][,,1] = model$recurrent_synapse_update[[i]][,,1] + t(prev_layer_hidden) %*% layer_f_delta_post_activation model$recurrent_synapse_update[[i]][,,2] = model$recurrent_synapse_update[[i]][,,2] + t(prev_layer_hidden) %*% layer_i_delta_post_activation model$recurrent_synapse_update[[i]][,,3] = model$recurrent_synapse_update[[i]][,,3] + t(prev_layer_hidden) %*% layer_c_delta_post_activation model$recurrent_synapse_update[[i]][,,4] = model$recurrent_synapse_update[[i]][,,4] + t(prev_layer_hidden) %*% layer_o_delta_post_activation model$time_synapse_update[[i]][,,1] = model$time_synapse_update[[i]][,,1] + t(x) %*% layer_f_delta_post_activation model$time_synapse_update[[i]][,,2] = model$time_synapse_update[[i]][,,2] + t(x) %*% layer_i_delta_post_activation model$time_synapse_update[[i]][,,3] = model$time_synapse_update[[i]][,,3] + t(x) %*% layer_c_delta_post_activation model$time_synapse_update[[i]][,,4] = model$time_synapse_update[[i]][,,4] + t(x) %*% layer_o_delta_post_activation model$bias_synapse_update[[i]][,1] = model$bias_synapse_update[[i]][,1] + colMeans(layer_f_delta_post_activation) model$bias_synapse_update[[i]][,2] = model$bias_synapse_update[[i]][,2] + colMeans(layer_i_delta_post_activation) model$bias_synapse_update[[i]][,3] = model$bias_synapse_update[[i]][,3] + colMeans(layer_c_delta_post_activation) model$bias_synapse_update[[i]][,4] = model$bias_synapse_update[[i]][,4] + colMeans(layer_o_delta_post_activation) layer_f_delta_pre_weight = layer_f_delta_pre_activation %*% t(array(model$recurrent_synapse[[i]][,,1],dim=c(dim(model$recurrent_synapse[[i]])[1:2]))) layer_i_delta_pre_weight = layer_i_delta_pre_activation %*% t(array(model$recurrent_synapse[[i]][,,2],dim=c(dim(model$recurrent_synapse[[i]])[1:2]))) layer_c_delta_pre_weight = layer_c_delta_pre_activation %*% t(array(model$recurrent_synapse[[i]][,,3],dim=c(dim(model$recurrent_synapse[[i]])[1:2]))) layer_o_delta_pre_weight = layer_o_delta_pre_activation %*% t(array(model$recurrent_synapse[[i]][,,4],dim=c(dim(model$recurrent_synapse[[i]])[1:2]))) future_layer_hidden_delta[[i]] = layer_o_delta_pre_weight + layer_c_delta_pre_weight + layer_i_delta_pre_weight + layer_f_delta_pre_weight layer_f_delta_pre_weight = layer_f_delta_pre_activation %*% t(array(model$time_synapse[[i]][,,1],dim=c(dim(model$time_synapse[[i]])[1:2]))) layer_i_delta_pre_weight = layer_i_delta_pre_activation %*% t(array(model$time_synapse[[i]][,,2],dim=c(dim(model$time_synapse[[i]])[1:2]))) layer_c_delta_pre_weight = layer_c_delta_pre_activation %*% t(array(model$time_synapse[[i]][,,3],dim=c(dim(model$time_synapse[[i]])[1:2]))) layer_o_delta_pre_weight = layer_o_delta_pre_activation %*% t(array(model$time_synapse[[i]][,,4],dim=c(dim(model$time_synapse[[i]])[1:2]))) layer_up_delta = layer_o_delta_pre_weight + layer_c_delta_pre_weight + layer_i_delta_pre_weight + layer_f_delta_pre_weight } } return(model) } backprop_gru = function(model,a,c,j,...){ model$last_layer_error[j,,] = c - model$store[[length(model$store)]][j,,,drop=F] model$last_layer_delta[j,,] = model$last_layer_error[j,,,drop = F] * sigmoid_output_to_derivative(model$store[[length(model$store)]][j,,,drop=F]) if(model$seq_to_seq_unsync){ model$last_layer_error[j,1:(model$time_dim_input - 1),] = 0 model$last_layer_delta[j,1:(model$time_dim_input - 1),] = 0 } model$error[j,model$current_epoch] <- apply(model$last_layer_error[j,,,drop=F],1,function(x){sum(abs(x))}) future_layer_hidden_delta = list() for(i in seq(length(model$hidden_dim))){ future_layer_hidden_delta[[i]] = matrix(0, nrow = length(j), ncol = model$hidden_dim[i]) } for (position in model$time_dim:1) { layer_up_delta = array(model$last_layer_delta[j,position,],dim=c(length(j),model$output_dim)) i = length(model$hidden_dim) layer_hidden = array(model$store[[i]][j,position,,1],dim=c(length(j),model$hidden_dim[i])) model$time_synapse_update[[i+1]] = model$time_synapse_update[[i+1]] + (t(layer_hidden) %*% layer_up_delta) model$bias_synapse_update[[i+1]] = model$bias_synapse_update[[i+1]] + colMeans(layer_up_delta) layer_up_delta = (layer_up_delta %*% t(model$time_synapse_update[[i+1]])) * sigmoid_output_to_derivative(layer_hidden) + future_layer_hidden_delta[[i]] for(i in length(model$hidden_dim):1){ if(i == 1){ x = array(a[,position,],dim=c(length(j),model$input_dim)) }else{ x = array(model$store[[i - 1]][j,position,,1],dim=c(length(j),model$synapse_dim[i])) } layer_hidden = array(model$store[[i]][j,position,,1],dim=c(length(j),model$hidden_dim[i])) if(position != 1){ prev_layer_hidden =array(model$store[[i]][j,position-1,,1],dim=c(length(j),model$hidden_dim[i])) }else{ prev_layer_hidden =array(0,dim=c(length(j),model$hidden_dim[i])) } layer_z = array(model$store[[i]][j,position,,2],dim=c(length(j), model$hidden_dim[i])) layer_r = array(model$store[[i]][j,position,,3],dim=c(length(j), model$hidden_dim[i])) layer_h = array(model$store[[i]][j,position,,4],dim=c(length(j), model$hidden_dim[i])) layer_hidden_delta = layer_up_delta + future_layer_hidden_delta[[i]] layer_h_delta_post_activation = layer_hidden_delta * layer_z layer_h_delta_pre_activation = layer_h_delta_post_activation * tanh_output_to_derivative(layer_h) layer_z_delta_post_split = layer_hidden_delta * layer_h layer_z_delta_post_1_minus = layer_hidden_delta * prev_layer_hidden layer_hidden_delta = layer_hidden_delta * (1 - layer_z) layer_z_delta_post_activation = (1 - layer_z_delta_post_1_minus) layer_z_delta_pre_activation = layer_z_delta_post_activation* sigmoid_output_to_derivative(layer_z) layer_z_delta_pre_weight_h = (layer_z_delta_pre_activation %*% t(model$recurrent_synapse[[i]][,,1]) ) layer_z_delta_pre_weight_x = (layer_z_delta_pre_activation %*% array(t(model$time_synapse[[i]][,,1]),dim = dim(model$time_synapse[[i]])[2:1])) model$recurrent_synapse_update[[i]][,,1] = model$recurrent_synapse_update[[i]][,,1] + t(prev_layer_hidden) %*% layer_z_delta_post_activation model$time_synapse_update[[i]][,,1] = model$time_synapse_update[[i]][,,1] + t(x) %*% layer_z_delta_post_activation model$bias_synapse_update[[i]][,1] = model$bias_synapse_update[[i]][,1] + colMeans(layer_z_delta_post_activation) layer_h_delta_pre_weight_h = (layer_h_delta_pre_activation %*% t(model$recurrent_synapse[[i]][,,3])) layer_h_delta_pre_weight_x = ( layer_h_delta_pre_activation %*% array(t(model$time_synapse[[i]][,,3]),dim = dim(model$time_synapse[[i]])[2:1])) model$recurrent_synapse_update[[i]][,,3] = model$recurrent_synapse_update[[i]][,,3] + t(prev_layer_hidden * layer_r) %*% layer_h_delta_post_activation model$time_synapse_update[[i]][,,3] = model$time_synapse_update[[i]][,,3] + t(x) %*% layer_h_delta_post_activation model$bias_synapse_update[[i]][,3] = model$bias_synapse_update[[i]][,3] + colMeans(layer_h_delta_post_activation) layer_r_delta_post_activation = prev_layer_hidden * layer_h_delta_pre_weight_h layer_r_delta_pre_activation = layer_r_delta_post_activation * sigmoid_output_to_derivative(layer_r) layer_hidden_delta = layer_hidden_delta + layer_r * layer_h_delta_pre_weight_h layer_r_delta_pre_weight_h = (layer_r_delta_pre_activation %*% t(model$recurrent_synapse[[i]][,,2])) layer_r_delta_pre_weight_x = (layer_r_delta_post_activation %*% array(t(model$time_synapse[[i]][,,2]),dim = dim(model$time_synapse[[i]])[2:1])) model$recurrent_synapse_update[[i]][,,2] = model$recurrent_synapse_update[[i]][,,2] + t(prev_layer_hidden) %*% layer_r_delta_post_activation model$time_synapse_update[[i]][,,2] = model$time_synapse_update[[i]][,,2] + t(x) %*% layer_r_delta_post_activation model$bias_synapse_update[[i]][,2] = model$bias_synapse_update[[i]][,2] + colMeans(layer_r_delta_post_activation) layer_r_and_z_delta_pre_weight_h = layer_r_delta_pre_weight_h + layer_z_delta_pre_weight_h layer_r_and_z_delta_pre_weight_x = layer_r_delta_pre_weight_x + layer_z_delta_pre_weight_x future_layer_hidden_delta[[i]] = layer_hidden_delta + layer_r_and_z_delta_pre_weight_h layer_up_delta = layer_r_and_z_delta_pre_weight_x + layer_h_delta_pre_weight_x } } return(model) }
get_hc_info <- function(varname, resplvl, Mlist, parelmts, lp) { all_lvls <- Mlist$group_lvls rel_lvls <- names(all_lvls)[all_lvls > all_lvls[resplvl]] rel_lvls_surv <- names(all_lvls)[all_lvls >= all_lvls[resplvl]] newrandom <- check_random_lvls( Mlist$random[[varname]], rel_lvls = if (Mlist$models[varname] %in% c("coxph", "survreg", "JM") & length(rel_lvls_surv) > 1L) { rel_lvls_surv } else { rel_lvls }) if (length(newrandom) > 0) { hc_columns <- lapply(newrandom, get_hc_columns, Mlist = Mlist) structure( orga_hc_parelmts( resplvl, intersect(rel_lvls, names(newrandom)), all_lvls = all_lvls, hc_columns = hc_columns, parelmts = parelmts, lp = lp ), warnings = rescale_ranefs_warning(lapply(hc_columns, attr, "incomplete"), Mlist$scale_pars, varname)) } } rescale_ranefs_warning <- function(incompl, scale_pars, varname) { nlapply(names(incompl), function(lvl) { if (any(incompl[[lvl]]) && any(!is.na(do.call(rbind, unname( scale_pars )))[names(incompl[[lvl]]), ])) { w <- warnmsg( "There are missing values in a variable for which a random effect is specified (%s). It will not be possible to re-scale the random effects %s and their variance covariance matrix %s back to the original scale of the data. If you are not interested in the estimated random effects or their (co)variances this is not a problem. The fixed effects estimates are not affected by this. If you are interested in the random effects or the (co)variances you need to specify that %s are not scaled (using the argument %s).", dQuote(names(incompl[[lvl]])[incompl[[lvl]]]), dQuote(paste0("b_", varname, "_", lvl)), dQuote(paste0("D_", varname, "_", lvl)), paste_and(dQuote(names(incompl[[lvl]]))), dQuote("scale_params") ) w } }) } check_random_lvls <- function(random, rel_lvls) { if (length(rel_lvls) == 0L) { return(NULL) } if (is.null(random)) { nlapply(rel_lvls, function(x) ~ 1) } else { rd <- remove_grouping(random) if (any(!names(rd) %in% rel_lvls)) { errormsg("You have specified random effects for levels on which there should not be random effects (%s).", dQuote(setdiff(names(rd), rel_lvls))) } else { rd } } } get_hc_columns <- function(rdfmla, Mlist) { Mlvls <- Mlist$Mlvls Mnam <- nlapply(Mlist$M, colnames) z_names <- get_dsgnmat_names(rdfmla, Mlist$data, Mlist$refs) inters <- Mlist$interactions[!names(Mlist$interactions) %in% z_names] in_z <- if (length(inters) > 0L) { nlapply(z_names, function(x) lapply(lapply(inters, attr, 'elements'), `%in%`, x)) } structure( nlapply(z_names, function(x) { list( main = if (x %in% names(Mlvls)) { setNames(match(x, Mnam[[Mlvls[x]]]), Mlvls[x]) }, interact = if (any(unlist(in_z[[x]]))) { w <- sapply(in_z[[x]], any) inters[w] } ) }), rd_intercept = attr(terms(rdfmla), 'intercept'), z_names = z_names, incomplete = lvapply(Mlist$data[, all_vars(rdfmla), drop = FALSE], function(x) any(is.na(x))) ) } get_dsgnmat_names <- function(formula, data, refs) { contr_list <- lapply(refs, attr, "contr_matrix") colnames( model.matrix(formula, data, contrasts.arg = contr_list[intersect(all_vars(formula), names(contr_list))])) } hc_rdslope_info <- function(hc_cols, parelmts) { hc_cols <- hc_cols[names(hc_cols) != "(Intercept)"] rd_slope_list <- lapply(names(hc_cols), function(var) { M_lvl <- names(hc_cols[[var]]$main) elmts <- parelmts[[M_lvl]] if (is.list(elmts)) { data.frame(rd_effect = var, term = var, matrix = M_lvl, cols = hc_cols[[var]]$main, parelmts = NA, stringsAsFactors = FALSE ) } else { data.frame(rd_effect = var, term = var, matrix = M_lvl, cols = hc_cols[[var]]$main, parelmts = ifelse(is.null(elmts[var]), NA, unname(elmts[var])), stringsAsFactors = FALSE ) } }) do.call(rbind, rd_slope_list) } hc_rdslope_interact <- function(hc_cols, parelmts, lvls) { hc_cols <- hc_cols[names(hc_cols) != "(Intercept)"] rd_slope_interact_coefs <- lapply(names(hc_cols), function(var) { if (any(lvapply(parelmts, is.list))) { do.call(rbind, lapply(hc_cols[[var]]$interact, function(x) { data.frame(rd_effect = var, term = attr(x, 'interaction'), matrix = names(x$elmts[attr(x, 'elements') != var]), cols = x$elmts[attr(x, 'elements') != var], parelmts = NA, stringsAsFactors = FALSE ) }) ) } else { do.call(rbind, lapply(hc_cols[[var]]$interact, function(x) { mat <- names(x$elmts)[attr(x, 'elements') != var] if (length(mat) > 1L) { elmt <- paste0(attr(x,"elements")[attr(x, 'elements') != var], collapse = ":") mat <- unlist(lapply(names(parelmts), function(p) { if (elmt %in% names(parelmts[[p]])) p })) col <- if (!is.null(mat)) { which(names(parelmts[[mat]]) == elmt) } } else { col <- x$elmts[attr(x, 'elements') != var] } if (!is.null(mat)) { data.frame(rd_effect = var, term = attr(x, 'interaction'), matrix = mat, cols = col, parelmts = unname(parelmts[[names(x$interterm)]][ attr(x, "interaction")]), stringsAsFactors = FALSE ) } }) ) } }) rd_slope_interact_coefs <- do.call(rbind, rd_slope_interact_coefs) if (!is.null(rd_slope_interact_coefs)) { subset(rd_slope_interact_coefs, matrix %in% paste0('M_', lvls)) } } orga_hc_parelmts <- function(resplvl, lvls, all_lvls, hc_columns, parelmts, lp) { hc_vars <- nlapply(lvls, function(lvl) { rd_slope_coefs <- hc_rdslope_info(hc_columns[[lvl]], parelmts) rd_slope_interact_coefs <- hc_rdslope_interact(hc_columns[[lvl]], parelmts, lvls) elmts <- parelmts[[paste0("M_", lvl)]][ !parelmts[[paste0("M_", lvl)]] %in% rbind(rd_slope_coefs, rd_slope_interact_coefs)$parelmts] rd_intercept_coefs <- if (!is.null(elmts) & attr(hc_columns[[lvl]], 'rd_intercept') == 1) { if (is.list(elmts) | length(elmts) == 0) { NULL } else { data.frame( rd_effect = "(Intercept)", term = names(elmts), matrix = paste0("M_", lvl), cols = lp[[paste0("M_", lvl)]][names(elmts)], parelmts = elmts, stringsAsFactors = FALSE ) } } structure( list(rd_intercept_coefs = rd_intercept_coefs, rd_slope_coefs = rd_slope_coefs, rd_slope_interact_coefs = rd_slope_interact_coefs ), rd_intercept = "(Intercept)" %in% names(hc_columns[[lvl]]), incomplete = attr(hc_columns[[lvl]], "incomplete"), z_names = attr(hc_columns[[lvl]], "z_names") ) }) used <- lapply(nlapply(hc_vars, do.call, what = rbind), "[[", "parelmts") othervars <- nlapply( names(all_lvls)[all_lvls <= min(all_lvls[lvls])], function(lvl) { other <- get_othervars_mat(lvl, parelmts, lp) nonprop <- get_othervars_mat(lvl, lapply(parelmts, 'attr', 'nonprop'), attr(lp, 'nonprop')) if (!inherits(other, 'list')) other <- other[!other$parelmts %in% unlist(used), ] list( other = if (all(dim(other) > 0)) other, nonprop = nonprop ) }) list(hcvars = hc_vars, othervars = lapply(othervars, "[[", "other"), nonprop = lapply(othervars, "[[", "nonprop") ) } get_othervars_mat <- function(lvl, parelmts, lp) { pe <- parelmts[[paste0("M_", lvl)]] linpred <- lp[[paste0("M_", lvl)]] if (length(pe) == 0) { NULL } else if (is.list(pe)) { lapply(pe, function(p) { data.frame(term = names(p), matrix = if (!is.null(linpred)) paste0("M_", lvl), cols = linpred[names(p)], parelmts = p, stringsAsFactors = FALSE) }) } else { data.frame(term = names(pe), matrix = if (!is.null(linpred)) paste0("M_", lvl), cols = linpred, parelmts = pe, stringsAsFactors = FALSE) } }
GetCDLImage <- function(aoi = NULL, year = NULL, type = NULL, format = 'png', crs = NULL, destfile = NULL, verbose = TRUE, tol_time = 20){ targetCRS <- "+proj=aea +lat_1=29.5 +lat_2=45.5 +lat_0=23 +lon_0=-96 +x_0=0 +y_0=0 +ellps=GRS80 +towgs84=0,0,0,0,0,0,0 +units=m +no_defs" if(is.null(aoi)) stop('aoi must be provided. See details. \n') if(is.null(year)) stop('year must be provided. See details. \n') if(is.null(type)) stop('type must be provided. See details. \n') if(type == 'p') stop('Cannot request statistics for a single point. \n') if(!type %in% c('f', 'ps', 'b', 's')) stop('Invalid type value. See details. \n') if(type == 'f'){ aoi <- as.character(aoi) if ((nchar(aoi) == 1)|(nchar(aoi) == 4)){ aoi <- paste0('0', aoi) } GetCDLImageF(fips = aoi, year = year, format = format, verbose = verbose, destfile = destfile, tol_time = tol_time) } if(type == 's'){ if(!is.null(crs)) stop('The coordinate system must be the Albers projection system. \n') GetCDLImageS(poly = aoi, year = year, format = format, verbose = verbose, destfile = destfile, tol_time = tol_time) } if(type == 'ps'){ if(length(aoi) < 6) stop('The aoi must be a numerical vector with at least 6 elements. \n') if(!is.null(crs)){ aoi <- convert_crs(aoi, crs)} GetCDLImagePs(points = aoi, year = year, format = format, verbose = verbose, destfile = destfile, tol_time = tol_time) } if(type == 'b'){ if (!is.numeric(aoi)) { if (!(class(aoi)[1] == "sf" | class(aoi)[2] == "sfc")) stop('aoi must be a numerical vector or a sf object. \n') if(is.na(sf::st_crs(aoi))) stop('The sf object for aoi does not contain crs. \n') aoi_crs <- sf::st_crs(aoi)[[2]] if(aoi_crs != targetCRS){aoi <- sf::st_transform(aoi, targetCRS)} GetCDLImageB(box = sf::st_bbox(aoi), year = year, format = format, verbose = verbose, destfile = destfile, tol_time = tol_time) }else{ if(length(aoi) != 4) stop('The aoi must be a numerical vector with 4 elements. \n') if(!is.null(crs)){ aoi <- convert_crs(aoi, crs)} GetCDLImageB(box = aoi, year = year, format = format, verbose = verbose, destfile = destfile, tol_time = tol_time) } } }
merge_named_lists <- function(list1, list2, fun=NULL) { if(!is.list(list1) || !is.list(list2)) stop("function merge_named_list requires two lists") if(is.null(fun) || !is.function(fun)) fun <- sum res_list <- list1 for(n in names(list2)) { if(!n %in% names(res_list)) res_list[[n]] <- list2[[n]] else res_list[[n]] <- fun(res_list[[n]],list2[[n]]) } return(res_list) } c_to_string <- function(var) { s <- "[" if(length(var)>0) for(i in 1:length(var)) { if(i<length(var)) s <- paste0(s,var[[i]],",") else s <- paste0(s,var[[i]]) } return(paste0(s,"]")) }
test_that("Validate GetVirtualReportSuiteSettings using legacy credentials", { skip_on_cran() SCAuth(Sys.getenv("USER", ""), Sys.getenv("SECRET", "")) gvrss <- GetVirtualReportSuiteSettings("vrs_zwitch0_vrs1") gvrss2 <- GetVirtualReportSuiteSettings(c("vrs_zwitch0_zwitchdevvrs", "vrs_zwitch0_vrs1")) expect_is(gvrss, "data.frame") expect_is(gvrss2, "data.frame") })
context("Testing test_docker_installation") test_that("Testing that test_docker_installation works", { skip_on_github_actions() skip_on_cran() expect_true(test_docker_installation()) expect_message(test_docker_installation(detailed = TRUE), "\u2714.*") })
library(jvcoords) set.seed(1) X1 <- matrix(rnorm(99), nrow = 33, ncol = 3) X2 <- matrix(rnorm(99), nrow = 3, ncol = 33) X3 <- matrix(rnorm(99), nrow = 99, ncol = 1) X4 <- matrix(1:6, 3, 2) for (x in list(X1, X2, X3, X4)) { s <- standardize(x) stopifnot(max(abs(colMeans(s$y))) < 1e-10) stopifnot(max(abs(apply(s$y, 2, var) - 1)) < 1e-10) stopifnot(max(abs(toCoords(s, x) - s$y)) < 1e-10) cat(dim(x), "to mat OK\n") stopifnot(max(abs(toCoords(s, x[1, ]) - s$y[1, ])) < 1e-10) cat(dim(x), "to vec OK\n") stopifnot(max(abs(fromCoords(s, s$y) - x)) < 1e-10) cat(dim(x), "from mat OK\n") stopifnot(max(abs(fromCoords(s, s$y[1, ]) - x[1, ])) < 1e-10) cat(dim(x), "from vec OK\n") Y <- matrix(rnorm(100 * s$q), 100, s$q) stopifnot(max(abs(Y - toCoords(s, fromCoords(s, Y)))) < 1e-10) cat(dim(x), "from&to mat OK\n") stopifnot(max(abs(Y[1, ] - toCoords(s, fromCoords(s, Y[1, ])))) < 1e-10) cat(dim(x), "from&to vec OK\n") }
data(satsolvers) vbsp = sum(parscores(satsolvers, vbs)) vbsm = sum(misclassificationPenalties(satsolvers, vbs)) vbss = sum(successes(satsolvers, vbs)) test_that("singleBest and vbs", { skip.expensive() vbsse = sum(apply(satsolvers$data[satsolvers$success], 1, max)) expect_equal(vbsse, 2125) expect_equal(vbss, 2125) vbsp1 = sum(parscores(satsolvers, vbs, 1)) vbsp1e = sum(apply(satsolvers$data[satsolvers$performance], 1, min)) expect_equal(vbsp1e, 1288664.971) expect_equal(vbsp1, 1288664.971) expect_equal(vbsp, 11267864.97) expect_equal(vbsm, 0) sbp = sum(parscores(satsolvers, singleBest)) sbm = sum(misclassificationPenalties(satsolvers, singleBest)) sbs = sum(successes(satsolvers, singleBest)) sbse = sum(satsolvers$data[,"clasp_success"]) expect_equal(sbse, 2048) expect_equal(sbs, 2048) sbp1 = sum(parscores(satsolvers, singleBest, 1)) sbp1e = sum(satsolvers$data["clasp"]) expect_equal(sbp1e, 1586266.044) expect_equal(sbp1, 1586266.044) sbme = sum(apply(satsolvers$data[satsolvers$performance], 1, function(x) { abs(x["clasp"] - min(x)) })) expect_equal(sbme, 297601.073) expect_equal(sbm, 297601.073) expect_equal(sbp, 14060266.04) }) folds = cvFolds(satsolvers) test_that("classify", { skip.expensive() res = classify(classifier=makeLearner("classif.OneR"), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = classify(classifier=list(makeLearner("classif.OneR"), makeLearner("classif.OneR"), makeLearner("classif.OneR")), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = classify(classifier=list(makeLearner("classif.OneR"), makeLearner("classif.OneR"), makeLearner("classif.OneR"), .combine=makeLearner("classif.OneR")), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) }) test_that("classifyPairs", { skip.expensive() res = classifyPairs(classifier=makeLearner("classif.OneR"), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = classifyPairs(classifier=makeLearner("classif.OneR"), data=folds, combine=makeLearner("classif.OneR")) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) }) test_that("cluster", { skip.expensive() res = cluster(clusterer=makeLearner("cluster.SimpleKMeans"), data=folds, pre=normalize) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = cluster(clusterer=makeLearner("cluster.SimpleKMeans"), data=folds, bestBy="successes", pre=normalize) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = cluster(clusterer=list(makeLearner("cluster.SimpleKMeans"), makeLearner("cluster.SimpleKMeans"), makeLearner("cluster.SimpleKMeans")), data=folds, pre=normalize) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = cluster(clusterer=list(makeLearner("cluster.SimpleKMeans"), makeLearner("cluster.SimpleKMeans"), makeLearner("cluster.SimpleKMeans"), .combine=makeLearner("classif.OneR")), data=folds, pre=normalize) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) }) test_that("regression", { skip.expensive() res = regression(regressor=makeLearner("regr.lm"), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = regression(regressor=makeLearner("regr.lm"), data=folds, combine=makeLearner("classif.OneR")) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = regression(regressor=makeLearner("regr.lm"), data=folds, combine=makeLearner("classif.OneR"), expand=function(x) { cbind(x, combn(c(1:ncol(x)), 2, function(y) { abs(x[,y[1]] - x[,y[2]]) })) }) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) }) test_that("regressionPairs", { skip.expensive() res = regressionPairs(regressor=makeLearner("regr.lm"), data=folds) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) res = regressionPairs(regressor=makeLearner("regr.lm"), data=folds, combine=makeLearner("classif.OneR")) expect_true(sum(parscores(folds, res)) > vbsp) expect_true(sum(misclassificationPenalties(folds, res)) > vbsm) expect_true(sum(successes(folds, res)) < vbss) expect_true(is.data.frame(res$predictor(satsolvers$data[satsolvers$features]))) }) test_that("perfScatterPlot", { skip.expensive() model = classify(classifier=makeLearner("classif.J48"), data=folds) library(ggplot2) p = perfScatterPlot(parscores, model, singleBest, folds, satsolvers) + scale_x_log10() + scale_y_log10() + xlab("J48") + ylab("single best") expect_false(is.null(p)) satsolvers$extra = c("foo") satsolvers$data$foo = 1:nrow(satsolvers$data) p = perfScatterPlot(parscores, model, singleBest, folds, satsolvers, pargs=aes(colour = foo)) + scale_x_log10() + scale_y_log10() + xlab("J48") + ylab("single best") expect_false(is.null(p)) }) test_that("tune", { skip.expensive() ps = makeParamSet(makeIntegerParam("M", lower = 1, upper = 100)) design = generateRandomDesign(10, ps) res = tuneModel(folds, classify, makeLearner("classif.J48"), design, parscores, nfolds = 3L, quiet = TRUE) expect_equal(class(res), "llama.model") expect_equal(attr(res, "type"), "classify") expect_true(res$parvals$M >= 1 && res$parvals$M <= 100) expect_true(all(sapply(res$inner.parvals, function(x) (x$M >= 1 && x$M <= 100)))) })
chao.sd <- function(x) { f.one <- sum(x[x==1]) f.two <- sum(x[x==2]) gamma <- f.two*(0.25*(f.one/f.two)^4+(f.one/f.two)^3+0.5*(f.one/f.two)^2) return(sqrt(gamma)) }
auto_name <- function(x, max_width = 40) { names(x) <- auto_names(x, max_width = max_width) x } auto_names <- function(x, max_width = 40) { x <- as.lazy_dots(x) nms <- names(x) %||% rep("", length(x)) missing <- nms == "" expr <- lapply(x[missing], `[[`, "expr") nms[missing] <- vapply(expr, deparse_trunc, width = max_width, FUN.VALUE = character(1), USE.NAMES = FALSE) nms } deparse_trunc <- function(x, width = getOption("width")) { if (is.symbol(x)) { return(as.character(x)) } text <- deparse(x, width.cutoff = width) if (length(text) == 1 && nchar(text) < width) return(text) paste0(substr(text[1], 1, width - 3), "...") }
"obounce" <- function (x, d) { ord <- order(x) xsort <- x[ord] n <- length(x) xnew <- xsort if (n > 1) { i1 <- 1 while (i1 < n) { x1 <- xsort[i1] i2 <- i1 + 1 for (j in i2:n) { nobounce <- TRUE jn <- n - j + i2 dj <- xsort[jn] - x1 dsought <- (jn - i1) * d if (dj < dsought) { jot <- (dsought - dj)/2 for (k in i1:jn) xnew[k] <- x1 - jot + (k - i1) * d i1 <- jn + 1 nobounce <- FALSE break } } if (nobounce) i1 <- i1 + 1 } if (min(diff(xnew)) < d * 0.999) { n1 <- (1:(n - 1))[diff(xnew) < d] cat("Error in bounce(). Improperly separated points are:", fill = TRUE) cat(paste(n1, ":", n1 + 1, sep = ""), fill = TRUE) cat(paste(xnew[n1], ":", xnew[n1 + 1], sep = ""), fill = TRUE) } } x[ord] <- xnew x }
sensIvreg <- function(ivregfit, coeftestIVres, variable, ...){ UseMethod("sensIvreg") }
summary.mslapmeg<- function(object,n=5,...){ dr<-data.frame(object[[1]],object[[2]],object[[3]]) colnames(dr)<-names(object)[-4] dr<-utils::head(dr[order(dr[,2]),],n) row.names(dr)<-NULL print(dr) }
test_that("tbl_format_header() results", { local_unknown_rows() local_foo_tbl() expect_snapshot({ tbl_format_header(tbl_format_setup(as_tbl(mtcars), width = 80)) tbl_format_header(tbl_format_setup(as_unknown_rows(trees), width = 30, n = 10)) "Narrow" tbl_format_header(tbl_format_setup(as_tbl(mtcars), width = 10)) "Custom tbl_sum()" tbl_format_header(tbl_format_setup(new_foo_tbl(), width = 30)) }) })
method_ids <- unique(data$method_id) %>% setdiff("error") plots <- map(method_ids, function(method_id) { print(method_id) data_method <- data %>% filter(method_id == !!method_id) model_method <- models %>% filter(method_id == !!method_id) data_noerror <- data_method %>% filter(error_status == "no_error") data_error <- data_method %>% filter(error_status != "no_error") pred_method <- data_pred %>% filter(method_id == !!method_id) data_noerror <- bind_rows( data_noerror, data_noerror %>% group_by(method_id, lnrow, lncol) %>% select_if(is.numeric) %>% summarise_if(is.numeric, mean, na.rm = TRUE) %>% mutate(orig_dataset_id = "mean") %>% ungroup() ) data_error <- bind_rows( data_error, data_error %>% group_by(method_id, lnrow, lncol) %>% select_if(is.numeric) %>% summarise_if(is.numeric, mean, na.rm = TRUE) %>% mutate(orig_dataset_id = "mean") %>% ungroup() ) g1 <- ggplot(data_method) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1, fill = error_status)) + scale_fill_manual(values = dynbenchmark::method_status_colours) + scale_x_nrow + scale_y_ncol + theme_classic() + theme(legend.position = "bottom") + labs(x = " facet_wrap(~ orig_dataset_id, ncol = 1) + coord_equal() if (nrow(data_noerror) > 0) { g2 <- ggplot(data_noerror) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1), fill = "darkgray", data_error) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1, fill = log10(time_method))) + scale_fill_distiller(palette = "RdYlBu") + scale_x_nrow + scale_y_ncol + theme_classic() + theme(legend.position = "bottom") + labs(x = " facet_wrap(~ orig_dataset_id, ncol = 1) + coord_equal() tmp_error <- bind_rows(data_error, data_noerror %>% filter(log10(max_mem) < 8)) g3 <- ggplot(data_noerror %>% filter(log10(max_mem) >= 8)) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1), fill = "darkgray", tmp_error) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1, fill = log10(max_mem))) + scale_fill_distiller(palette = "RdYlBu") + scale_x_nrow + scale_y_ncol + theme_classic() + theme(legend.position = "bottom") + labs(x = " facet_wrap(~ orig_dataset_id, ncol = 1) + coord_equal() g4a <- ggplot(pred_method %>% select(lnrow, lncol, time_lpred)) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1, fill = time_lpred)) + scale_fill_distiller(palette = "RdYlBu") + scale_x_nrow + scale_y_ncol + theme_classic() + theme(legend.position = "bottom") + labs(x = " coord_equal() g4b <- ggplot(pred_method) + geom_rect(aes(xmin = lnrow - .1, xmax = lnrow + .1, ymin = lncol - .1, ymax = lncol + .1, fill = mem_lpred)) + scale_fill_distiller(palette = "RdYlBu") + scale_x_nrow + scale_y_ncol + theme_classic() + theme(legend.position = "bottom") + labs(x = " coord_equal() patchwork::wrap_plots( patchwork::wrap_plots( g1 + labs(title = "Execution information"), g2 + labs(title = "Timings grid"), g3 + labs(title = "Memory grid"), nrow = 1 ), patchwork::wrap_plots( g4a + labs(title = "Predicted timings"), g4b + labs(title = "Predicted memory"), ncol = 1 ), nrow = 1, widths = c(3, 1) ) + patchwork::plot_annotation( title = paste0("Scalability results for ", data_method$method_name[[1]]), theme = theme(title = element_text(size = 20)) ) } else { patchwork::wrap_plots( g1 + labs(title = "Execution information") ) + patchwork::plot_annotation( title = paste0("Scalability results for ", data_method$method_name[[1]]), theme = theme(title = element_text(size = 20)) ) } }) dir.create(result_file("results"), showWarnings = FALSE) dir.create(result_file("results/error_class_plots"), showWarnings = FALSE) map(seq_along(method_ids), function(i) { mid <- method_ids[[i]] pl <- plots[[i]] cat("Plotting ", mid, "\n", sep = "") ggsave(result_file(c("results/", mid, ".png")), pl, width = 12, height = 14, dpi = 100) })
df2m <- function(x) { if(!is.null(x)) { xattr <- attributes(x) nxa <- names(xattr) x$intnr <- x$paramnr <- x$varname <- NULL cn <- colnames(x) x <- as.matrix(x) rownames(x) <- 1L:nrow(x) colnames(x) <- rep(cn, length.out = ncol(x)) for(k in 1L:length(nxa)) if(all(nxa[k] != c("dim", "dimnames", "class", "names", "row.names"))) { attr(x, nxa[k]) <- xattr[[k]] } } return(x) }
library(readr) library(dplyr) library(tidyr) library(magrittr) library(ggplot2) CDC_parser <- function(year, url) { all_deaths_name <- paste0("deaths_", substr(year, 3, 4)) all_deaths_save <- paste0("all_deaths_", substr(year, 3, 4), ".RData") gun_name <- paste0("guns_", substr(year, 3, 4)) gun_save <- paste0("gun_deaths_", substr(year, 3, 4), ".RData") suicide_name <- paste0("suicide_", substr(year, 3, 4)) suicide_save <- paste0("suicide_", substr(year, 3, 4), ".RData") layout <- fwf_widths(c(19,1,40,2,1,1,2,2,1,4,1,2,2,2,2,1,1,1,16,4,1,1,1,1,34,1,1,4,3,1,3,3,2,1,281,1,2,1,1,1,1,33,3,1,1), col_names = c("drop1", "res_status", "drop2", "education_89", "education_03", "education_flag", "month", "drop3", "sex", "detail_age", "age_flag", "age_recode", "age_recode2", "age_group", "age_infant", "death_place", "marital", "day_of_week", "drop4", "data_year", "at_work", "death_manner", "burial", "autopsy", "drop5", "activity", "injury_place", "underlying_cause", "cause_recode358", "drop6", "cause_recode113", "cause_recode130", "cause_recode39", "drop7", "multiple_causes", "drop8", "race", "race_bridged", "race_flag", "race_recode", "race_recode2", "drop9", "hispanic", "drop10", "hispanic_recode")) temp <- tempfile() download.file(url, temp, quiet = T) raw_file <- read_fwf(unzip(temp), layout) raw_file <- raw_file %>% select(-contains("drop")) assign(eval(all_deaths_name), raw_file) save(list = all_deaths_name, file = all_deaths_save) suicide_code <- list() for (i in 1:24) { suicide_code[[i]] <- paste0("X", i + 59) } suicide_code[length(suicide_code)+1] <- "U03" suicide_code[length(suicide_code)+1] <- "Y870" suicide <- raw_file %>% filter(underlying_cause %in% suicide_code) %>% mutate(gun = ifelse(underlying_cause %in% c("X72", "X73", "X74"), 1, 0), year = year) assign(eval(suicide_name), suicide) save(list = suicide_name, file = suicide_save) rm(suicide) rm(list = suicide_name) guns <- raw_file %>% filter(underlying_cause %in% c("W32", "W33", "W34", "X72", "X73", "X74", "U014", "X93", "X94", "X95", "Y22", "Y23", "Y24", "Y350")) rm(raw_file) guns <- guns %>% mutate(intent = ifelse(underlying_cause %in% c("W32", "W33", "W34"), "Accidental", ifelse(underlying_cause %in% c("X72", "X73", "X74"), "Suicide", ifelse(underlying_cause %in% c("*U01.4", "X93", "X94", "X95", "Y350"), "Homicide", ifelse(underlying_cause %in% c("Y22", "Y23", "Y24"), "Undetermined", NA)))), police = ifelse(underlying_cause == "Y350", 1, 0), weapon = ifelse(underlying_cause %in% c("W32", "X72", "X93", "Y22"), "Handgun", ifelse(underlying_cause %in% c("W33", "X73", "X94", "Y23"), "Rifle etc", "Other/unknown")), year = year) guns <- guns %>% mutate(age = ifelse(substr(detail_age, 1, 1) == "1", as.numeric(substr(detail_age, 2, 4)), ifelse(detail_age == 9999, NA, 0)), age = ifelse(age == 999, NA, age)) assign(eval(gun_name), guns) save(list = gun_name, file = gun_save) rm(guns) rm(list = gun_name) } year <- 2013 url <- "ftp://ftp.cdc.gov/pub/Health_Statistics/NCHS/Datasets/DVS/mortality/mort2013us.zip" CDC_parser(year, url) load("gun_deaths_14.RData") load("gun_deaths_13.RData") load("gun_deaths_12.RData") all_guns <- rbind(guns_12, guns_13, guns_14) all_guns <- all_guns %>% filter(res_status != 4) all_guns <- all_guns %>% mutate(place = factor(injury_place, labels = c("Home", "Residential institution", "School/instiution", "Sports", "Street", "Trade/service area", "Industrial/construction", "Farm", "Other specified", "Other unspecified")), education = ifelse(education_flag == 1, cut(as.numeric(education_03), breaks = c(0, 2, 3, 5, 8, 9)), cut(as.numeric(education_89), breaks = c(0, 11, 12, 15, 17, 99))), education = factor(education, labels = c("Less than HS", "HS/GED", "Some college", "BA+", NA)), race = ifelse(hispanic > 199 & hispanic <996, "Hispanic", ifelse(race == "01", "White", ifelse(race == "02", "Black", ifelse(as.numeric(race) >= 4 & as.numeric(race) <= 78, "Asian/Pacific Islander","Native American/Native Alaskan")))), race = ifelse(is.na(race), "Unknown", race)) %>% select(year, month, intent, police, sex, age, race, hispanic, place, education) all_guns %>% filter(intent == "Suicide") %>% group_by(year) %>% summarize(suicides = length(year)) all_guns %>% filter(intent == "Homicide", age >= 15, age < 35, sex == "M") %>% group_by(year) %>% summarize(homicides = length(year)) save(all_guns, file = "all_guns.RData") write.csv(all_guns, file = "full_data.csv")
variance_drv = function(data, years = 10) { n = years U = 1 + data u = mean(U) u2 = moment(U, central = FALSE, absolute = FALSE, order = 2) app1 = rep(NA, n - 1) for (i in 1:(n - 1)) app1[i]=moment(U, central = FALSE, absolute = FALSE, order = 2*i) p1 = sum(app1) app2 = matrix(NA, n,n) for (r in 1:nrow(app2)) for (s in 1:ncol(app2)) app2[r,s]=moment(U, central = FALSE, absolute = FALSE, order = sum(r+s)) for (r in 1:nrow(app2)) for (s in 1:ncol(app2)) if (s<=r) app2[r,s]=0 app2[,n]=0 p2 = 2*sum(app2) app3=rep(NA, n - 1) for (i in 1:(n - 1)) app3[i]=moment(U, central = FALSE, absolute = FALSE, order = i) p3 =(sum(app3))^2 p4 =moment(U, central = FALSE, absolute = FALSE, order = 2*n) un=moment(U, central = FALSE, absolute = FALSE, order = n) p5=un^2 app6=rep(NA,(2*n)-(n+1)) for (i in 1:length(app6)) app6[i]=moment(U, central = FALSE, absolute = FALSE, order = n+i) p6=2*sum(app6) app7=rep(NA,n-1) for (i in 1:length(app7)) app7[i]=moment(U, central = FALSE, absolute = FALSE, order = i) p7=2*un*sum(app7) var=p1+p2-p3+p4-p5+p6-p7 return(var) }
getNamedArgs_OdbcDriver <- function(dsn = NULL, ..., timezone = "UTC", driver = NULL, server = NULL, database = NULL, uid = NULL, pwd = NULL, .connection_string = NULL) { list( dsn = dsn, ..., timezone = timezone, driver = driver, server = server, database = database, uid = uid, .connection_string = .connection_string ) }
tLagPropOdds <- function(data, ..., ti = NULL, td = NULL, itmax = 500, tol = 1e-5) { inputs <- .verifyInputs(df = data, ti = ti, td = td) ipwObj <- .ipw(uv = inputs$uv, cats = inputs$cats, txOpts = inputs$txOpts, itmax = itmax, tol = tol) res <- .aipw(uv = inputs$uv, ti = inputs$ti, td = inputs$td, ipwObj = ipwObj, txOpts = inputs$txOpts, uniqueCensor = inputs$uniqueCensor) class(x = res) <- 'tLagObj' attr(x = res, which = "type") <- inputs$type return( res ) }
context("EM") theta0 <- list(A = matrix(0.5), B = matrix(0.5, 1, 7), C = matrix(0.5), D = matrix(0.5, 1, 7), Q = matrix(1), R = matrix(1), mu1 = matrix(1), V1 = matrix(1)) obs <- log(ldsr:::P1annual$Qa) mu <- mean(obs) y <- t(obs - mu) N <- 85 uInst <- vInst <- t(ldsr:::P1pc[322:406]) u <- v <- t(NPpc[601:813]) foreach::registerDoSEQ() test_that("Numerical results are correct for the instrumental period in the first two iterations for P1", { smooth1 <- ldsr:::Kalman_smoother(y, uInst, vInst, theta0) theta1 <- ldsr:::Mstep(y, uInst, vInst, smooth1) smooth2 <- ldsr:::Kalman_smoother(y, uInst, vInst, theta1) theta2 <- ldsr:::Mstep(y, uInst, vInst, smooth2) expect_equal(smooth1$lik, -11.678657, tolerance = 1e-6) expect_equal(smooth1$X[c(1, 85)], c(1.293356, -0.987671), tolerance = 1e-6) expect_equal(theta1$A[1], 0.606066, tolerance = 1e-6) expect_equal(theta1$C[1], -0.005995, tolerance = 1e-6) expect_equal(theta1$Q[1], 3.640236, tolerance = 1e-6) expect_equal(smooth2$lik, -0.114224, tolerance = 1e-6) expect_equal(theta2$A[1], 0.603945, tolerance = 1e-6) expect_equal(theta2$C[1], -0.012004, tolerance = 1e-6) expect_equal(theta2$Q[1], 3.644322, tolerance = 1e-6) }) test_that("Convergence is correct for the instrumental period", { fit <- ldsr:::LDS_EM(y, uInst, vInst, theta0, 100, 1e-5) expect_equal(length(fit$liks), 68) expect_equal(fit$lik, -0.039093, tolerance = 1e-6) }) test_that("Fixed restart works", { fit <- LDS_reconstruction(NPannual, u, v, start.year = 1800, init = make_init(nrow(u), nrow(v), 2)) expect_is(fit, "list") }) test_that("Randomized restarts works", { fit <- LDS_reconstruction(NPannual, u, v, start.year = 1800, num.restarts = 2) expect_is(fit, "list") }) test_that("Cross validation works with randomized restarts", { cv <- cvLDS(NPannual, u, v, start.year = 1800, num.restarts = 2, Z = make_Z(NPannual$Qa, 2)) expect_is(cv, "list") }) test_that("u can be NULL", { fit <- LDS_reconstruction(NPannual, u = NULL, v, start.year = 1800, num.restarts = 2) expect_is(fit, "list") cv <- cvLDS(NPannual, u = NULL, v, start.year = 1800, num.restarts = 2, Z = make_Z(NPannual$Qa, 2)) expect_is(cv, "list") }) test_that("v can be NULL", { fit <- LDS_reconstruction(NPannual, u, v = NULL, start.year = 1800, num.restarts = 2) expect_is(fit, "list") cv <- cvLDS(NPannual, u, v = NULL, start.year = 1800, num.restarts = 2, Z = make_Z(NPannual$Qa, 2)) expect_is(cv, "list") }) test_that("u and v can have different nrows", { fit <- LDS_reconstruction(NPannual, u[1:2, ], v, start.year = 1800, num.restarts = 2) expect_is(fit, "list") cv <- cvLDS(NPannual, u[1:2, ], v, start.year = 1800, num.restarts = 2, Z = make_Z(NPannual$Qa, 2)) expect_is(cv, "list") })
context("Haversine distance") test_that("Bankstown airport to Sydney airport approximately 17628m", { expect_lt(haversine_distance(-33 - 56/60 - 46/3600, 151 + 10/60 + 38/3600, -33 - 55/60 - 28/3600, 150 + 59/60+18/3600) / 17.628 - 1, 0.01) }) test_that("Broken Hill airport to Sydney airport approximately 932158", { expect_lt(haversine_distance(-33 - 56/60 - 46/3600, 151 + 10/60 + 38/3600, -32 - 00/60 - 05/3600, 141 + 28/60 + 18/3600) / 932.158 - 1, 0.01) })
library(testthat) library(PReMiuM) test_check("PReMiuM")
sim.morpho <- function(tree, characters, states = 1, model = "ER", rates, substitution = c(stats::runif, 2, 2), invariant = TRUE, verbose = FALSE) { check.class(tree, "phylo") check.class(characters, "numeric") check.length(characters, 1, " must be a single numeric value.") check.class(states, "numeric") if(sum(states) != 1) { stop.call("", "States argument must sum up to 1.") } if(length(states) > 1 && model == "HKY") { states <- 1 warning("The HKY model only allows the use of two states characters (binary).") } if(!is(model, "function")) { model <- toupper(model) implemented_models <- c("ER", "HKY", "MIXED") check.method(model, implemented_models, "The model") model_name <- model if(!is(model, "function") && model_name == "ER") { model <- rTraitDisc.mk substitution <- c(stats::runif, 1, 1) } if(!is(model, "function") && model_name == "HKY") { model <- gen.seq.HKY.binary } if(!is(model, "function") && model_name == "MIXED") { model <- MIXED.model } } else { stop.call("", "User functions are not supported yet for the model argument.\nTry using \"HKY\", \"ER\" or \"MIXED\".") } if(length(rates) == 1) { check.class(rates, "function") } else { check.class(rates[[1]], "function") test <- NULL ; try(test <- sample.distribution(1, rates), silent = TRUE) if(length(test) != 1) { stop.call("", "Error in rates argument format. Should be c(function, arg1, arg2, ...).") } } if(length(substitution) == 1) { check.class(substitution, "function") } else { check.class(substitution[[1]], "function") test <- NULL ; try(test <- sample.distribution(1, substitution), silent = TRUE) if(length(test) != 1) { stop.call("", "Error in substitution argument format. Should be c(function, arg1, arg2, ...).") } } check.class(invariant, "logical") check.class(verbose, "logical") if(verbose == TRUE) cat(paste("Generating a matrix of ", characters, " characters for ", Ntip(tree), " taxa:", sep="")) matrix <- replicate(characters, model(tree = tree, states = states, rates = rates, substitution = substitution, verbose = verbose)) if(verbose == TRUE) cat("Done.\n") if(invariant == FALSE) { if(any(apply(matrix, 2, is.invariant))) { if(verbose == TRUE) cat("Re-simulating ", length(which(apply(matrix, 2, is.invariant)) == TRUE), " invariant characters:", sep="") while(any(apply(matrix, 2, is.invariant))) { matrix[, which(apply(matrix, 2, is.invariant) == TRUE)] <- replicate(length(which(apply(matrix, 2, is.invariant) == TRUE)), model(tree = tree, states = states, rates = rates, substitution = substitution, verbose = verbose)) if(verbose == TRUE) cat(".") } if(verbose == TRUE) cat("Done.\n") } } if(length(tree$tip.label) != 0) { rownames(matrix) <- tree$tip.label } return(matrix) }
NULL create_ranking <- function(orderings){ if(is.vector(orderings)){ stopifnot(validate_permutation(orderings)) return(order(orderings)) } else if(is.matrix(orderings)){ n_items <- ncol(orderings) orderings <- split(orderings, f = seq_len(nrow(orderings))) check <- lapply(orderings, validate_permutation) if(!Reduce(`&&`, check)){ stop(paste("orderings must contain proper permutations. Problem row(s):", which(!check))) } rankings <- lapply(orderings, function(x) { missing_items <- setdiff(1:n_items, x) candidates <- matrix(1:n_items, ncol = n_items, nrow = n_items) candidates[, missing_items] <- NA_real_ inds <- outer(X = x, Y = 1:n_items, FUN = "==") inds[1, colSums(inds, na.rm = TRUE) == 0] <- TRUE inds[is.na(inds)] <- FALSE candidates[inds] } ) return(t(matrix(unlist(rankings), ncol = length(rankings)))) } else { stop("orderings must be a vector or matrix") } } create_ordering <- function(rankings){ create_ranking(rankings) }
source("ESEUR_config.r") library("igraph") unloadNamespace("sna") vehicles=read.graph(paste0(ESEUR_dir, "ecosystems/Braha/Braha_VehicleNetworkinPajek.net"), format="pajek") software=read.graph(paste0(ESEUR_dir, "ecosystems/Braha/Braha_SoftwareNetworkinPajek.net"), format="pajek") pharmaceutical=read.graph(paste0(ESEUR_dir, "ecosystems/Braha/Braha_PharmaceuticaNetwork.txt"), format="pajek") hospital=read.graph(paste0(ESEUR_dir, "ecosystems/Braha/Braha_SixteenStoryHospital.txt"), format="pajek") pal_col=rainbow_hcl(3) graph_prop=function(net_graph) { t1=vcount(net_graph) t2=ecount(net_graph) t3=average.path.length(net_graph) t4=transitivity(net_graph) t6=mean(degree(net_graph, mode="out")) t7=graph.density(net_graph) return(cbind(Nodes=t1, Edges=t2, "Average path length"=t3, "Clustering coeff"=t4, Degree=t6, Density=t7)) } tab=graph_prop(hospital) tab=rbind(tab, graph_prop(pharmaceutical)) tab=rbind(tab, graph_prop(software)) tab=rbind(tab, graph_prop(vehicles)) rownames(tab)=c("Hospital", "Pharmaceutical", "Software", "Vehicles") library("ascii") print(ascii(tab, include.rownames=TRUE, include.colnames=TRUE))
isEuclidean = function(x) { return(x$edge.weight.type %in% c("EUC_2D", "EUC_3D")) }
logspec2cov<-function(ebeta,vbeta,SARIMA=list(sigma2=1),lags,subdivisions=100){ nb<-length(ebeta) acv<-c() pb<-txtProgressBar(min=0,max=lags,style= 3) for(k in 0:lags){ setTxtProgressBar(pb,k) dumfun<-function(x){ g0<-log(SARIMAspec(SARIMA,freq=x)$spec) B<-basis(x,nb) mu<-B%*%ebeta+g0 s2<-rowSums((B%*%vbeta)*B) exp(mu+0.5*s2)*cos(2*pi*k*x) } acv[k+1]<-2*pi*integrate(dumfun,0,0.5,rel.tol=1e-2,subdivisions=subdivisions)$value } close(pb) return(acv) }
context("scatter_plot") test_that("scatter_plot works", { g = scatter_plot(mtcars, "cyl", "wt") expect_equal(nrow(g$data), 32) g = scatter_plot(mtcars, "as.character(cyl)", "wt", "'a'") expect_equal(nrow(g$data), 32) g = scatter_plot(mtcars, "as.character(cyl)", "wt", "am") expect_equal(nrow(g$data), 32) })
msaedbns <- function (formula, vardir, weight,cluster,nonsample, samevar = FALSE, MAXITER = 100, PRECISION = 1e-04, data) { result = list(MSAE_Eblup_sampled = NA,MSAE_Eblup_all = NA, MSE_Eblup_sampled = NA, MSE_Eblup_all = NA, randomEffect_sampled = NA, randomEffect_all = NA, Rmatrix_sampled = NA, fit = list(method = NA, convergence = NA, iterations = NA, estcoef = NA, refvar = NA, informationFisher = NA), difference_benchmarking = list(Estimation_sampled = NA, Estimation_all = NA, Aggregation_sampled = NA, Aggregation_all = NA, MSE_DB_sampled = NA, MSE_DB_all = NA, g4.a = NA, g4.b = NA)) if (!(TRUE %in% data[,"nonsample"])){ stop("this msaedbns() function is used for at least 1 observation has no sample, check your 'nonsample' variable or use msaedb() instead ") } if (length(formula)<=1){ stop("this msaedbns() function is used for at least 2 response variables, numbers of your response variables is ",length(formula),". use saedbns() function instead") } r <- length(formula) RIn_function <- function(vardir, n,r){ it <- 0 it2 <- 0 RIn <- list() rmat2 <- matrix(0,n,n) for (i in 1:r){ for (j in 1:r){ it <- it +1 if (i>j){ RIn[[it+it2]] <- rmat2 it <- it-1 it2 <- it2+1 }else { RIn[[it+it2]] <- diag(vardir[,it])} } } RIN <- list() for ( i in 1:r){ if (i == 1){ RIN[[i]] <- RIn[[i]] for (j in 1:(r-1)){ RIN[[i]] <- cbind(RIN[[i]],RIn[[j+1]]) } } else { RIN[[i]] <- RIn[[i*r-r+1]] for (j in 1:(r-1)){ RIN[[i]] <- cbind(RIN[[i]],RIn[[(i*r-r+1)+j]]) } } } RR <- do.call(rbind,RIN) RR <- (t(RR)+RR)*(matrix(1,n*r,n*r)-diag(0.5,n*r)) RIn<- return(RR) } index <- cbind(rep(1:dim(data)[1])) data <- cbind(index,data) data_sampled <- data[which(data$nonsample == FALSE), ] formuladata <- formula for(i in 1:r) {formuladata[[i]] <- model.frame(formula[[i]], na.action = na.omit, data_sampled )} y.vec <- unlist(lapply(formuladata, function(x){x[1][1]})) x.matrix <- formula for(i in 1:r) {x.matrix[[i]] <- model.matrix(formula[[i]], na.action = na.omit, data_sampled)} x.matrix = Reduce(adiag,x.matrix) w.matrix_temp = as.matrix(data_sampled[,weight]) w.matrix <- matrix(0,dim(w.matrix_temp)[1],r) for (i in 1:dim(w.matrix)[1]) { for (j in 1:r){ w.matrix[i,j] <- w.matrix_temp[i,j]/sum(w.matrix_temp[,j]) } } n = length(y.vec)/r dfnonsample <- data[which(data$nonsample == TRUE), ] anns <- dfnonsample$index vardirns <- dfnonsample[,vardir] x.matrixns <- formula for(i in 1:r) {x.matrixns[[i]] <- model.matrix(formula[[i]], na.action = na.omit, dfnonsample)} x.matrixns = Reduce(adiag,x.matrixns) if (any(is.na(data[, weight]))) stop("Object weight contains NA values.") if (!all(weight %in% names(data))) stop("Object weight is not appropiate with data") if (length(weight) != r) stop("Length of weight is not appropiate, the length must be ",r) if (any(is.na(data[, vardir]))) stop("Object vardir contains NA values.") if (!all(vardir %in% names(data))) stop("Object vardir is not appropiate with data") if (length(vardir) != sum(1:r)) stop("Length of vardir is not appropiate, the length must be ", sum(1:r)) RIn = RIn_function(data_sampled[, vardir],n,r) for (i in 1:r) { if (attr(attributes(formuladata[[i]])$terms, "response") == 1) textformula = paste(formula[[i]][2], formula[[i]][1], formula[[i]][3]) else textformula = paste(formula[[i]][1], formula[[i]][2]) if (length(na.action(formuladata[[i]])) > 0) { stop("Argument formula= ", textformula, " contains NA values.") } } varnames_Y <- lapply(formula, function(x) {x[[2]]}) In = diag(n) Ir = diag(r) d.sigma <- lapply(formula, function(x){x=matrix(0,r,r)}) for (i in 1:r) {d.sigma[[i]][i, i] = 1} d.SIGMA <- lapply(d.sigma, function(x){kronecker(x,In)}) convergence = TRUE if (samevar) { Varu <- median(diag(RIn)) k <- 0 diff <- rep(PRECISION + 1, r) while (any(diff > PRECISION) & (k < MAXITER)) { Varu1<- Varu G <- kronecker(Varu, Ir) GIn <- kronecker(G, In) SIGMA<- (GIn + RIn) SIGMA_inv <- solve(SIGMA) Xt_Si<- t(SIGMA_inv %*% x.matrix) Q <- solve(Xt_Si %*% x.matrix,tol = 1e-30) P <- SIGMA_inv - t(Xt_Si) %*% Q %*% Xt_Si Py <- P %*% y.vec s <- (-0.5) * sum(diag(P)) + 0.5 * (t(Py) %*% Py) F <- 0.5 * sum(diag(P %*% P)) Varu <- Varu1 + solve(F) %*% s diff <- abs((Varu - Varu1)/Varu1) k <- k + 1 } Varu = as.vector((rep(max(Varu,0), r))) names(Varu) = varnames_Y if (k >= MAXITER && diff >= PRECISION) { convergence = FALSE } GIn <- kronecker(diag(Varu), In) SIGMA <- (GIn + RIn) SIGMA_inv <- solve(SIGMA) Xt_Si <- t(SIGMA_inv %*% x.matrix) Q <- solve(Xt_Si %*% x.matrix) P <- SIGMA_inv - t(Xt_Si) %*% Q %*% Xt_Si Py <- P %*% y.vec beta.REML <- Q %*% Xt_Si %*% y.vec resid <- y.vec - x.matrix %*% beta.REML MSAE_Eblup<- data.frame(matrix(x.matrix %*% beta.REML +GIn %*% SIGMA_inv %*% resid,n, r)) colnames(MSAE_Eblup) = varnames_Y std.err.beta <- sqrt(diag(Q)) tvalue <- beta.REML/std.err.beta pvalue <- 2 * pnorm(abs(tvalue), lower.tail = FALSE) coef <- cbind(beta.REML, std.err.beta, tvalue, pvalue) colnames(coef) = c("beta", "std.error", "t.statistics","p.value") Bi <- RIn%*%solve(SIGMA) m <- dim(x.matrix)[1] p <- dim(x.matrix)[2] I <- diag(m) g1d <- diag(Bi%*%GIn) g2d <- diag(Bi%*%x.matrix%*%Q%*%t(x.matrix)%*%t(Bi)) dg <- SIGMA_inv - (I-Bi) %*% SIGMA_inv g3d <- diag(dg %*% SIGMA %*% t(dg))/F W <- diag(as.vector(w.matrix)) g4.a<- matrix(0,m,m) for (i in 1:r){ g4.a <- g4.a + d.SIGMA[[i]]*sum(diag(d.SIGMA[[i]]%*%W%*%Bi%*%SIGMA%*%t(W)%*%t(Bi))) } g4.a <- diag(g4.a) g4.b <- matrix(0,r,r) for (l in 0:(r-1)) { for (i in ((l*n)+1):((l+1)*n)) { xdi <- matrix(x.matrix[i, ], nrow = 1, ncol = p) for (j in ((l*n)+1):((l+1)*n)) { xdj <- matrix(x.matrix[j, ], nrow = 1, ncol = p) g4.b<- g4.b + d.sigma[[l+1]]*as.numeric(W[i,i]*W[j,j]*Bi[i,i]*Bi[j,j]*as.numeric(xdi %*% Q %*% t(xdj))) } } } g4.b <- diag(kronecker(g4.b,In)) g4d <- g4.a - g4.b g4.a <- as.data.frame(matrix(g4.a,n,r)) g4.a <- apply(g4.a, 2, median) names(g4.a) <- varnames_Y g4.b <- as.data.frame(matrix(g4.b,n,r)) g4.b <- apply(g4.b, 2, median) names(g4.b) <- varnames_Y MSE_Eblup <- g1d + g2d + 2 * g3d MSE_DB <- g1d + g2d + 2 * g3d + g4d MSE_Eblup <- data.frame(matrix(MSE_Eblup, n, r)) MSE_DB <- data.frame(matrix(MSE_DB, n, r)) names(MSE_Eblup) = varnames_Y names(MSE_DB) = varnames_Y } else { Varu <- apply(matrix(diag(RIn), n, r), 2, median) k <- 0 diff <- rep(PRECISION + 1, r) while (any(diff > rep(PRECISION, r)) & (k < MAXITER)) { Varu1 <- Varu G <- diag(as.vector(Varu1)) GIn <- kronecker(G, In) SIGMA <- GIn + RIn SIGMA_inv <- solve(SIGMA) Xt_Si <- t(SIGMA_inv %*% x.matrix) Q <- solve(Xt_Si %*% x.matrix) P <- SIGMA_inv - t(Xt_Si) %*% Q %*% Xt_Si Py <- P %*% y.vec s <- vector() for (i in 1:r){s[i] <- (-0.5) * sum(diag(P %*% d.SIGMA[[i]])) + 0.5 * (t(Py) %*% d.SIGMA[[i]] %*% Py)} F <- matrix(NA,r,r) for (i in 1:r){ for (j in 1:r){ F[j,i] <- 0.5*sum(diag(P %*% d.SIGMA[[i]] %*% P %*% d.SIGMA[[j]])) } } Varu <- Varu1 + solve(F) %*% s diff <- abs((Varu - Varu1)/Varu1) k <- k + 1 } Varu <- as.vector(sapply(Varu, max,0)) names(Varu) = varnames_Y if (k >= MAXITER && diff >= PRECISION) { convergence = FALSE } G <- diag(as.vector(Varu)) GIn <- kronecker(G, In) SIGMA <- GIn + RIn SIGMA_inv <- solve(SIGMA) Xt_Si <- t(SIGMA_inv %*% x.matrix) Q <- solve(Xt_Si %*% x.matrix) P <- SIGMA_inv - t(Xt_Si) %*% Q %*% Xt_Si Py <- P %*% y.vec beta.REML <- Q %*% Xt_Si %*% y.vec resid <- y.vec - x.matrix %*% beta.REML MSAE_Eblup <- data.frame(matrix(x.matrix %*% beta.REML +GIn %*% SIGMA_inv %*% resid,n, r)) colnames(MSAE_Eblup) = varnames_Y std.err.beta <- sqrt(diag(Q)) tvalue <- beta.REML/std.err.beta pvalue <- 2 * pnorm(abs(tvalue), lower.tail = FALSE) coef <- cbind(beta.REML, std.err.beta, tvalue, pvalue) colnames(coef)= c("beta", "std.error", "t.statistics","p.value") F_inv <- solve(F) Bi <- RIn%*%solve(SIGMA) m <- dim(x.matrix)[1] p <- dim(x.matrix)[2] I <- diag(m) g1d <- diag(Bi%*%GIn) g2d <- diag(Bi%*%x.matrix%*%Q%*%t(x.matrix)%*%t(Bi)) dg <- lapply(d.SIGMA, function(x) x %*% SIGMA_inv - GIn %*% SIGMA_inv %*% x %*% SIGMA_inv) g3d = list() for (i in 1:r) { for (j in 1:r) { g3d[[(i - 1) * r + j]] = F_inv[i, j] * (dg[[i]] %*% SIGMA %*% t(dg[[j]])) } } g3d <- diag(Reduce("+", g3d)) W <- diag(as.vector(w.matrix)) g4.a <- matrix(0,m,m) for (i in 1:r){ g4.a<- g4.a + d.SIGMA[[i]]*sum(diag(d.SIGMA[[i]]%*%W%*%Bi%*%SIGMA%*%t(W)%*%t(Bi))) } g4.a <- diag(g4.a) g4.b <- matrix(0,r,r) for (l in 0:(r-1)) { for (i in ((l*n)+1):((l+1)*n)) { xdi <- matrix(x.matrix[i, ], nrow = 1, ncol = p) for (j in ((l*n)+1):((l+1)*n)) { xdj <- matrix(x.matrix[j, ], nrow = 1, ncol = p) g4.b<- g4.b + d.sigma[[l+1]]*as.numeric(W[i,i]*W[j,j]*Bi[i,i]*Bi[j,j]*as.numeric(xdi %*% Q %*% t(xdj))) } } } g4.b <- diag(kronecker(g4.b,In)) g4d <- g4.a - g4.b g4.a <- as.data.frame(matrix(g4.a,n,r)) g4.a <- apply(g4.a, 2, median) names(g4.a) <- varnames_Y g4.b <- as.data.frame(matrix(g4.b,n,r)) g4.b <- apply(g4.b, 2, median) names(g4.b) <- varnames_Y MSE_Eblup <- g1d + g2d + 2 * g3d MSE_DB <- g1d + g2d + 2 * g3d + g4d MSE_Eblup <- data.frame(matrix(MSE_Eblup, n, r)) MSE_DB <- data.frame(matrix(MSE_DB, n, r)) names(MSE_Eblup) = varnames_Y names(MSE_DB) = varnames_Y } randomEffect <- GIn%*%SIGMA_inv%*%resid randomEffect <- as.data.frame(matrix(randomEffect, n, r)) names(randomEffect) <- varnames_Y XBns <- matrix(x.matrixns%*%beta.REML,length(anns),r) XBns <- cbind(XBns,dfnonsample[,cluster]) estrEff <- cbind(randomEffect,data_sampled[,cluster],nonsample=data_sampled$nonsample,data_sampled$index) avrEffc <- matrix(0,max(data[,cluster]),r) for (i in 1:r){ for (j in 1:max(data[,cluster])){ if (!(j %in% estrEff[,i+r])){ newline <- rep(NA,dim(estrEff)[2]) newline[1:r] <-0 newline[i+r] <- j estrEff <- rbind(estrEff,newline) } } } for (i in 1:r){ avrEffc[,i] <- sapply(split(estrEff[,i], estrEff[,i+r]), mean) } colnames(avrEffc) <- varnames_Y avrEffc <- cbind(cluster = c(1:max(data[,cluster])), avrEffc) EBLUPCluster <- matrix(0,length(anns),r) for (i in 1:length(anns)){ for (j in 1:r){ EBLUPCluster[i,j] <- XBns[i,j]+avrEffc[XBns[i,j+r],j+1] } } colnames(EBLUPCluster) <- varnames_Y EBLUPCluster <- data.frame(an = anns,EBLUPCluster ) totalArea <- dim(MSAE_Eblup)[1]+dim(EBLUPCluster)[1] idx <- cbind(index = rep(1:totalArea)) MSAE_Eblup_temp <- cbind(index=data_sampled$index,MSAE_Eblup) MSAE_Eblup_all <- merge(x=as.matrix(idx), y=MSAE_Eblup_temp, by = "index", all.x=TRUE) MSAE_Eblup_all <- MSAE_Eblup_all[,-1] for (i in 1:totalArea){ for (j in 1:length(anns)){ if (i==anns[j]){ MSAE_Eblup_all[i,] <- EBLUPCluster[which(EBLUPCluster$an == i), ][,-1] } } } y.vec <- matrix(y.vec, n,r) colnames(y.vec) = varnames_Y W <- as.matrix(w.matrix) alfa <- ginv(t(W))%*%(t(W)%*%y.vec-t(W)%*%as.matrix(MSAE_Eblup)) MSAE_DB <- as.data.frame(MSAE_Eblup + alfa) colnames(MSAE_DB) <- varnames_Y Aggregation_Direct <- colSums(as.matrix(y.vec)*(W)) Aggregation_DB <- colSums(as.matrix(MSAE_DB)*(W)) Aggregation_EBLUP <- colSums(as.matrix(MSAE_Eblup)*(W)) Aggregation <- matrix(unlist(rbind(Aggregation_Direct,Aggregation_DB,Aggregation_EBLUP)),3,r) rownames(Aggregation) <- c("Aggregation_Direct","Aggregation_DB","Aggregation_EBLUP") colnames(Aggregation) <- varnames_Y y.direct <- y.vec colnames(y.direct) = varnames_Y W_direct = as.matrix(w.matrix) W_all = as.matrix(data[,weight]) alfa_all <- ginv(t(W_all))%*%(t(W_direct)%*%y.direct-t(W_all)%*%as.matrix(MSAE_Eblup_all)) MSAE_DB_all <- as.data.frame(MSAE_Eblup_all + alfa_all) colnames(MSAE_DB_all) <- varnames_Y Aggregation_Direct <- colSums(as.matrix(y.direct)*(W_direct)) Aggregation_DB <- colSums(as.matrix(MSAE_DB_all)*(W_all)) Aggregation_EBLUP <- colSums(as.matrix(MSAE_Eblup_all)*(W_all)) Aggregation_all <- matrix(unlist(rbind(Aggregation_Direct,Aggregation_DB,Aggregation_EBLUP)),3,r) rownames(Aggregation_all) <- c("Aggregation_Direct","Aggregation_DB","Aggregation_EBLUP") colnames(Aggregation_all) <- varnames_Y v <- matrix(diag(RIn),n,r) colnames(v) <- varnames_Y SampledV <- cbind(v,data_sampled[,cluster],an = data_sampled$index,nonsample=data_sampled$nonsample) avVardir <- matrix(0,max(data[,cluster]),r) for (i in 1:r){ for (j in 1:max(data[,cluster])){ if (!(j %in% SampledV[,i+r])){ newline <- rep(NA,dim(SampledV)[2]) newline[1:r] <-0 newline[i+r] <- j SampledV <- rbind(SampledV,newline) } } } for (i in 1:r){ avVardir[,i] <- sapply(split(SampledV[,i], SampledV[,r+i]), mean) } colnames(avVardir) <- varnames_Y avVardir <- cbind(cluster = c(1:max(data[,cluster])), avVardir) vardirns <- cbind(dfnonsample[, vardir][,1:r],dfnonsample[,cluster],an =dfnonsample$index) vardir.ns <- matrix(0,length(anns),r) for (i in 1:length(anns)){ for (j in 1:r){ vardir.ns[i,j] <- avVardir[vardirns[i,j+r],j+1] } } RInns <- diag(as.vector(vardir.ns)) GInns <- kronecker(diag(Varu),diag(length(anns))) Bins <- RInns%*%solve(GInns+RInns) g1dns <- Bins%*%GInns g1dns <- matrix(diag(g1dns),length(anns),r) SIGMAns <- GInns + RInns SIGMA_invns <- solve(SIGMAns) Xt_Sins <- t(SIGMA_invns %*% x.matrixns) Qns <- ginv(Xt_Sins%*%x.matrixns) xqxns <- (x.matrixns)%*%Qns%*%t(x.matrixns) g2dns <- (Bins%*%xqxns%*%t(Bins)) g2dns <- matrix(diag(g2dns),length(anns),r) g3eblup <- matrix(g3d,n,r) colnames(g3eblup) <- varnames_Y Sampledg3d <- cbind(g3eblup,data_sampled[,cluster],an = data_sampled$index ,nonsample=data_sampled$nonsample) avg3d <- matrix(0,max(data[,cluster]),r) for (i in 1:r){ for (j in 1:max(data[,cluster])){ if (!(j %in% Sampledg3d[,i+r])){ newline <- rep(NA,dim(Sampledg3d)[2]) newline[1:r] <-0 newline[i+r] <- j Sampledg3d <- rbind(Sampledg3d,newline) } } } for (i in 1:r){ avg3d[,i] <- sapply(split(Sampledg3d[,i], Sampledg3d[,r+i]), mean) } colnames(avg3d) <- varnames_Y avg3d <- cbind(cluster = c(1:max(data[,cluster])), avg3d) g3dns <- matrix(0,length(anns),r) for (i in 1:length(anns)){ for (j in 1:r){ g3dns[i,j] <-avg3d[vardirns[i,j+r],j+1] } } MSE_Eblupns = g1dns+g2dns+2*g3dns MSE_Eblupns <- data.frame(an=anns,MSE_Eblupns) MSE_Eblup_temp <- cbind(index=data_sampled$index,MSE_Eblup) MSE_Eblup_all <- merge(x=as.matrix(idx), y=MSE_Eblup_temp, by = "index", all.x=TRUE) MSE_Eblup_all <- MSE_Eblup_all[,-1] for (i in 1:totalArea){ for (j in 1:length(anns)){ if (i==anns[j]){ MSE_Eblup_all[i,] <- MSE_Eblupns[which(MSE_Eblupns$an == i), ][,-1] } } } g4dns <- colMeans(matrix(g4d,n,r)) g4dns <- matrix(NA,totalArea,r) for (i in 1:totalArea){ g4dns[i,] <- colMeans(matrix(g4d,n,r)) } MSE_DB_all <-MSE_Eblup_all+g4dns randomEffectns <- matrix(0,length(anns),r) randomEffectns <- cbind(randomEffectns,dfnonsample[,cluster],an =dfnonsample$index) for (i in 1:length(anns)){ for (j in 1:r){ randomEffectns[i,j] <- randomEffectns[i,j]+avrEffc[XBns[i,j+r],j+1] } } randomEffectns <- randomEffectns[,1:r] randomEffectns <- data.frame(an=anns,randomEffectns) randomEffect_temp <- cbind(index=data_sampled$index,randomEffect) randomEffect_all <- merge(x=as.matrix(idx), y=randomEffect_temp, by = "index", all.x=TRUE) randomEffect_all <- randomEffect_all[,-1] for (i in 1:totalArea){ for (j in 1:length(anns)){ if (i==anns[j]){ randomEffect_all[i,] <- randomEffectns[which(randomEffectns$an == i), ][,-1] } } } result$MSAE_Eblup_sampled = MSAE_Eblup result$MSAE_Eblup_all = MSAE_Eblup_all result$MSE_Eblup_sampled = MSE_Eblup result$MSE_Eblup_all = MSE_Eblup_all result$randomEffect_sampled = signif(randomEffect, digits = 5) result$randomEffect_all = signif(randomEffect_all, digits = 5) result$Rmatrix_sampled = signif(RIn, digits = 5) result$fit$method = "REML" result$fit$convergence = convergence result$fit$iterations = k result$fit$estcoef = signif(coef, digits = 5) result$fit$refvar = signif(data.frame(t(Varu)), digits = 5) result$fit$informationFisher = signif(F, digits = 5) result$difference_benchmarking$Estimation_sampled = MSAE_DB result$difference_benchmarking$Estimation_all = MSAE_DB_all result$difference_benchmarking$Aggregation_sampled = Aggregation result$difference_benchmarking$Aggregation_all = Aggregation_all result$difference_benchmarking$MSE_DB_sampled = MSE_DB result$difference_benchmarking$MSE_DB_all = MSE_DB_all result$difference_benchmarking$g4.a = g4.a result$difference_benchmarking$g4.b = g4.b return(result) }
normalize_height = function(las, algorithm, na.rm = FALSE, use_class = c(2L,9L), ..., add_lasattribute = FALSE, Wdegenerated = TRUE) { UseMethod("normalize_height", las) } normalize_height.LAS = function(las, algorithm, na.rm = FALSE, use_class = c(2L,9L), ..., add_lasattribute = FALSE, Wdegenerated = TRUE) { assert_is_a_bool(na.rm) assert_is_a_bool(add_lasattribute) assert_is_a_bool(Wdegenerated) if (is(algorithm, "RasterLayer")) { Zground <- raster::extract(algorithm, coordinates(las), ...) isna <- is.na(Zground) nnas <- sum(isna) if (nnas > 0 && na.rm == FALSE) stop(glue::glue("{nnas} points were not normalizable because the DTM contained NA values. Process aborted.")) } else if (is.function(algorithm)) { assert_is_algorithm(algorithm) assert_is_algorithm_spi(algorithm) if (any(as.integer(use_class) != use_class)) stop("'add_class' is not a vector of integers'", call. = FALSE) use_class <- as.integer(use_class) if (!"Classification" %in% names(las@data)) stop("No field 'Classification' found. This attribute is required to interpolate ground points.", call. = FALSE) . <- Z <- Zref <- X <- Y <- Classification <- NULL ground <- las@data[Classification %in% c(use_class), .(X,Y,Z)] if (nrow(ground) == 0) stop("No ground points found. Impossible to compute a DTM.", call. = FALSE) ground <- check_degenerated_points(ground, Wdegenerated) lidR.context <- "normalize_height" ground <- LAS(ground, las@header, proj4string = las@proj4string, check = FALSE, index = las@index) Zground <- algorithm(ground, las@data) isna <- is.na(Zground) nnas <- sum(isna) if (nnas > 0 & na.rm == FALSE) stop(glue::glue("{nnas} points were not normalizable. Process aborted."), call. = FALSE) } else { stop(glue::glue("Parameter 'algorithm' is a {class(algorithm)}. Expected type is 'RasterLayer' or 'function'"), call. = FALSE) } zoffset <- las@header@PHB[["Z offset"]] zscale <- las@header@PHB[["Z scale factor"]] if (!"Zref" %in% names(las@data)) las@data[["Zref"]] <- las@data[["Z"]] las@data[["Z"]] <- las@data[["Z"]] - Zground if (add_lasattribute && is.null(las@header@VLR$Extra_Bytes[["Extra Bytes Description"]][["Zref"]])) las <- add_lasattribute_manual(las, name = "Zref", desc = "Elevation above sea level", type = "int", offset = zoffset, scale = zscale) if (nnas > 0 && na.rm == TRUE) { las <- filter_poi(las, !isna) message(glue::glue("{nnas} points were not normalizable and removed.")) } fast_quantization(las@data[["Z"]], zscale, zoffset) las <- lasupdateheader(las) las@index$sensor <- las@index$sensor + NLAS return(las) } normalize_height.LAScluster = function(las, algorithm, na.rm = FALSE, use_class = c(2L,9L), ..., add_lasattribute = FALSE, Wdegenerated = TRUE) { buffer <- NULL x <- readLAS(las) if (is.empty(x)) return(NULL) x <- normalize_height(x, algorithm, na.rm, use_class, ..., add_lasattribute = add_lasattribute, Wdegenerated = Wdegenerated) x <- filter_poi(x, buffer == 0) return(x) } normalize_height.LAScatalog = function(las, algorithm, na.rm = FALSE, use_class = c(2L,9L), ..., add_lasattribute = FALSE, Wdegenerated = TRUE) { opt_select(las) <- "*" options <- list(need_buffer = TRUE, drop_null = TRUE, need_output_file = TRUE, automerge = TRUE) output <- catalog_apply(las, normalize_height, algorithm = algorithm, na.rm = na.rm, use_class = use_class, ..., add_lasattribute = add_lasattribute, Wdegenerated = Wdegenerated, .options = options) return(output) } unnormalize_height = function(las) { stopifnotlas(las) if ("Zref" %in% names(las@data)) { las@data[["Z"]] <- las@data[["Zref"]] las@data[["Zref"]] <- NULL las <- lasupdateheader(las) } else message("No attribute 'Zref' found. Un-normalizisation is impossible.") if (las@index$sensor > NLAS) las@index$sensor <- las@index$sensor - NLAS return(las) } setMethod("-", c("LAS", "RasterLayer"), function(e1, e2) { return(normalize_height(e1,e2)) }) setOldClass("lidRAlgorithm") setMethod("-", c("LAS", "lidRAlgorithm"), function(e1, e2) { return(normalize_height(e1,e2)) }) check_degenerated_points = function(points, Wdegenerated = TRUE) { . <- X <- Y <- Z <- NULL dup_xyz = duplicated(points, by = c("X", "Y", "Z")) dup_xy = duplicated(points, by = c("X", "Y")) ndup_xyz = sum(dup_xyz) ndup_xy = sum(dup_xy & !dup_xyz) if (ndup_xyz > 0 && Wdegenerated) warning(glue::glue("There were {ndup_xyz} degenerated ground points. Some X Y Z coordinates were repeated. They were removed."), call. = FALSE) if (ndup_xy > 0 && Wdegenerated) warning(glue::glue("There were {ndup_xy} degenerated ground points. Some X Y coordinates were repeated but with different Z coordinates. min Z were retained."), call. = FALSE) if (ndup_xy > 0 | ndup_xyz > 0) points = points[, .(Z = min(Z)), by = .(X,Y)] return(points) }
getOptimalFeatureSet <- function(filt.data, ordered.genes, elbow.pt = 25, k = 10, num.pcs = 20, error = 0) { mean_knn_vec <- c() minNumGenes = "" numStepsUnchangedMin = 0 message("Determining optimal feature set...") pb <- utils::txtProgressBar(min = elbow.pt, max = length(ordered.genes), style = 3) for(num_genes in seq(from = elbow.pt, to = length(ordered.genes), by = 25)) { neighbour_feature_genes <- ordered.genes[1:num_genes] log.feature.data <- filt.data[neighbour_feature_genes, ] suppressWarnings({ temp.seurat <- Seurat::CreateSeuratObject(counts = log.feature.data) Seurat::VariableFeatures(temp.seurat) <- neighbour_feature_genes temp.seurat <- Seurat::ScaleData(object = temp.seurat, features = neighbour_feature_genes, verbose = FALSE) temp.seurat <- Seurat::RunPCA(object = temp.seurat, features = neighbour_feature_genes, verbose = FALSE)}) pca.data <- as.matrix(temp.seurat@[email protected][, 1:min(num.pcs, ncol(temp.seurat@[email protected]))]) rownames(pca.data) <- colnames(log.feature.data) system.time( my.knn <- RANN::nn2( data = pca.data, k = (k + 1), treetype = "kd", searchtype = "standard", eps = error ) ) nn.dists <- my.knn$nn.dists rownames(nn.dists) <- rownames(pca.data) nn.dists <- nn.dists[,-1] sdVec <- stats::na.omit(temp.seurat@reductions$pca@stdev[1:num.pcs]) length_scale <- sqrt(sum(sdVec ^ 2)) mean_nn_dist <- mean(x = nn.dists) scaled_mean_nn_dist <- mean_nn_dist / length_scale names(scaled_mean_nn_dist) <- num_genes mean_knn_vec <- append(mean_knn_vec, scaled_mean_nn_dist) if (which.min(mean_knn_vec) != minNumGenes) { minNumGenes = which.min(mean_knn_vec) numStepsUnchangedMin = 0 } else { numStepsUnchangedMin = numStepsUnchangedMin + 1 } utils::setTxtProgressBar(pb = pb, value = num_genes) } optimal_feature_genes <- ordered.genes[1:as.numeric(names(minNumGenes))] message(" ") message("Done.") return(list("optimal.feature.genes" = optimal_feature_genes, "density.index" = mean_knn_vec)) }
fweibullgpd <- function(x, phiu = TRUE, useq = NULL, fixedu = FALSE, pvector = NULL, std.err = TRUE, method = "BFGS", control = list(maxit = 10000), finitelik = TRUE, ...) { call <- match.call() np = 5 check.quant(x, allowna = TRUE, allowinf = TRUE) check.logic(phiu) check.posparam(useq, allowvec = TRUE, allownull = TRUE) check.logic(fixedu) check.logic(std.err) check.optim(method) check.control(control) check.logic(finitelik) if (any(!is.finite(x))) { warning("non-finite cases have been removed") x = x[is.finite(x)] } if (any(x <= 0)) { warning("non-positive values have been removed") x = x[x > 0] } check.quant(x) n = length(x) if ((method == "L-BFGS-B") | (method == "BFGS")) finitelik = TRUE if (fixedu & is.null(useq)) stop("for fixed threshold approach, useq must be specified (as scalar or vector)") if (is.null(useq)) { check.nparam(pvector, nparam = np, allownull = TRUE) if (is.null(pvector)) { initfweibull = fitdistr(x, "weibull", lower = c(1e-8, 1e-8)) pvector[1] = initfweibull$estimate[1] pvector[2] = initfweibull$estimate[2] pvector[3] = as.vector(quantile(x, 0.9)) initfgpd = fgpd(x, pvector[3], std.err = FALSE) pvector[4] = initfgpd$sigmau pvector[5] = initfgpd$xi } } else { check.nparam(pvector, nparam = np - 1, allownull = TRUE) if (length(useq) != 1) { useq = useq[sapply(useq, FUN = function(u, x) sum(x > u) > 5, x = x)] check.posparam(useq, allowvec = TRUE) nllhu = sapply(useq, profluweibullgpd, pvector = pvector, x = x, phiu = phiu, method = method, control = control, finitelik = finitelik, ...) if (all(!is.finite(nllhu))) stop("thresholds are all invalid") u = useq[which.min(nllhu)] } else { u = useq } if (fixedu) { if (is.null(pvector)) { initfweibull = fitdistr(x, "weibull", lower = c(1e-8, 1e-8)) pvector[1] = initfweibull$estimate[1] pvector[2] = initfweibull$estimate[2] initfgpd = fgpd(x, u, std.err = FALSE) pvector[3] = initfgpd$sigmau pvector[4] = initfgpd$xi } } else { if (is.null(pvector)) { initfweibull = fitdistr(x, "weibull", lower = c(1e-8, 1e-8)) pvector[1] = initfweibull$estimate[1] pvector[2] = initfweibull$estimate[2] pvector[3] = u initfgpd = fgpd(x, pvector[3], std.err = FALSE) pvector[4] = initfgpd$sigmau pvector[5] = initfgpd$xi } else { pvector[5] = pvector[4] pvector[4] = pvector[3] pvector[3] = u } } } if (fixedu) { nllh = nluweibullgpd(pvector, u, x, phiu) if (is.infinite(nllh)) { pvector[4] = 0.1 nllh = nluweibullgpd(pvector, u, x, phiu) } if (is.infinite(nllh)) stop("initial parameter values are invalid") fit = optim(par = as.vector(pvector), fn = nluweibullgpd, u = u, x = x, phiu = phiu, finitelik = finitelik, method = method, control = control, hessian = TRUE, ...) wshape = fit$par[1] wscale = fit$par[2] sigmau = fit$par[3] xi = fit$par[4] } else { nllh = nlweibullgpd(pvector, x, phiu) if (is.infinite(nllh)) { pvector[5] = 0.1 nllh = nlweibullgpd(pvector, x, phiu) } if (is.infinite(nllh)) stop("initial parameter values are invalid") fit = optim(par = as.vector(pvector), fn = nlweibullgpd, x = x, phiu = phiu, finitelik = finitelik, method = method, control = control, hessian = TRUE, ...) wshape = fit$par[1] wscale = fit$par[2] u = fit$par[3] sigmau = fit$par[4] xi = fit$par[5] } conv = TRUE if ((fit$convergence != 0) | any(fit$par == pvector) | (abs(fit$value) >= 1e6)) { conv = FALSE warning("check convergence") } pu = pweibull(u, wshape, wscale) if (phiu) { phiu = 1 - pu se.phiu = NA } else { phiu = mean(x > u, na.rm = TRUE) se.phiu = sqrt(phiu * (1 - phiu) / n) } if (std.err) { qrhess = qr(fit$hessian) if (qrhess$rank != ncol(qrhess$qr)) { warning("observed information matrix is singular") se = NULL invhess = NULL } else { invhess = solve(qrhess) vars = diag(invhess) if (any(vars <= 0)) { warning("observed information matrix is singular") invhess = NULL se = NULL } else { se = sqrt(vars) } } } else { invhess = NULL se = NULL } if (!exists("nllhu")) nllhu = NULL list(call = call, x = as.vector(x), init = as.vector(pvector), fixedu = fixedu, useq = useq, nllhuseq = nllhu, optim = fit, conv = conv, cov = invhess, mle = fit$par, se = se, rate = phiu, nllh = fit$value, n = n, wshape = wshape, wscale = wscale, u = u, sigmau = sigmau, xi = xi, phiu = phiu, se.phiu = se.phiu) } lweibullgpd <- function(x, wshape = 1, wscale = 1, u = qweibull(0.9, wshape, wscale), sigmau = sqrt(wscale^2 * gamma(1 + 2/wshape) - (wscale * gamma(1 + 1/wshape))^2), xi = 0, phiu = TRUE, log = TRUE) { check.quant(x, allowna = TRUE, allowinf = TRUE) check.param(wshape) check.param(wscale) check.param(u) check.param(sigmau) check.param(xi) check.phiu(phiu, allowfalse = TRUE) check.logic(log) if (any(!is.finite(x))) { warning("non-finite cases have been removed") x = x[is.finite(x)] } if (any(x <= 0)) { warning("non-positive values have been removed") x = x[x > 0] } check.quant(x) n = length(x) check.inputn(c(length(wshape), length(wscale), length(u), length(sigmau), length(xi), length(phiu)), allowscalar = TRUE) xu = x[which(x > u)] nu = length(xu) xb = x[which(x <= u)] nb = length(xb) if (n != nb + nu) { stop("total non-finite sample size is not equal to those above threshold and those below or equal to it") } if ((wscale <= 0) | (wshape <= 0) | (sigmau <= 0) | (u <= 0) | (u <= min(x)) | (u >= max(x))) { l = -Inf } else { pu = pweibull(u, wshape, wscale) if (is.logical(phiu)) { if (phiu) { phiu = 1 - pu } else { phiu = nu / n } } phib = (1 - phiu) / pu syu = 1 + xi * (xu - u) / sigmau if ((min(syu) <= 0) | (phiu <= 0) | (phiu >= 1) | (pu < .Machine$double.eps) | (pu <= 0) | (pu >= 1)) { l = -Inf } else { l = lgpd(xu, u, sigmau, xi, phiu) l = l + (wshape - 1) * sum(log(xb)) - sum(xb^wshape) / wscale^wshape + nb * log(wshape) - nb * wshape * log(wscale) + nb * log(phib) } } if (!log) l = exp(l) l } nlweibullgpd <- function(pvector, x, phiu = TRUE, finitelik = FALSE) { np = 5 check.nparam(pvector, nparam = np) check.quant(x, allowna = TRUE, allowinf = TRUE) check.phiu(phiu, allowfalse = TRUE) check.logic(finitelik) wshape = pvector[1] wscale = pvector[2] u = pvector[3] sigmau = pvector[4] xi = pvector[5] nllh = -lweibullgpd(x, wshape, wscale, u, sigmau, xi, phiu) if (finitelik & is.infinite(nllh)) { nllh = sign(nllh) * 1e6 } nllh } profluweibullgpd <- function(u, pvector, x, phiu = TRUE, method = "BFGS", control = list(maxit = 10000), finitelik = TRUE, ...) { np = 5 check.nparam(pvector, nparam = np - 1, allownull = TRUE) check.posparam(u) check.quant(x, allowna = TRUE, allowinf = TRUE) check.phiu(phiu, allowfalse = TRUE) check.optim(method) check.control(control) check.logic(finitelik) if (any(!is.finite(x))) { warning("non-finite cases have been removed") x = x[is.finite(x)] } if (any(x <= 0)) { warning("non-positive values have been removed") x = x[x > 0] } check.quant(x) if (!is.null(pvector)) { nllh = nluweibullgpd(pvector, u, x, phiu) if (is.infinite(nllh)) pvector = NULL } if (is.null(pvector)) { initfweibull = fitdistr(x, "weibull", lower = c(1e-8, 1e-8)) pvector[1] = initfweibull$estimate[1] pvector[2] = initfweibull$estimate[2] initfgpd = fgpd(x, u, std.err = FALSE) pvector[3] = initfgpd$sigmau pvector[4] = initfgpd$xi nllh = nluweibullgpd(pvector, u, x, phiu) } if (is.infinite(nllh)) { pvector[4] = 0.1 nllh = nluweibullgpd(pvector, u, x, phiu) } if (is.infinite(nllh)) { warning(paste("initial parameter values for threshold u =", u, "are invalid")) fit = list(par = rep(NA, np), value = Inf, counts = 0, convergence = NA, message = "initial values invalid", hessian = rep(NA, np)) } else { fit = optim(par = as.vector(pvector), fn = nluweibullgpd, u = u, x = x, phiu = phiu, finitelik = finitelik, method = method, control = control, hessian = TRUE, ...) } if (finitelik & is.infinite(fit$value)) { fit$value = sign(fit$value) * 1e6 } fit$value } nluweibullgpd <- function(pvector, u, x, phiu = TRUE, finitelik = FALSE) { np = 5 check.nparam(pvector, nparam = np - 1) check.posparam(u) check.quant(x, allowna = TRUE, allowinf = TRUE) check.phiu(phiu, allowfalse = TRUE) check.logic(finitelik) wshape = pvector[1] wscale = pvector[2] sigmau = pvector[3] xi = pvector[4] nllh = -lweibullgpd(x, wshape, wscale, u, sigmau, xi, phiu) if (finitelik & is.infinite(nllh)) { nllh = sign(nllh) * 1e6 } nllh }
randomReturns <- function(na, ns, sd, mean = 0, rho = 0) { ans <- rnorm(ns*na) dim(ans) <- c(na, ns) if (!identical(rho, 0)) { if (length(rho == 1L)) { C <- array(rho, dim = c(na, na)) diag(C) <- 1 } else C <- rho ans <- t(chol(C)) %*% ans } ans <- ans*sd ans <- ans + mean t(ans) }
Lg.pond<-function(liste.mat,ponde){ Lg.pond<-Lg(liste.mat) Lg.pond<-sweep(Lg.pond,1,STATS=ponde,FUN="*") Lg.pond<-sweep(Lg.pond,2,STATS=ponde,FUN="*") return(Lg.pond) }
knitr::opts_chunk$set(message=FALSE, error=FALSE, warning=FALSE, comment=NA) savefigs <- FALSE library("rprojroot") root<-has_file(".ROS-Examples-root")$make_fix_file() library("rstanarm") library("ggplot2") theme_set(bayesplot::theme_default(base_family = "sans")) mile <- read.csv(root("Mile/data","mile.csv"), header=TRUE) head(mile) fit <- stan_glm(seconds ~ year, data = mile, refresh = 0) print(fit, digits=2) print(1007 -.393*c(1900,2000)) print(coef(fit)[1] + coef(fit)[2]*c(1900,2000), digits=4) if (savefigs) pdf(root("Mile/figs","aplusbx1a.pdf"), height=3.5, width=5) a <- 0.15 b <- 0.4 par(mar=c(3,3,1,1), mgp=c(2,.5,0), tck=-.01) plot(c(0,2.2), c(0,a+2.2*b), pch=20, cex=.5, main="y = a + bx (with b > 0)", bty="l", type="n", xlab="x", ylab="y", xaxt="n", yaxt="n", xaxs="i", yaxs="i") axis(1, c(0,1,2)) axis(2, c(a,a+b,a+2*b), c("a","a+b","a+2b")) abline(a, b) if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","aplusbx1b.pdf"), height=3.5, width=5) a <- 0.95 b <- -0.4 par(mar=c(3,3,1,1), mgp=c(2,.5,0), tck=-.01) plot(c(0,2.2), c(0,a+.2), pch=20, cex=.5, main="y = a + bx (with b < 0)", bty="l", type="n", xlab="x", ylab="y", xaxt="n", yaxt="n", xaxs="i", yaxs="i") axis(1, c(0,1,2)) axis(2, c(a,a+b,a+2*b), c("a","a+b","a+2b")) abline(a, b) if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","aplusbx2a.pdf"), height=3.5, width=5) par(mar=c(3,3,1,1), mgp=c(2,.5,0), tck=-.01) curve(1007 - 0.393*x, from=0, to=2.1, xlab="x", ylab="y", bty="l", xaxs="i", main="y = 1007 - 0.393x") if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","aplusbx2b.pdf"), height=3.5, width=5) par(mar=c(3,3,1,1), mgp=c(2,.5,0), tck=-.01) curve(1007 - 0.393*x, from=0, to=100, xlab="x", ylab="y", bty="l", xaxs="i", main="y = 1007 - 0.393x") if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","aplusbx3.pdf"), height=3.5, width=5) par(mar=c(3,3,1,1), mgp=c(2,.5,0), tck=-.01) curve(1007 - 0.393*x, from=1900, to=2000, xlab="Year", ylab="Time (seconds)", bty="l", xaxs="i", main="Approx. trend of record times in the mile run", ylim=c(215, 265)) text(1960, 246, "y = 1007 - 0.393x") if (savefigs) dev.off() ggplot(aes(x=year, y=seconds), data=mile) + geom_point(shape=1, size=2) + geom_abline(intercept=fit$coefficients[1], slope=fit$coefficients[2]) + labs(x="Year", y="Time (seconds)", title = "Approx. trend of record times in the mile run") if (savefigs) pdf(root("Mile/figs","mile1a.pdf"), height=3.5, width=5) plot(mile$year, mile$seconds, main="World record times in the mile run") if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","mile1b.pdf"), height=3.5, width=5) par(mar=c(3,3,3,1), mgp=c(2,.5,0), tck=-.01) plot(mile$year, mile$seconds, bty="l", main="World record times in the mile run", xlab="Year", ylab="Seconds") if (savefigs) dev.off() if (savefigs) pdf(root("Mile/figs","mile2.pdf"), height=3.5, width=5) par(mar=c(3,3,3,1), mgp=c(2,.5,0), tck=-.01) plot(mile$year, mile$seconds, bty="l", main="World record times in the mile run", xlab="Year", ylab="Seconds") curve(coef(fit)[1] + coef(fit)[2]*x, add=TRUE) if (savefigs) dev.off()
test_that("expect error when n = 0 or n < 0", { expect_error(rm_latest_packages(n = 0)) expect_error(rm_latest_packages(n = -1)) expect_error(rm_latest_packages(n = -1)) expect_error(rm_latest_packages(n = -100)) }) test_that("expect error when n not numeric or not length 1", { expect_error(rm_latest_packages(n = "hello world")) expect_error(rm_latest_packages(n = c(32, 2323))) expect_error(rm_latest_packages(n = mtcars)) })
options(digits=12) if(!require("optimx"))stop("this test requires package optimx.") if(!require("setRNG"))stop("this test requires setRNG.") test.rng <- list(kind="Wichmann-Hill", normal.kind="Box-Muller", seed=c(979,1479,1542)) old.seed <- setRNG(test.rng) cat("optimx test chen-x.f ...\n") chen.f <- function(x) { v <- log(x) + exp(x) f <- (v - sqrt(v^2 + 5e-04))/2 sum (f * f) } p0 <- rexp(50) system.time(ans.optx <- optimx(par=p0, fn=chen.f, lower=0, control=list(all.methods=TRUE,save.failures=TRUE,maxit=2500)))[1] print(ans.optx)
test_that("gm_mean returns a numeric", { expect_identical(gm_mean(numeric(0)), NaN) expect_identical(gm_mean(1), 1) expect_identical(gm_mean(-1), NaN) expect_identical(gm_mean(c(1, -1)), NaN) expect_identical(gm_mean(NA_real_), NA_real_) expect_identical(gm_mean(NA_real_, na.rm = TRUE), NaN) expect_identical(gm_mean(c(1, NA)), NA_real_) expect_identical(gm_mean(c(1, NA), na.rm = TRUE), 1) expect_identical(gm_mean(0), 0) expect_identical(gm_mean(0, zero.propagate = FALSE), NaN) expect_identical(gm_mean(c(1, 0)), 0) expect_identical(gm_mean(c(NA_real_, 0)), 0) expect_identical(gm_mean(c(NA_real_, 0), zero.propagate = FALSE), NA_real_) expect_identical(gm_mean(c(NA_real_, 0), na.rm = TRUE), 0) expect_identical(gm_mean(c(NA_real_, 0), na.rm = TRUE, zero.propagate = FALSE), NaN) expect_identical(gm_mean(c(1, 0), zero.propagate = FALSE), 1) expect_identical(gm_mean(1L), 1) expect_error(gm_mean("1")) expect_identical(round(gm_mean(c(13, 5, 70, 80))), 25) })
draw.selic = function(){ selic = BETSget(4189) target = BETSget(432) start = c(2006,1) if(!is.null(start)){ selic = window(selic, start = start) } else{ start = start(selic) } inx = grep("-15$",target[,1]) first = target[1,1] target = ts(target[inx,2], start = as.numeric(c(format(first,"%Y"),format(first,"%m"))), frequency = 12) target = window(target, start = start, frequency = 12) lims = chart.add_basic(ts = selic, title = "Base Interest Rate (SELIC)", subtitle = "Accumulated in the Month, in Annual Terms", col = "darkolivegreen", arr.pos = "h", leg.pos = "none") chart.add_extra(target, ylim = lims[3:4], xlim = lims[1:2], arr.pos = "none", leg.pos = "none", col = "darkgray") legend("bottomleft", c("SELIC", "Target"), lty=c(1,2), lwd=c(2.5,2.5),col=c("darkolivegreen", "darkgray"), bty = "n", cex = 0.9) chart.add_notes(selic, ylim = lims[3:4], xlim = lims[1:2]) }
globalVariables(c('PROVINCE', 'SHARE', 'PNS', 'NATIONAL_SHARE', 'PNS_WEIGHTED')) psns <- function(tidy_votes, method = 'Jones-Mainwaring') { if (!ncol(tidy_votes) == 3) { stop('Data frame must have exactly 3 columns') } if (!identical(names(tidy_votes), c('PROVINCE', 'PARTY', 'VOTES'))) { stop('Data frame names must be PROVINCE, PARTY and VOTES') } if (!method %in% c('Jones-Mainwaring', 'Golosov')) { stop('Not a valid method') } tidy_votes %>% group_by(PROVINCE) %>% mutate(SHARE = VOTES/sum(VOTES)) %>% group_by(PARTY) %>% summarize(PNS = pns(SHARE, method), VOTES = sum(VOTES)) %>% mutate(NATIONAL_SHARE = VOTES/sum(VOTES), PNS_WEIGHTED = PNS*NATIONAL_SHARE) %>% ungroup() %>% summarise(pns = sum(PNS_WEIGHTED)) %>% pull() }
ddistr <- function(x, meanvalue, distr=c("poisson", "nbinom"), distrcoefs, ...){ distr <- match.arg(distr) result <- switch(distr, "poisson"=dpois(x, lambda=meanvalue, ...), "nbinom"=dnbinom(x, mu=meanvalue, size=distrcoefs[[1]], ...) ) return(result) } pdistr <- function(q, meanvalue, distr=c("poisson", "nbinom"), distrcoefs, ...){ distr <- match.arg(distr) result <- switch(distr, "poisson"=ppois(q, lambda=meanvalue, ...), "nbinom"=pnbinom(q, mu=meanvalue, size=distrcoefs[[1]], ...) ) return(result) } qdistr <- function(p, meanvalue, distr=c("poisson", "nbinom"), distrcoefs, ...){ distr <- match.arg(distr) result <- switch(distr, "poisson"=qpois(p, lambda=meanvalue, ...), "nbinom"=qnbinom(p, mu=meanvalue, size=distrcoefs[[1]], ...) ) return(result) } rdistr <- function(n, meanvalue, distr=c("poisson", "nbinom"), distrcoefs){ distr <- match.arg(distr) result <- switch(distr, "poisson"=rpois(n, lambda=meanvalue), "nbinom"=rnbinom(n, mu=meanvalue, size=distrcoefs[[1]]) ) return(result) } sddistr <- function(meanvalue, distr=c("poisson", "nbinom"), distrcoefs){ distr <- match.arg(distr) result <- switch(distr, "poisson"=sqrt(meanvalue), "nbinom"=sqrt(meanvalue + meanvalue^2/distrcoefs[[1]]) ) return(result) } ardistr <- function(response, meanvalue, distr=c("poisson", "nbinom"), distrcoefs){ result <- switch(distr, "poisson"=3/2*(response^(2/3)-meanvalue^(2/3))/meanvalue^(1/6), "nbinom"=(3/distrcoefs[["size"]]*((1+response*distrcoefs[[1]])^(2/3) - (1+meanvalue*distrcoefs[[1]])^(2/3)) + 3*(response^(2/3)-meanvalue^(2/3))) / (2*(meanvalue+meanvalue^2*distrcoefs[[1]])^(1/6)) ) return(result) } checkdistr <- function(distr=c("poisson", "nbinom"), distrcoefs){ distr <- match.arg(distr) if(distr=="nbinom"){ if(missing(distrcoefs) || length(distrcoefs)!=1) stop("For the negative binomial parameter (only) the dispersion parameter 'size' has to be provided in argument 'distrcoefs'") if(distrcoefs[[1]]<=0) stop("The additional dispersion parameter for the negative binomial distribution has to be greater than zero") } }
context("Exponential functions") test_that("Raw moments for the exponential distribution work correctly", { expect_equal(pexp(2, rate = 1), mexp(truncation = 2)) x <- rexp(1e5, rate = 1) expect_equal(mean(x), mexp(r = 1, lower.tail = FALSE), tolerance = 1e-1) expect_equal(sum(x[x > quantile(x, 0.1)]) / length(x), mexp(r = 1, truncation = quantile(x, 0.1), lower.tail = FALSE), tolerance = 1e-1) })
expected <- eval(parse(text="\"\\\" \\\\t\\\\n\\\\\\\"\\\\\\\\'`><=%;,|&{()}\\\"\"")); test(id=0, code={ argv <- eval(parse(text="list(\" \\t\\n\\\"\\\\'`><=%;,|&{()}\", 0L, \"\\\"\", 0L, FALSE)")); .Internal(encodeString(argv[[1]], argv[[2]], argv[[3]], argv[[4]], argv[[5]])); }, o=expected);
context("Read HMR files") test_that("test that can read HMR file", { expect_true(file.exists(system.file("extdata", "nanosims_data", "hmr", package = "lans2r"))) expect_true(is(hmr <- load_HMR(system.file("extdata", "nanosims_data", "hmr", package = "lans2r"), prefix = "", suffix = ".hmr_txt"), "data.frame")) expect_equal({ summary <- hmr %>% select(-step, -voltage, -cts) %>% distinct() summary$ion }, c("1H", "2H")) expect_equal(summary$trolley, c(" expect_equal(summary$B, c("998.7", "998.7")) expect_equal(summary$R, c("130.53", "184.90")) expect_equal(summary$M, c("1.025", "2.056")) })
setClass("CoImp", representation(Missing.data.matrix = "matrix" ,Perc.miss = "matrix" ,Estimated.Model = "list" ,Estimation.Method = "character" ,Index.matrix.NA = "matrix" ,Smooth.param = "vector" ,Imputed.data.matrix = "matrix" ,Estimated.Model.Imp = "list" ,Estimation.Method.Imp = "character" ), prototype = list(Missing.data.matrix = matrix(0,0,0) ,Perc.miss = matrix(0,0,0) ,Estimated.Model = list() ,Estimation.Method = character() ,Index.matrix.NA = matrix(0,0,0) ,Smooth.param = vector() ,Imputed.data.matrix = matrix(0,0,0) ,Estimated.Model.Imp = list() ,Estimation.Method.Imp = character() ) ) setMethod( f="plot", signature(x = "CoImp",y = "missing"), definition=function(x, y, plot.legend = TRUE, args.legend = list(y = 110, cex = 0.8), plot.name = NULL, ...){ par(mfrow=c(1,1)); bar.plot(tab = [email protected], legend.plot = plot.legend, args.legend = args.legend, ...) X <- [email protected] smoothing <- [email protected] n.marg <- ncol(X) fit0_nn <- list() for(i in 1:n.marg){ fit0_nn[[i]] <- locfit::locfit( ~ locfit::lp(X[,i], nn=smoothing[i], deg=1)) } fit0 <- fit0_nn alpha <- smoothing f.x <- list() for(j in 1:n.marg){ f.x[[j]] <- function(x){predict(fit0[[j]], newdata=x)} knorm <- try(integrate(f.x[[j]], lower=0, upper=Inf),silent=TRUE) if(knorm[[1]]==0 | inherits(knorm, "try-error")==TRUE){knorm[[1]] <- 0.001} f.x[[j]] <- function(x){predict(fit0[[j]], newdata=x)/as.numeric(knorm[[1]])} } if(n.marg<=3){ dev.new(); par(mfrow=c(1,ceiling(n.marg))) }else{ if(n.marg >3 && n.marg<=6){ dev.new(); par(mfrow=c(2,ceiling(n.marg/2))) }else{ dev.new(); par(mfrow=c(3,ceiling(n.marg/3))) } } par(mai=c(0.5,0.5,0.3,0.5)) for(i in 1:n.marg){ j <- i minimo <- min(X[complete.cases(X[,i]),i]) massimo <- max(X[complete.cases(X[,i]),i]) opt1 <- f.x[[i]](optimize(f.x[[i]], c(minimo,massimo), maximum=TRUE)$maximum) his <- hist(X[,i], plot=FALSE) opt2 <- max(his$density) opt <- max(opt1,opt2) plot(his, freq=FALSE, ylim=c(0,opt), main="", xlab="", ylab="") plot(f.x[[i]], lwd=2, xlim=c(minimo-1, massimo+1),ylim=c(0,opt), col="blue", add=TRUE) if(is.null(plot.name)){ title(main = paste("Variable X", i,sep="")) }else{ title(main = plot.name[i]) } } } ) setMethod( f="show", signature="CoImp", definition=function(object){ out <- object cat (" Main output of the function CoImp \n") cat (" -------------------------------------------------------------------------- \n") cat (" Percentage of missing and available data : \n") print(out@"Perc.miss") cat (" -------------------------------------------------------------------------- \n") cat (" Imputed data matrix : \n") print(out@"Imputed.data.matrix") cat (" -------------------------------------------------------------------------- \n") } ) CoImp <- function(X, n.marg = ncol(X), x.up = NULL, x.lo = NULL, q.up = rep(0.85, n.marg), q.lo = rep(0.15, n.marg), type.data = "continuous", smoothing = rep(0.5, n.marg), plot = TRUE, model = list(normalCopula(0.5, dim=n.marg), claytonCopula(10, dim=n.marg), gumbelCopula(10, dim=n.marg), frankCopula(10, dim=n.marg), tCopula(0.5, dim=n.marg,...), rotCopula(claytonCopula(10,dim=n.marg), flip=rep(TRUE,n.marg)),...), start. = NULL, ...){ if(!is.matrix(X)) stop("Tha data should be a matrix") if(n.marg<=1) stop("The data matrix should contain at least two variables") if(nrow(X)<1) stop("The data matrix should contain at least one observation") if(any(is.na(X))==FALSE) stop("The data matrix should contain at least one missing value") if(sum(complete.cases(X))==0) stop("The data matrix should contain at least one complete record") if(type.data != "discrete" & type.data != "continuous") stop("The data must be either continuous or discrete") if(type.data == "discrete") warning("The variables are treated as continuous and rounded off.") if(!is.null(x.up) & !is.null(q.up)) stop("Specify either x.up xor q.up") if(!is.null(x.lo) & !is.null(q.lo)) stop("Specify either x.lo xor q.lo") if(!is.null(q.up) & (any(q.up<=0) || any(q.up>=1))) stop("q.up must lie in (0, 1)") if(!is.null(q.lo) & (any(q.lo<=0) || any(q.lo>=1))) stop("q.lo must lie in (0, 1)") if(is.null(x.up) & is.null(q.up)) stop("Specify either x.up xor q.up") if(is.null(x.lo) & is.null(q.lo)) stop("Specify either x.lo xor q.lo") fit0_nn <- list() for(i in 1:n.marg){ fit0_nn[[i]] <- locfit::locfit( ~ locfit::lp(X[,i], nn=smoothing[i], deg=1)) } fit0 <- fit0_nn alpha <- smoothing names(alpha) <- c(paste("x",1:n.marg,sep="")) f.x <- list() F.x <- list() for(j in 1:n.marg){ f.x[[j]] <- function(x){predict(fit0[[j]], newdata=x)} knorm <- try(integrate(f.x[[j]], lower=0, upper=Inf),silent=TRUE) if(knorm[[1]]==0 | inherits(knorm, "try-error")==TRUE){knorm[[1]] <- 0.001} f.x[[j]] <- function(x){predict(fit0[[j]], newdata=x)/as.numeric(knorm[[1]])} F.x[[j]] <- function(x){ifelse(!is.na(x),integrate(f.x[[j]], lower=0, upper=x)$value,return(NA))} } ind.miss <- which(is.na(X), arr.ind = TRUE) if(nrow(ind.miss)>1){ind.miss <- ind.miss[order(ind.miss[,1]),]} ind.cols.na <- split(ind.miss[,2],ind.miss[,1]) num.rows.na <- length(ind.cols.na) n.mod <- length(model) loglik <- double(length=n.mod) metodo.fin <- double(length=n.mod) metodo.optim.fin <- double(length=n.mod) for(i in 1:n.mod){ metodo <- "ml" metodo.c <- "BFGS" udat.na <- fit.margin(dataset=t(X), param=list(dimc=n.marg)) udat <- udat.na[complete.cases(udat.na),] fitc <- try(fitCopula(data=udat, copula=model[[i]], start=start., method=metodo, optim.method=metodo.c), silent=TRUE) if(inherits(fitc, "try-error")==TRUE){ metodo <- c("mpl", "itau", "irho") repeat{ if(length(metodo)==0 || inherits(fitc, "try-error")==FALSE) break fitc <- try(fitCopula(data = udat, copula = model[[i]], start = start., method = metodo[[1]]), silent = TRUE) metodo <- setdiff(metodo, metodo[[1]]) } } if(inherits(fitc, "try-error")==TRUE){ metodo.c <- c("Nelder-Mead", "CG", "L-BFGS-B", "SANN") repeat{ if(length(metodo.c)==0 || inherits(fitc, "try-error")==FALSE) break metodo <- c("ml","mpl","itau","irho") repeat{ if(length(metodo)==0 || inherits(fitc, "try-error")==FALSE) break fitc <- try(fitCopula(data = udat, copula = model[[i]], start = start., method = metodo[[1]], optim.method=metodo.c[[1]]), silent = TRUE) metodo <- setdiff(metodo, metodo[[1]]) } metodo.c <- setdiff(metodo.c, metodo.c[[1]]) } } if (inherits(fitc, "try-error") || is.nan(suppressWarnings(loglikCopula(param=fitc@estimate, u=udat, copula=model[[i]])))) { loglik[i] <- -10000 }else{ loglik[i] <- suppressWarnings(loglikCopula(param=fitc@estimate, u=udat, copula=model[[i]])) } if(length(metodo)==0){ metodo.fin[i] <- 0 }else{ metodo.fin[i] <- metodo[[1]] } if(length(metodo.c)==0){ metodo.optim.fin[i] <- 0 }else{ metodo.optim.fin[i] <- metodo.c[[1]] } } best <- which(loglik==max(loglik[which(!is.na(loglik))]))[[1]] mod.fin.base <- model[[best]] metodo.fin.base <- metodo.fin[[best]] metodo.optim.fin.base <- metodo.optim.fin[[best]] if(metodo.fin.base=="ml"){ udat.na <- fit.margin(dataset=t(X), param=list(dimc=n.marg)) udat <- udat.na[complete.cases(udat.na),] }else{ udat.na <- fit.margin2(dataset=t(X), param=list(dimc=n.marg)) udat <- udat.na[complete.cases(udat.na),] } mod.fin <- try(fitCopula(data=udat, copula=mod.fin.base, start=start., method=metodo.fin.base, optim.method=metodo.optim.fin.base),silent=TRUE) if (inherits(mod.fin, "try-error")) { stop("Imputation failed") }else{ if(class(mod.fin.base)=="rotExplicitCopula" | class(mod.fin.base)=="rotCopula"){ mod.fin.base@copula@parameters <- mod.fin@estimate }else{ mod.fin.base@parameters <- mod.fin@estimate } } dati.fin <- X x.min <- apply(X, 2, min, na.rm=TRUE) x.max <- apply(X, 2, max, na.rm=TRUE) if(is.null(x.up)){ x.up <- diag(apply(X, 2, quantile, p=q.up, na.rm=TRUE)) } if(is.null(x.lo)){ x.lo <- diag(apply(X, 2, quantile, p=q.lo, na.rm=TRUE)) } for(i in 1:num.rows.na){ cat("\r Number of imputed rows: ", i, "\n"); cols.na <- ind.cols.na[[i]] cols.no.na <- seq(1:n.marg)[-cols.na] rows.na <- as.numeric(names(ind.cols.na))[i] y <- X[rows.na,] lcn <- length(cols.na) meanX <- colMeans(X,na.rm=TRUE) medianX <- apply(X=X, FUN=median, MARGIN=2, na.rm=TRUE) zz <- y fcond <- function(x){ zz[cols.na] <- x fcond.mod(x, y=zz, ind=cols.na, model=mod.fin.base, distr=F.x, dens=f.x) } fcond2 <- Vectorize(fcond) if(lcn==n.marg) stop("It cannot impute a full NA record") a <- x.min[cols.na] b <- x.max[cols.na] aa <- x.lo[cols.na] bb <- x.up[cols.na] if(lcn==1){ maxf <- suppressWarnings(optimize(fcond2, interval=c(a, b), maximum=TRUE)$max) if(maxf>=aa & maxf<=bb){ umissM <- hitormiss(FUN=fcond, p=lcn, h=fcond(maxf), a=aa, b=bb) }else{ umissM <- hitormiss(FUN=fcond, p=lcn, h=fcond(maxf), a=a, b=b) } }else{ maxf <- suppressWarnings(try(optim(par=meanX[cols.na], fn=fcond, lower=a, upper=b, control = list(fnscale=-1))$par,silent=TRUE)) if(inherits(maxf, "try-error")==TRUE){ maxf <- suppressWarnings(optim(par=medianX[cols.na], fn=fcond, lower=a, upper=b, control = list(fnscale=-1))$par) } if(all(maxf>=aa) & all(maxf<=bb)){ umissM <- suppressWarnings(hitormiss(FUN=fcond,p=lcn,h=fcond(maxf),a=aa,b=bb)) }else{ umissM <- suppressWarnings(hitormiss(FUN=fcond,p=lcn,h=fcond(maxf),a=a,b=b)) } } dati.fin[rows.na,cols.na] <- umissM } loglik.imp <- double(length=n.mod) metodo.fin.imp <- double(length=n.mod) metodo.optim.fin.imp <- double(length=n.mod) if(type.data=="discrete"){ dati.fin <- round(dati.fin,0) } for(i in 1:n.mod){ metodo <- "ml" metodo.c <- "BFGS" udat.na.imp <- fit.margin(dataset=t(dati.fin), param=list(dimc=n.marg)) udat.imp <- udat.na.imp[complete.cases(udat.na.imp),] fitc.imp <- try(fitCopula(data=udat.imp, copula=model[[i]], start=start., method=metodo, optim.method=metodo.c), silent=TRUE) if(inherits(fitc.imp, "try-error")==TRUE){ metodo <- c("mpl","itau","irho") repeat{ if(length(metodo)==0 || inherits(fitc.imp, "try-error")==FALSE) break fitc.imp <- try(fitCopula(data = udat.imp, copula = model[[i]], start = start., method = metodo[[1]]), silent = TRUE) metodo <- setdiff(metodo, metodo[[1]]) } } if(inherits(fitc.imp, "try-error")==TRUE){ metodo.c <- c("Nelder-Mead", "CG", "L-BFGS-B", "SANN") repeat{ if(length(metodo.c)==0 || inherits(fitc.imp, "try-error")==FALSE) break metodo <- c("ml","mpl","itau","irho") repeat{ if(length(metodo)==0 || inherits(fitc.imp, "try-error")==FALSE) break fitc.imp <- try(fitCopula(data = udat.imp, copula = model[[i]], start = start., method = metodo[[1]], optim.method=metodo.c[[1]]), silent = TRUE) metodo <- setdiff(metodo, metodo[[1]]) } metodo.c <- setdiff(metodo.c, metodo.c[[1]]) } } if (inherits(fitc.imp, "try-error") || is.nan(suppressWarnings(loglikCopula(param=fitc.imp@estimate, u=udat.imp, copula=model[[i]])))) { loglik.imp[i] <- -10000 }else{ loglik.imp[i] <- suppressWarnings(loglikCopula(param=fitc.imp@estimate, u=udat.imp, copula=model[[i]])) } if(length(metodo)==0){ metodo.fin.imp[i] <- 0 }else{ metodo.fin.imp[i] <- metodo[[1]] } if(length(metodo.c)==0){ metodo.optim.fin.imp[i] <- 0 }else{ metodo.optim.fin.imp[i] <- metodo.c[[1]] } } best.imp <- which(loglik.imp==max(loglik.imp[which(!is.na(loglik.imp))]))[[1]] mod.fin.base.imp <- model[[best.imp]] metodo.fin.base.imp <- metodo.fin.imp[[best.imp]] metodo.optim.fin.base.imp <- metodo.optim.fin.imp[[best.imp]] if(metodo.fin.base.imp=="ml"){ udat.na.imp <- fit.margin(dataset=t(dati.fin), param=list(dimc=n.marg)) udat.imp <- udat.na.imp[complete.cases(udat.na.imp),] }else{ udat.na.imp <- fit.margin2(dataset=t(dati.fin), param=list(dimc=n.marg)) udat.imp <- udat.na.imp[complete.cases(udat.na.imp),] } mod.fin.imp <- try(fitCopula(data=udat.imp, copula=mod.fin.base.imp, start=start., method=metodo.fin.base.imp, optim.method=metodo.optim.fin.base.imp),silent=TRUE) if (inherits(mod.fin.imp, "try-error")) { stop("Imputation failed") }else{ if(class(mod.fin.base.imp)=="rotExplicitCopula" | class(mod.fin.base.imp)=="rotCopula"){ mod.fin.base.imp@copula@parameters <- mod.fin.imp@estimate }else{ mod.fin.base.imp@parameters <- mod.fin.imp@estimate } } perc.miss <- round(colMeans(is.na(X)*100),2) perc.data <- round(rbind(100-perc.miss, perc.miss),3) rownames(perc.data) <- c("Data","Missing") ifelse(is.null(colnames(X)), colnames(perc.data) <- paste("X",c(1:n.marg),sep=""), colnames(perc.data) <- colnames(X)) if(is.null(colnames(X))) colnames(X) <- paste("X",c(1:n.marg),sep="") ifelse(is.null(colnames(X)), colnames(dati.fin) <- paste("X",c(1:n.marg),sep=""), colnames(dati.fin) <- colnames(X)) if(class(mod.fin.base)=="rotExplicitCopula" | class(mod.fin.base)=="rotCopula"){ mod.fin.base <- mod.fin.base@copula } if(class(mod.fin.base.imp)=="rotExplicitCopula" | class(mod.fin.base.imp)=="rotCopula"){ mod.fin.base.imp <- mod.fin.base.imp@copula } mod.pre <- list(model = mod.fin.base@class, dimension = mod.fin.base@dimension, parameter = mod.fin.base@parameters, number = best) mod.post <- list(model = mod.fin.base.imp@class, dimension = mod.fin.base.imp@dimension, parameter = mod.fin.base.imp@parameters, number = best.imp) out <- new("CoImp") [email protected] <- X; [email protected] <- perc.data; [email protected] <- mod.pre; [email protected] <- metodo.fin.base; [email protected] <- ind.miss; [email protected] <- alpha; [email protected] <- dati.fin; [email protected] <- mod.post; [email protected] <- metodo.fin.base.imp; if(plot==TRUE) plot(out) return(out); }
\donttest{ data(DengueSimR02) r.max<-seq(20,1000,20) r.min<-seq(0,980,20) type<-2-(DengueSimR02[,"time"]<120) tmp<-cbind(DengueSimR02,type=type) typed.pi<-get.pi.typed(tmp,typeA=1,typeB=2,r=r.max,r.low=r.min) }
context("Primary Inputs of locFDR BF theoretic function cor") test_that("Absent of BetaHat and SE will throw error", { expect_error(analytic_locFDR_BF_cor(1:10), "BetaHat or SE vector is missing!") expect_error(analytic_locFDR_BF_cor(SpikeVar=0.3), "BetaHat or SE vector is missing!") expect_error(analytic_locFDR_BF_cor(1:10, 1:10), "Correlation matrix is missing!") }) test_that("Throws error if BetaHat is not a numeric vector of length more than 1 and no missing value", { expect_error(analytic_locFDR_BF_cor(1, 1:10, ExampleDataCor$cor), "Number of elements in the BetaHat vector must be more than 1!") expect_error(analytic_locFDR_BF_cor(NA, 1:10, ExampleDataCor$cor), "BetaHat must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(c(NA,1), 1:10, ExampleDataCor$cor), "BetaHat for one or more phenotypes are missing!") expect_error(analytic_locFDR_BF_cor("AB", 1:10, ExampleDataCor$cor), "BetaHat must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(c("A", 1), 1:10, ExampleDataCor$cor), "BetaHat must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(matrix(0,2,2), 1:10, ExampleDataCor$cor), "BetaHat must be a vector.") expect_error(analytic_locFDR_BF_cor(data.frame(rep(1:10)), 1:10, ExampleDataCor$cor), "BetaHat must be a vector.") expect_warning(analytic_locFDR_BF_cor(matrix(1:10, 10, 1), 1:10, ExampleDataCor$cor), "BetaHat is a matrix!") }) test_that("Throws error if SE is not a positive numeric vector of length more than 1 and no missing value", { expect_error(analytic_locFDR_BF_cor(1:10, 1, ExampleDataCor$cor), "Number of elements in the SE vector must be more than 1!") expect_error(analytic_locFDR_BF_cor(1:10, NA, ExampleDataCor$cor), "SE must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(1:10, c(NA,1), ExampleDataCor$cor), "SE for one or more phenotypes are missing!") expect_error(analytic_locFDR_BF_cor(1:10, "AB", ExampleDataCor$cor), "SE must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(1:10, c("A", 1), ExampleDataCor$cor), "SE must be a numeric vector.") expect_error(analytic_locFDR_BF_cor(1:10, matrix(0,2,2), ExampleDataCor$cor), "SE must be a vector.") expect_error(analytic_locFDR_BF_cor(1:10, data.frame(rep(1:10)), ExampleDataCor$cor), "SE must be a vector.") expect_error(analytic_locFDR_BF_cor(1:10, c(-1, 2,3), ExampleDataCor$cor), "One or more elements in the SE vector are not positive!") expect_warning(analytic_locFDR_BF_cor(1:10, matrix(1:10, 10, 1), ExampleDataCor$cor), "SE is a matrix!") }) test_that("Throws error if Beta and SE are not of same length", { expect_error(analytic_locFDR_BF_cor(1:10, 1:15, ExampleDataCor$cor), "BetaHat and SE vectors must have the same number of elements!") expect_error(analytic_locFDR_BF_cor(1:100, 1:15, ExampleDataCor$cor), "BetaHat and SE vectors must have the same number of elements!") })
context("Testing anova and haplo.glm") tmp <- Sys.setlocale("LC_ALL", "C") tmp <- Sys.getlocale() options(stringsAsFactor=FALSE) label <-c("DQB","DRB","B") data(hla.demo) y <- hla.demo$resp y.bin <- 1*(hla.demo$resp.cat=="low") geno <- as.matrix(hla.demo[,c(17,18,21:24)]) geno <- setupGeno(geno, miss.val=c(0,NA)) my.data <- data.frame(geno=geno, age=hla.demo$age, male=hla.demo$male, y=y, y.bin=y.bin) seed <- c(17, 53, 1, 40, 37, 0, 62, 56, 5, 52, 12, 1) set.seed(seed) fit.hla.gaus.gender <- haplo.glm(y ~ male + geno, family = gaussian, na.action="na.geno.keep", data=my.data, locus.label=label, control = haplo.glm.control(haplo.min.count=10)) coeff.hla.gender <- summary(fit.hla.gaus.gender)$coefficients set.seed(seed) fit.hla.gaus.inter <- haplo.glm(y ~ male * geno, family = gaussian, na.action="na.geno.keep", data=my.data, locus.label=label, control = haplo.glm.control(haplo.min.count = 10)) coeff.hla.inter <- summary(fit.hla.gaus.inter)$coefficients if(0) { saveRDS(fit.hla.gaus.gender, "fit.gaus.gender.rds") saveRDS(fit.hla.gaus.inter, "fit.gaus.inter.rds") } fit.gender <- readRDS("fit.gaus.gender.rds") fit.inter <- readRDS("fit.gaus.inter.rds") coeffgender <- summary(fit.gender)$coefficients coeffinter <- summary(fit.inter)$coefficients test_that("Basic haplo.glm anova and glm coefficients", { expect_equal(coeff.hla.gender, expected=coeffgender, tolerance=1e-3) expect_equal(coeff.hla.inter, expected=coeffinter, tolerance=1e-3) })
gridfunction<-function(npoints,linf,lsup){ npar=length(linf) xgrid=matrix(0,npoints,npar) for(i in 1:npar){ xgrid[,i]=seq(linf[i], lsup[i], length.out = npoints) } grid.l=data.frame(xgrid) gridoutput=make.surface.grid(grid.l) return(gridoutput[,]) }
MDCSIS=function(X,Y,nsis=(dim(X)[1])/log(dim(X)[1])){ if (dim(X)[1]!=length(Y)) { stop("X and Y should have same number of rows!") } if (missing(X)|missing(Y)) { stop("The data is missing!") } if (TRUE%in%(is.na(X)|is.na(Y)|is.na(nsis))) { stop("The input vector or matrix cannot have NA!") } if (inherits(Y,"Surv")) { stop("MDCSIS can not implemented with object of Surv") } corr=c(); n=dim(X)[1]; p=dim(X)[2]; Y_ij=Y%*%t(Y) for (k in 1:p){ X_matrix=matrix(X[,k],n,n) X_ij=abs(X_matrix-t(X_matrix)) covxy=mean(X_ij*Y_ij) covx=mean(X_ij*X_ij) covy=mean(Y_ij*Y_ij) corr[k]=abs(covxy)/sqrt(covx*covy) } A=order(corr,decreasing=TRUE) return (A[1:nsis]) }
days_frost <- function(mintemps, fendates, lastday = 181){ mintemps <- mintemps %>% filter(mintemps$DOY<=lastday) Datescrit_10 <- rep(NA,lastday) Datescrit_90 <- rep(NA,lastday) len = length(fendates$DOY) for (i in 1:len){ Datescrit_10[fendates$DOY[i]]=fendates$LT_10[i] Datescrit_90[fendates$DOY[i]]=fendates$LT_90[i] } Tcritant_LT10 <- rep(fendates$LT_10[1], fendates$DOY[1]-1) Tcritant_LT90 <- rep(fendates$LT_90[1], fendates$DOY[1]-1) Tcritpost_LT10 <- rep(fendates$LT_10[len], lastday-fendates$DOY[len]) Tcritpost_LT90 <- rep(fendates$LT_90[len], lastday-fendates$DOY[len]) Tcrit_gap_10 <- zoo(Datescrit_10) Tcrit_gap_90 <- zoo(Datescrit_90) Tcrit_fgap_10 <- na.approx(Tcrit_gap_10) Tcrit_fgap_90 <- na.approx(Tcrit_gap_90) Tcritcent_10 <- coredata(Tcrit_fgap_10) Tcritcent_90 <- coredata(Tcrit_fgap_90) mintemps$LT_10 <- c(Tcritant_LT10,Tcritcent_10,Tcritpost_LT10) mintemps$LT_90 <- c(Tcritant_LT90,Tcritcent_90,Tcritpost_LT90) mintemps <- mintemps %>% mutate(LT_0 = (LT_10-LT_90)/8+LT_10, LT_100 = LT_0-(LT_10-LT_90)*10/8, Dam = ifelse((LT_0-Tmin)/(LT_0-LT_100)<0,0, ifelse((LT_0-Tmin)/(LT_0-LT_100)>1,1, (LT_0-Tmin)/(LT_0-LT_100))) ) return(mintemps) }
knitr::opts_chunk$set( collapse = TRUE, comment = " echo = TRUE, message = FALSE, warning = FALSE, fig.align="center", fig.height= 6, fig.width = 6 ) library(tci) data("eleveld_pk") data("eleveld_pd") pkpd_eb <- merge(eleveld_pk, eleveld_pd) prior_pars_id1 <- eleveld_poppk(df = pkpd_eb[1,]) prior_pars_id1 pars_pk_id1 <- unlist(prior_pars_id1[,c("V1","V2","V3","CL","Q2","Q3","KE0")]) pars_pd_id1 <- unlist(prior_pars_id1[,c("CE50","GAMMA","GAMMA2","BIS0","BIS0")]) olc_inf_id1 <- tci_pd(pdresp = c(50,50), tms = c(0,5), pkmod = pkmod3cptm, pdmod = emax_eleveld, pdinv = inv_emax_eleveld, pars_pk = pars_pk_id1, pars_pd = pars_pd_id1) plot(olc_inf_id1) eb_pars_pk_id1 <- unlist(pkpd_eb[1,c("CL","Q2","Q3","V1","V2","V3","KE0")]) eb_pars_pd_id1 <- unlist(pkpd_eb[1,c("E50","GAM","GAM1","EMAX","EMAX")]) eb_sigma_id1 <- unlist(pkpd_eb[1,"RESD"]) eb_bd_id1 <- unlist(pkpd_eb[1,"ALAG1"]) * 60 set.seed(1) datasim_id1 <- gen_data(inf = olc_inf_id1, pkmod = pkmod3cptm, pdmod = emax_eleveld, pars_pk0 = eb_pars_pk_id1, pars_pd0 = eb_pars_pd_id1, sigma_add = eb_sigma_id1, delay = eb_bd_id1) plot(datasim_id1) cl_targets <- function(time, target){ data.frame(time = time, target = target) } cl_updates <- function(time, full_data = TRUE, plot_progress = FALSE){ data.frame(time = time, full_data = full_data, plot_progress = plot_progress) } targets = cl_targets(time = seq(0,10,1/6), target = 50) updates <- cl_updates(time = seq(2,10,2)) prior_par_list <- list( pars_pkpd = prior_pars_id1[c("CL","Q2","Q3","V1","V2","V3", "KE0","CE50","GAMMA","GAMMA2", "BIS0","BIS0")], pk_ix = 1:7, pd_ix = 8:12, fixed_ix = 9:12, err = prior_pars_id1[1,"SIGMA"], sig = eleveld_vcov(prior_pars_id1, rates = FALSE)[[1]] ) true_par_list <- list(pars_pkpd = pkpd_eb[1,c("CL","Q2","Q3","V1", "V2","V3","KE0", "E50","GAM","GAM1", "EMAX","EMAX")], pk_ix = 1:7, pd_ix = 8:12, fixed_ix = 9:12, err = pkpd_eb[1,"RESD"], delay = pkpd_eb[1,"ALAG1"]) bayes_sim <- bayes_control(targets = targets, updates = updates, prior = prior_par_list, true_pars = true_par_list) plot(bayes_sim)
OuterPara <- function(m, nu, N, eps){ cm <- sqrt(m / nu) d2 <- as.numeric(compute_zl(nu, eps)[1]) zl <- as.numeric(compute_zl(nu, eps)[2]) zu <- zl + d2 h <- d2/(N - 1) zvec <- seq(zl, zu, by = h) wvec <- transf(zvec) / cm psinu.zvec <- Func_psi_nu(zvec, nu) cons1 <- sqrt(2/m) * exp(lgamma(nu/2) - lgamma(m/2)) cons2 <- (2/m) * exp(lgamma(nu/2) - lgamma(m/2)) exp.w <- sqrt(2/m) * exp(lgamma((m + 1)/2) - lgamma(m/2)) out <- list(h=h, cons1=cons1, cons2=cons2, exp.w=exp.w, wvec=wvec, psinu.zvec=psinu.zvec) }
if (requiet("testthat") && requiet("performance") && requiet("lme4")) { data(sleepstudy, package = "lme4") m1.1 <- glm(Reaction ~ Days, data = sleepstudy, family = gaussian()) m1.2 <- glm(Reaction ~ Days, data = sleepstudy, family = gaussian("log")) m1.3 <- glm(Reaction ~ Days, data = sleepstudy, family = gaussian("inverse")) m2.1 <- glm(Reaction ~ Days, data = sleepstudy, family = inverse.gaussian()) m2.2 <- glm(Reaction ~ Days, data = sleepstudy, family = inverse.gaussian("log")) m2.3 <- glm(Reaction ~ Days, data = sleepstudy, family = inverse.gaussian("inverse")) cp <- compare_performance(m1.1, m1.2, m1.3, m2.1, m2.2, m2.3) test_that("rmse", { expect_equal(cp$RMSE, c(47.4489, 47.39881, 47.38701, 47.41375, 47.39979, 47.38705), tolerance = 1e-3) }) }
"seas.sum" <- function(x, var, width = 11, start.day = 1, prime, a.cut = 0.3, na.cut = 0.2) { orig <- as.character(substitute(x))[[1]] if (missing(var)) var <- c("precip", "rain", "snow", "leak", "evap", "ezwat", "et", "runoff", "air", "soil") var <- names(x)[names(x) %in% var] if (missing(prime)) prime <- ifelse("precip" %in% var, "precip", var[1]) sc <- seas.df.check(x, orig, c(prime, var)) if (is.na(a.cut) || a.cut <= 0) a.cut = FALSE x$fact <- mkseas(x, width, start.day) x$ann <- mkann(x, start.day) bins <- levels(x$fact) num <- length(bins) years <- levels(x$ann) ann <- data.frame(year=years, active=NA, days=NA, na=NA) seas <- array(dim=c(length(years), num, length(var)), dimnames=list(years, bins, var)) days <- array(dim=c(length(years), num), dimnames=list(years, bins)) na <- days if (is.na(a.cut) || !a.cut) { a.cut <- FALSE } else { active <- seas is.active <- function(test) { tot <- numeric(length(test)) tot[is.na(test)] <- NA tot[test > a.cut] <- 1 na.rm <- ifelse(sum(is.na(tot)) / length(tot) < na.cut[2], TRUE, FALSE) return(sum(tot, na.rm=na.rm)) } } if (length(na.cut) == 1) na.cut <- rep(na.cut, 2) sum.is.num <- function(x)sum(is.finite(x)) ann$days <- attr(x$ann, "year.lengths") if (a.cut) ann$active <- tapply(x[,prime], x$ann, is.active) else ann$active <- NULL ann$na <- tapply(x[,prime], x$ann, sum.is.num) for (p in var) ann[,p] <- tapply(x[,p], x$ann, sum, na.rm=TRUE) td <- function(y) table(mkseas(width=width, year=y, calendar=sc$calendar)) days[,] <- t(sapply(ann$days, td)) for (y in 1:length(years)) { s <- x[x$ann == years[y],, drop=FALSE] if (nrow(s) > 0) { na[y,] <- tapply(s[,prime], s$fact, sum.is.num) for (p in var) { seas[y,,p] <- tapply(s[,p], s$fact, sum, na.rm=TRUE) if (a.cut) active[y,,p] <- tapply(s[,p], s$fact, is.active) } } } ann$na[is.na(ann$na)] <- 0 ann$na <- ann$days - ann$na na[is.na(na)] <- 0 na <- days - na ann.na <- ann$na / ann$days > na.cut[1] seas.na <- na/days > na.cut[2] ann[ann.na, var] <- NA seas[,,var][seas.na] <- NA if (a.cut) { ann[ann.na, "active"] <- NA active[,,var][seas.na] <- NA } l <- list(ann=ann, seas=seas, active=NA, days=days, na=na) if (a.cut) l$active <- active else l$active <- NULL l$start.day <- start.day l$years <- years l$var <- var l$units <- list() l$long.name <- list() for (v in var) { l$units[[v]] <- attr(x[[v]], "units") l$long.name[[v]] <- attr(x[[v]], "long.name") if (is.null(l$long.name[[v]])) l$long.name[[v]] <- v } l$prime <- prime l$width <- width l$bins <- bins l$bin.lengths <- attr(x$fact, "bin.lengths") l$year.range <- attr(x$ann, "year.range") l$na.cut <- na.cut l$a.cut <- a.cut l$id <- sc$id l$name <- sc$name attr(l, "class") <- "seas.sum" return(l) }
github.m3it.covid19data <- function(level) { if(!level %in% 1:2) return(NULL) url <- "https://raw.githubusercontent.com/M3IT/COVID-19_Data/master/Data/COVID19_Data_Hub.csv" x <- read.csv(url, na.strings = c("NA","")) x$date <- as.Date(x$date) x <- x[x$administrative_area_level == level,] return(x) }
update_SS <- function(z, S, hyperprior=NULL){ S_up <- S mu0 <- S[["mu"]] kappa0 <- S[["kappa"]] nu0 <- S[["nu"]] lambda0 <- S[["lambda"]] if(length(dim(z))>1 & dim(z)[2]>1){ n <- ncol(z) zbar <- apply(X=z, MARGIN=1, FUN=mean) kappa1 <- kappa0 + n nu1 <- nu0 + n mu1 <- n/(kappa0 + n)*zbar + kappa0/(kappa0 + n)*mu0 varz <- tcrossprod(z-zbar) if(!is.null(hyperprior)){ g0 <- nu0 lambda0 <- wishrnd(n=nu0+g0, Sigma=solve(solve(lambda0)+solve(hyperprior[["Sigma"]]))) } lambda1 <- (lambda0 + kappa0*n/(kappa0 + n)*tcrossprod(zbar - mu0) + varz) }else{ kappa1 <- kappa0 + 1 nu1 <- nu0 + 1 mu1 <- (kappa0/(kappa0 + 1)*mu0 + 1/(kappa0 + 1)*z)[,1] if(!is.null(hyperprior)){ g0 <- nu0 lambda0 <- wishrnd(n=nu0+g0, Sigma=solve(solve(lambda0)+solve(hyperprior[["Sigma"]]))) } lambda1 <- lambda0 + kappa0/(kappa0 + 1)*tcrossprod(z[,1] - mu0) } S_up[["mu"]] <- mu1 S_up[["kappa"]] <- kappa1 S_up[["nu"]] <- nu1 S_up[["lambda"]] <- lambda1 return(S_up) }
LassoPath <- function (data, formula) { X <- model.matrix(formula, data) y <- model.frame(formula, data)[, 1] get_lambdas <- cv.glmnet(X, y, family="binomial", type.measure="auc", nfolds=3) glmnet.output <- glmnet(X, y, alpha = 1, family = "binomial", lambda = get_lambdas$lambda, standardize=TRUE, intercept = FALSE, type.logistic = "modified.Newton") dimension <- glmnet.output$df coeff <- t(as.matrix(glmnet.output$beta)) lambda <- glmnet.output$lambda path <- cbind(lambda, dimension, coeff) class(path) <- "LassoPath" return(path) }
GE_translate_inputs <- function(beta_list, rho_list, prob_G, cov_Z=NULL, cov_W=NULL, corr_G=NULL) { if (length(beta_list) != 6 | length(rho_list) != 6 | class(beta_list) != 'list' | class(rho_list) != 'list') { stop('Input vectors not the right size!') } num_G <- length(beta_list[[2]]) num_I <- length(beta_list[[4]]) num_Z <- length(beta_list[[5]]); if(num_Z == 1 & beta_list[[5]][1] == 0) {num_Z <- 0} num_W <- length(beta_list[[6]]); if(num_W == 1 & beta_list[[6]][1] == 0) {num_W <- 0} if (num_G != num_I | num_G != length(prob_G)) { stop('Discordance between effect sizes for G and probabilities of G') } rho_GE <- rho_list[[1]]; rho_GZ <- rho_list[[2]]; rho_EZ <- rho_list[[3]] rho_GW <- rho_list[[4]]; rho_EW <- rho_list[[5]]; rho_ZW <- rho_list[[6]] if (length(rho_GE) != num_G) { stop('Incompatible number of elements in beta/rho_list') } if (num_Z > 0) { if (length(rho_GZ) != num_Z*num_G | length(rho_EZ) != num_Z) { stop('Incompatible number of elements in beta/rho_list') } if (num_W > 0) { if (length(rho_ZW) != num_Z*num_W) { stop('Incompatible number of elements in beta/rho_list') } } } if (num_W > 0) { if (length(rho_GW) != num_G*num_W | length(rho_EW) != num_W) { stop('Incompatible number of elements in beta/rho_list') } } if (num_G > 1) { if (ncol(corr_G) != num_G | nrow(corr_G) != num_G) { stop('Incompatible number of elements in beta/rho_list') } } if (num_G > 1) { G_bin_struct <- corr_G cprob <- tryCatch(bindata::bincorr2commonprob(margprob = prob_G, bincorr=G_bin_struct), error=function(e) e) if ('error' %in% class(cprob)) { stop ('You specified an invalid corr_G structure') } sigma_struct <- tryCatch(bindata::commonprob2sigma(commonprob=cprob), error=function(e) e) if ('error' %in% class(sigma_struct)) { stop ('You specified an invalid corr_G structure') } G_segment <- matrix(data=0, nrow=2*num_G, ncol=2*num_G) for (i in 1:num_G) { odd_seq <- seq(from=1, to=(2*num_G-1), by=2) even_seq <- odd_seq + 1 G_segment[i*2-1, odd_seq] <- sigma_struct[i, ] G_segment[i*2, even_seq] <- sigma_struct[i, ] } } else { G_segment <- diag(x=1, nrow=2, ncol=2) } w_vec <- qnorm(1-prob_G) r_GE <- rho_GE / (2*dnorm(w_vec)) GE_segment <- rep(r_GE, each=2) if (num_Z != 0) { GZ_segment <- matrix(data=NA, nrow=2*num_G, ncol=num_Z) for (i in 1:num_G) { r_GZ <- rho_GZ[((i-1)*num_Z+1):(i*num_Z)] / (2*dnorm(w_vec[i])) GZ_segment[i*2-1, ] <- r_GZ GZ_segment[i*2, ] <- r_GZ } } if (num_W != 0) { GW_segment <- matrix(data=NA, nrow=2*num_G, ncol=num_W) for (i in 1:num_G) { r_GW <- rho_GW[((i-1)*num_W+1):(i*num_W)] / (2*dnorm(w_vec[i])) GW_segment[i*2-1, ] <- r_GW GW_segment[i*2, ] <- r_GW } } MVN_sig_tot <- matrix(data=NA, nrow=(2*num_G+num_Z+num_W+1), ncol=(2*num_G+num_Z+num_W+1)) MVN_sig_tot[1:(2*num_G), 1:(2*num_G)] <- G_segment MVN_sig_tot[(2*num_G+1), 1:(2*num_G)] <- GE_segment MVN_sig_tot[1:(2*num_G), (2*num_G+1)] <- GE_segment MVN_sig_tot[(2*num_G+1), (2*num_G+1)] <- 1 if (num_Z > 0 & num_W > 0) { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), 1:(2*num_G)] <- t(GZ_segment) MVN_sig_tot[1:(2*num_G), (2*num_G+2):(2*num_G+num_Z+1)] <- GZ_segment MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), 1:(2*num_G)] <- t(GW_segment) MVN_sig_tot[1:(2*num_G), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- GW_segment MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+1)] <- rho_EZ MVN_sig_tot[(2*num_G+1), (2*num_G+2):(2*num_G+num_Z+1)] <- rho_EZ if (num_Z == 1) { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+2):(2*num_G+num_Z+1)] <- 1 } else { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+2):(2*num_G+num_Z+1)] <- cov_Z } MVN_sig_tot[(2*num_G+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- rho_EW MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+1)] <- rho_EW ZW_segment <- matrix(data=NA, nrow=num_Z, ncol=num_W) for (i in 1:num_Z) { ZW_segment[i, ] <- rho_ZW[((i-1)*num_W+1):(i*num_W)] } MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- ZW_segment MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+2):(2*num_G+num_Z+1)] <- t(ZW_segment) if (num_W == 1) { MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- 1 } else { MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- cov_W } } if (num_Z > 0 & num_W == 0) { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), 1:(2*num_G)] <- t(GZ_segment) MVN_sig_tot[1:(2*num_G), (2*num_G+2):(2*num_G+num_Z+1)] <- GZ_segment MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+1)] <- rho_EZ MVN_sig_tot[(2*num_G+1), (2*num_G+2):(2*num_G+num_Z+1)] <- rho_EZ if (num_Z == 1) { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+2):(2*num_G+num_Z+1)] <- 1 } else { MVN_sig_tot[(2*num_G+2):(2*num_G+num_Z+1), (2*num_G+2):(2*num_G+num_Z+1)] <- cov_Z } } if (num_Z == 0 & num_W > 0) { MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), 1:(2*num_G)] <- t(GW_segment) MVN_sig_tot[1:(2*num_G), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- GW_segment MVN_sig_tot[(2*num_G+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- rho_EW MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+1)] <- rho_EW if (num_W == 1) { MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- 1 } else { MVN_sig_tot[(2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1), (2*num_G+num_Z+2):(2*num_G+num_Z+num_W+1)] <- cov_W } } if (!isSymmetric(MVN_sig_tot)) {stop("Problem building covariance matrix!")} test_data <- tryCatch(mvtnorm::rmvnorm(n=1, sigma=MVN_sig_tot), warning=function(w) w, error=function(e) e) if (class(test_data)[1] != 'matrix') {stop('You specified an impossible covariance matrix!')} return(list(sig_mat_total=MVN_sig_tot)) }
SVN <- function(level){ x <- NULL if(level==1){ x1 <- gov.si(level = level) x2 <- github.cssegisanddata.covid19(country = "Slovenia") %>% select(-c("confirmed", "deaths")) x3 <- ourworldindata.org(id = "SVN") %>% select(-c("tests", "hosp", "icu")) x <- x1 %>% full_join(x2, by = "date") %>% full_join(x3, by = "date") } return(x) }