Datasets:

lanesket
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[](){expression}<LSEP>[litteral](str){repdata}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mvncovar1}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LSEP>[](symbol){time}<LSEP>[](symbol){group}<LSEP>[](symbol){chains}<LSEP>[](symbol){iter}<LSEP>[](symbol){data}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timepoints}<LSEP>[](symbol){time}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gendergrp}<LSEP>[](symbol){group}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){mvncov}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){beta1}<LEND>[argument 1; call](){}<LSEP>[](symbol){dnorm}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){beta2}<LEND>[argument 1; call](){}<LSEP>[](symbol){dnorm}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 2; 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call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){R}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 7; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma2}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[call](){}<LSEP>[](symbol){inverse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega2}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N1}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Z}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 1; call](){}<LSEP>[](symbol){dmnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mu1}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 9; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mu1}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta1}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){beta2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){age}<LSEP>[](symbol){j}<LEND>[statement 10; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 1; call](){}<LSEP>[](symbol){dwish}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){R}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 11; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma1}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[call](){}<LSEP>[](symbol){inverse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){d13}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){beta1}<LSEP>[](symbol){beta3}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){datam}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){gendergrp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dataf}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){gendergrp}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){Age}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LSEP>[](symbol){}<LSEP>[](symbol){timepoints}<LEND>[statement 6; assign](){=}<LSEP>[](symbol){z}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){dataf}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LEND>[statement 7; assign](){=}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){as.matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){datam}<LSEP>[](symbol){}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LEND>[statement 8; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){z}<LEND>[litteral](NULL){NULL}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){colnames}<LSEP>[](symbol){y}<LEND>[litteral](NULL){NULL}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){Age}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Age}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){z}<LEND>[statement 11; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){Age}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){mvncovardata}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){Age}<LEND>[argument 1; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){datam}<LEND>[argument 2; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){Age}<LEND>[argument 3; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){dataf}<LEND>[](symbol){z}<LSEP>[](symbol){y}<LSEP>[](symbol){Age}<LEND>[argument 7; call](){}<LSEP>[](symbol){matrix}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LSEP>[argument 4; litteral](real){0.000000}<LSEP>[argument 5; litteral](real){1.000000}<LSEP>[argument 6; litteral](real){0.000000}<LSEP>[argument 7; litteral](real){0.000000}<LSEP>[argument 8; litteral](real){0.000000}<LSEP>[argument 9; litteral](real){0.000000}<LSEP>[argument 10; litteral](real){1.000000}<LSEP>[argument 11; litteral](real){0.000000}<LSEP>[argument 12; litteral](real){0.000000}<LSEP>[argument 13; litteral](real){0.000000}<LSEP>[argument 14; litteral](real){0.000000}<LSEP>[argument 15; litteral](real){1.000000}<LEND>[argument 1; litteral](real){4.000000}<LSEP>[argument 2; litteral](real){4.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){inits}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.000000}<LEND>[statement 14; assign](){=}<LSEP>[](symbol){param}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mu1}<LSEP>[argument 1; litteral](str){mu2}<LSEP>[argument 2; litteral](str){Omega1}<LSEP>[argument 3; litteral](str){Omega2}<LSEP>[argument 4; litteral](str){Sigma1}<LSEP>[argument 5; litteral](str){Sigma2}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){v1.sim.mvncov}<LEND>[call](){}<LSEP>[](symbol){jags}<LSEP>[](symbol){mvncovardata}<LSEP>[](symbol){inits}<LSEP>[](symbol){mvncov}<LSEP>[](symbol){param}<LSEP>[](symbol){chains}<LSEP>[](symbol){iter}<LEND>[argument 6; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){iter}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){mvncovar1out}<LSEP>[](symbol){v1.sim.mvncov}<LEND>[statement 17; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){mvncovar1out}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){utils}<LSEP>[](symbol){globalVariables}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){N2}<LSEP>[argument 1; litteral](str){M2}<LSEP>[argument 2; litteral](str){beta3}<LSEP>[argument 3; litteral](str){beta2}<LSEP>[argument 4; litteral](str){beta4}<LSEP>[argument 5; litteral](str){age}<LSEP>[argument 6; litteral](str){inverse}<LSEP>[argument 7; litteral](str){Omega2}<LSEP>[argument 8; litteral](str){N1}<LSEP>[argument 9; litteral](str){M1}<LSEP>[argument 10; litteral](str){beta1}<LSEP>[argument 11; litteral](str){Omega1}<LSEP>[argument 12; litteral](str){Gender}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){mvncovar2}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){m}<LSEP>[](symbol){n}<LSEP>[](symbol){time}<LSEP>[](symbol){group}<LSEP>[](symbol){chains}<LSEP>[](symbol){iter}<LSEP>[](symbol){data}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){timepoints}<LSEP>[](symbol){time}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){gendergrp}<LSEP>[](symbol){group}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){covar2mod}<LEND>[](){function}<LSEP>[parameters; litteral](NULL){NULL}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){dnorm}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 1; call](){}<LSEP>[](symbol){~}<LSEP>[](symbol){beta2}<LEND>[argument 1; call](){}<LSEP>[](symbol){dnorm}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.001000}<LEND>[statement 2; 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block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mu2}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta2}<LSEP>[](symbol){beta4}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){age}<LSEP>[](symbol){j}<LEND>[statement 5; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega2}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 1; call](){}<LSEP>[](symbol){dwish}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){R}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 6; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma2}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[call](){}<LSEP>[](symbol){inverse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega2}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 7; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){N1}<LEND>[body; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Z}<LSEP>[](symbol){i}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 1; call](){}<LSEP>[](symbol){dmnorm}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mu1}<LSEP>[](symbol){}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 8; control flow](){for}<LSEP>[](symbol){j}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){mu1}<LSEP>[](symbol){j}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta}<LEND>[argument 1; call](){}<LSEP>[](symbol){}<LSEP>[](symbol){beta2}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){age}<LSEP>[](symbol){j}<LEND>[statement 9; call](){}<LSEP>[](symbol){~}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M1}<LEND>[argument 1; call](){}<LSEP>[](symbol){dwish}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){R}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[argument 1; litteral](real){4.000000}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Sigma1}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[argument 2; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){M2}<LEND>[call](){}<LSEP>[](symbol){inverse}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){Omega1}<LSEP>[](symbol){}<LSEP>[](symbol){}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){delta}<LEND>[call](){}<LSEP>[](symbol){+}<LSEP>[](symbol){beta2}<LSEP>[](symbol){beta4}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){datam}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){gendergrp}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){dataf}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){data}<LEND>[argument 1; 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litteral](str){slurm}<LSEP>[argument 2; litteral](NULL){NULL}<LSEP>[argument 3; litteral](NULL){NULL}<LSEP>[argument 4; litteral](NULL){NULL}<LEND>[argument 5; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](str){}<LEND>[argument 6; litteral](str){R}<LSEP>[argument 7; litteral](NULL){NULL}<LSEP>[argument 8; litteral](str){ecFlow}<LSEP>[argument 9; litteral](NULL){NULL}<LSEP>[argument 10; litteral](NULL){NULL}<LSEP>[argument 11; litteral](str){01:00:00}<LSEP>[argument 12; litteral](real){6.000000}<LEND>[argument 13; call](){}<LSEP>[](symbol){list}<LSEP>[argument 0; litteral](str){}<LEND>[argument 14; litteral](logical){TRUE}<LSEP>[argument 15; litteral](real){10.000000}<LSEP>[argument 16; litteral](str){none}<LEND>[statement 18; control flow](){if}<LSEP>[](symbol){on_cluster}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.list}<LSEP>[](symbol){cluster}<LEND>[true branch; 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assign](){<-}<LSEP>[](symbol){cluster}<LSEP>[](symbol){default_cluster}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){remote_ecflow_suite_dir}<LSEP>[](symbol){ecflow_suite_dir}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){is_data_dir_shared}<LSEP>[litteral](logical){FALSE}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){is_ecflow_suite_dir_shared}<LSEP>[litteral](logical){FALSE}<LEND>[statement 24; control flow](){if}<LSEP>[](symbol){on_cluster}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){localhost_name}<LEND>[call](){}<LSEP>[](symbol){system}<LSEP>[argument 0; litteral](str){hostname -f}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 1; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){Sys.which}<LSEP>[argument 0; litteral](str){ecflow_client}<LEND>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){ecFlow must be installed in or...}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){queue_host}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){queue_host}<LSEP>[](symbol){localhost_name}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){queue_host}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){localhost}<LSEP>[argument 1; litteral](str){127.0.0.1}<LSEP>[](symbol){localhost_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LEND>[argument 0; call](){}<LSEP>[](symbol){paste0}<LSEP>[argument 0; litteral](str){^}<LSEP>[](symbol){localhost_name}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){queue_host}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){queue_host}<LSEP>[](symbol){localhost_name}<LEND>[statement 3; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){queue_type}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){slurm}<LSEP>[argument 1; litteral](str){pbs}<LSEP>[argument 2; litteral](str){lsf}<LSEP>[argument 3; litteral](str){host}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The only supported 'queue_type...}<LEND>[statement 4; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; 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control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){lib_dir}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The component 'lib_dir', of th...}<LSEP>[argument 1; litteral](str){a character string.}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.logical}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){bidirectional}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The component 'bidirectional' ...}<LEND>[statement 8; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){bidirectional}<LEND>[true branch; 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call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){r_module}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){r_module}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The component 'r_module' of th...}<LSEP>[argument 1; litteral](str){and contain no blank spaces.}<LEND>[statement 12; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){CDO_module}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; 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assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){r_module}<LEND>[call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){r_module}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){CDO_module}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){ecflow_module}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The component 'ecflow_module' ...}<LEND>[statement 14; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){ecflow_module}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LSEP>[argument 0; litteral](str){ }<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){ecflow_module}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){stop}<LSEP>[argument 0; litteral](str){The component 'ecflow_module' ...}<LSEP>[argument 1; litteral](str){one character, and contain no ...}<LEND>[statement 15; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){is.null}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; litteral](str){cores_per_job}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){cluster}<LSEP>[argument 1; 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call](){}<LSEP>[](symbol){options}<LSEP>[](symbol){oldw}<LEND>[statement 43; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){list.weis2}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){best.layout}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x1}<LEND>[call](){}<LSEP>[](symbol){merge}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){x2}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){x1}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){des}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){des}<LEND>[statement 2; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){y}<LEND>[](symbol){x}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){vw}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x1}<LEND>[argument 1; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x2}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){x3}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){apply}<LSEP>[](symbol){vw}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){abs}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){y}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){x4}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){vw}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){which}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){x3}<LEND>[argument 1; call](){}<LSEP>[](symbol){min}<LSEP>[](symbol){x3}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){as.vector}<LEND>[argument 0; call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){x4}<LEND>[statement 6; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){res}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.Random.seed}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](integer){403}<LSEP>[argument 1; litteral](integer){10}<LSEP>[argument 2; litteral](integer){568137784}<LSEP>[argument 3; litteral](integer){1476767515}<LSEP>[argument 4; litteral](integer){1179761785}<LSEP>[argument 5; litteral](integer){1103537352}<LEND>[argument 6; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){607255306}<LEND>[argument 7; litteral](integer){2065863985}<LSEP>[argument 8; litteral](integer){3442019}<LEND>[argument 9; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){2132719822}<LEND>[argument 10; litteral](integer){685150340}<LSEP>[argument 11; litteral](integer){1319955655}<LSEP>[argument 12; litteral](integer){869482397}<LSEP>[argument 13; litteral](integer){1187924756}<LEND>[argument 14; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](integer){1864001094}<LEND>[argument 15; litteral](integer){418672645}<LSEP>[argument 16; 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litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){rlnorm}<LSEP>[argument 0; litteral](real){10000.000000}<LSEP>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){bfd}<LEND>[call](){}<LSEP>[](symbol){benford}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){negative}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){test}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){list}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){Mean Mantissa}<LSEP>[argument 1; litteral](str){Var Mantissa}<LSEP>[argument 2; litteral](str){Ex. 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litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){bfd}<LEND>[call](){}<LSEP>[](symbol){benford}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){both}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 4; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LSEP>[argument 1; litteral](str){none}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_error}<LEND>[argument 0; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LSEP>[argument 1; litteral](str){xxx}<LEND>[statement 6; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mantissa}<LSEP>[argument 1; litteral](str){abs diff}<LSEP>[argument 2; litteral](str){second order}<LEND>[statement 7; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mantissa}<LSEP>[argument 1; litteral](str){abs diff}<LSEP>[argument 2; litteral](str){second order}<LSEP>[argument 3; litteral](str){summation}<LEND>[statement 8; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mantissa}<LSEP>[argument 1; litteral](str){abs diff}<LSEP>[argument 2; litteral](str){second order}<LSEP>[argument 3; litteral](str){summation}<LSEP>[argument 4; litteral](str){chi square}<LEND>[statement 9; call](){}<LSEP>[](symbol){plot}<LSEP>[](symbol){bfd}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){mantissa}<LSEP>[argument 1; litteral](str){abs diff}<LSEP>[argument 2; litteral](str){second order}<LSEP>[argument 3; litteral](str){summation}<LSEP>[argument 4; litteral](str){chi square}<LSEP>[argument 5; litteral](str){ex summation}<LEND>[statement 10; call](){}<LSEP>[](symbol){expect_that}<LSEP>[](symbol){bfd}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LEND>[argument 0; call](){}<LSEP>[](symbol){benford}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){both}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){Exact printing, this sould not...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[](symbol){skip_on_travis}<LEND>[statement 2; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){rlnorm}<LSEP>[argument 0; litteral](real){1000.000000}<LSEP>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){bfd}<LEND>[call](){}<LSEP>[](symbol){benford}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](str){both}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){print}<LEND>[call](){}<LSEP>[](symbol){capture.output}<LEND>[argument 0; call](){}<LSEP>[](symbol){print}<LSEP>[](symbol){bfd}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){test_print}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){}<LSEP>[argument 1; litteral](str){Benford object:}<LSEP>[argument 2; litteral](str){ }<LSEP>[argument 3; litteral](str){Data: data }<LSEP>[argument 4; litteral](str){Number of observations used = ...}<LSEP>[argument 5; litteral](str){Number of obs. for second orde...}<LSEP>[argument 6; litteral](str){First digits analysed = 2}<LSEP>[argument 7; litteral](str){}<LSEP>[argument 8; litteral](str){Mantissa: }<LSEP>[argument 9; litteral](str){}<LSEP>[argument 10; litteral](str){ Statistic Value}<LSEP>[argument 11; litteral](str){ Mean 0.476}<LSEP>[argument 12; litteral](str){ Var 0.084}<LSEP>[argument 13; litteral](str){ Ex.Kurtosis -1.205}<LSEP>[argument 14; litteral](str){ Skewness 0.076}<LSEP>[argument 15; litteral](str){}<LSEP>[argument 16; litteral](str){}<LSEP>[argument 17; litteral](str){The 5 largest deviations: }<LSEP>[argument 18; litteral](str){}<LSEP>[argument 19; litteral](str){ digits absolute.diff}<LSEP>[argument 20; litteral](str){1 10 13.61}<LSEP>[argument 21; litteral](str){2 18 12.52}<LSEP>[argument 22; litteral](str){3 31 9.21}<LSEP>[argument 23; litteral](str){4 11 9.21}<LSEP>[argument 24; litteral](str){5 15 8.03}<LSEP>[argument 25; litteral](str){}<LSEP>[argument 26; litteral](str){Stats:}<LSEP>[argument 27; litteral](str){}<LSEP>[argument 28; litteral](str){\tPearson's Chi-squared test}<LSEP>[argument 29; litteral](str){}<LSEP>[argument 30; litteral](str){data: data}<LSEP>[argument 31; litteral](str){X-squared = 83.095, df = 89, p...}<LSEP>[argument 32; litteral](str){}<LSEP>[argument 33; litteral](str){}<LSEP>[argument 34; litteral](str){\tMantissa Arc Test}<LSEP>[argument 35; litteral](str){}<LSEP>[argument 36; litteral](str){data: data}<LSEP>[argument 37; litteral](str){L2 = 0.0013529, df = 2, p-valu...}<LSEP>[argument 38; litteral](str){}<LSEP>[argument 39; litteral](str){Mean Absolute Deviation (MAD):...}<LSEP>[argument 40; litteral](str){MAD Conformity - Nigrini (2012...}<LSEP>[argument 41; litteral](str){Distortion Factor: -6.228274}<LSEP>[argument 42; litteral](str){}<LSEP>[argument 43; litteral](str){Remember: Real data will never...}<LEND>[statement 8; call](){}<LSEP>[](symbol){expect_that}<LSEP>[](symbol){print}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LSEP>[](symbol){test_print}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){Regular printing -- no compari...}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){rlnorm}<LSEP>[argument 0; litteral](real){1000.000000}<LSEP>[argument 1; litteral](real){10.000000}<LSEP>[argument 2; litteral](real){10.000000}<LEND>[statement 2; 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[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){benford.analysis}<LEND>[call](){}<LSEP>[](symbol){context}<LSEP>[argument 0; litteral](str){Extracting Digits}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){Exctracting digits from made u...}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){213.000000}<LSEP>[argument 1; litteral](real){65468.000000}<LSEP>[argument 2; litteral](real){878942.000000}<LSEP>[argument 3; litteral](real){132456.000000}<LSEP>[argument 4; litteral](real){6878.000000}<LSEP>[argument 5; litteral](real){32132.000000}<LSEP>[argument 6; litteral](real){45665.000000}<LSEP>[argument 7; litteral](real){41656.000000}<LSEP>[argument 8; litteral](real){138744.000000}<LSEP>[argument 9; litteral](real){23465.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){digits1}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; 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litteral](real){6878.000000}<LSEP>[argument 5; litteral](real){3213.000000}<LSEP>[argument 6; litteral](real){4566.000000}<LSEP>[argument 7; litteral](real){4165.000000}<LSEP>[argument 8; litteral](real){1387.000000}<LSEP>[argument 9; litteral](real){2346.000000}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){as.integer}<LSEP>[](symbol){data}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){digits3}<LEND>[call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){extract.digits}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](real){3.000000}<LEND>[](symbol){data.digits}<LEND>[statement 11; call](){}<LSEP>[](symbol){expect_that}<LSEP>[](symbol){digits3}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){213.000000}<LSEP>[argument 1; litteral](real){654.000000}<LSEP>[argument 2; litteral](real){878.000000}<LSEP>[argument 3; litteral](real){132.000000}<LSEP>[argument 4; litteral](real){687.000000}<LSEP>[argument 5; litteral](real){321.000000}<LSEP>[argument 6; litteral](real){456.000000}<LSEP>[argument 7; litteral](real){416.000000}<LSEP>[argument 8; litteral](real){138.000000}<LSEP>[argument 9; litteral](real){234.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){set.seed}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){rnorm}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){rd1}<LEND>[call](){}<LSEP>[](symbol){extract.digits}<LSEP>[](symbol){x}<LEND>[statement 15; call](){}<LSEP>[](symbol){expect_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rd1}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){rd2}<LEND>[call](){}<LSEP>[](symbol){extract.digits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](str){negative}<LEND>[statement 17; call](){}<LSEP>[](symbol){expect_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rd2}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){<}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[statement 18; assign](){<-}<LSEP>[](symbol){rd3}<LEND>[call](){}<LSEP>[](symbol){extract.digits}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){FALSE}<LEND>[statement 19; call](){}<LSEP>[](symbol){expect_that}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){rd3}<LEND>[argument 1; call](){}<LSEP>[](symbol){equals}<LEND>[argument 0; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){DF}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){data}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){data}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){>=}<LSEP>[](symbol){data}<LSEP>[argument 1; litteral](real){10.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){collapsed}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LSEP>[](symbol){data}<LEND>[argument 1; call](){}<LSEP>[](symbol){^}<LSEP>[argument 0; litteral](real){10.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){trunc}<LEND>[argument 0; call](){}<LSEP>[](symbol){log10}<LSEP>[](symbol){data}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){DF}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; 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[](){expression}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}<LSEP>[litteral](NULL){NULL}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){VERSION}<LEND>[call](){}<LSEP>[](symbol){commandArgs}<LSEP>[argument 0; litteral](logical){TRUE}<LEND>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.exists}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){../windows/rsvg-%s/include/lib...}<LSEP>[](symbol){VERSION}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<}<LEND>[argument 0; call](){}<LSEP>[](symbol){getRversion}<LEND>[argument 1; litteral](str){3.3.0}<LEND>[true branch; call](){}<LSEP>[](symbol){setInternet2}<LEND>[statement 1; call](){}<LSEP>[](symbol){download.file}<LEND>[argument 0; call](){}<LSEP>[](symbol){sprintf}<LSEP>[argument 0; litteral](str){https://github.com/rwinlib/rsv...}<LSEP>[](symbol){VERSION}<LEND>[argument 1; litteral](str){lib.zip}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[statement 2; call](){}<LSEP>[](symbol){dir.create}<LSEP>[argument 0; litteral](str){../windows}<LSEP>[argument 1; litteral](logical){FALSE}<LEND>[statement 3; call](){}<LSEP>[](symbol){unzip}<LSEP>[argument 0; litteral](str){lib.zip}<LSEP>[argument 1; litteral](str){../windows}<LEND>[statement 4; call](){}<LSEP>[](symbol){unlink}<LSEP>[argument 0; litteral](str){lib.zip}
[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){rsvg}
[](){expression}<LSEP>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){spelling}<LSEP>[](symbol){spell_check_test}<LEND>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](logical){FALSE}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){rsvg}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){svg}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){css}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){rsvg_raw}<LSEP>[](symbol){svg}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){css}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){out}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.numeric}<LSEP>[](symbol){out}<LEND>[argument 1; litteral](real){255.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){dim}<LSEP>[](symbol){out}<LEND>[statement 2; call](){}<LSEP>[](symbol){aperm}<LSEP>[](symbol){out}<LEND>[assign](){<-}<LSEP>[](symbol){rsvg_raw}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){svg}<LSEP>[](symbol){width}<LSEP>[](symbol){height}<LSEP>[](symbol){css}<LEND>[body; block](){}<LSEP>[statement 0; 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[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){SportsAnalytics}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){archetypes}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){RColorBrewer}<LEND>[assign](){<-}<LSEP>[](symbol){col_pal}<LEND>[call](){}<LSEP>[](symbol){brewer.pal}<LSEP>[argument 0; litteral](real){7.000000}<LSEP>[argument 1; litteral](str){Set1}<LEND>[assign](){<-}<LSEP>[](symbol){col_black}<LEND>[call](){}<LSEP>[](symbol){rgb}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.200000}<LEND>[call](){}<LSEP>[](symbol){data}<LSEP>[argument 0; litteral](str){EURO4PlayerSkillsSep11}<LEND>[assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){EURO4PlayerSkillsSep11}<LEND>[argument 1; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){Position}<LSEP>[argument 1; 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[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){SportsAnalytics}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){archetypes}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){RColorBrewer}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[argument 0; litteral](str){vcd}<LEND>[assign](){<-}<LSEP>[](symbol){col_pal}<LEND>[call](){}<LSEP>[](symbol){brewer.pal}<LSEP>[argument 0; litteral](real){7.000000}<LSEP>[argument 1; litteral](str){Set1}<LEND>[assign](){<-}<LSEP>[](symbol){col_black}<LEND>[call](){}<LSEP>[](symbol){rgb}<LSEP>[argument 0; litteral](real){0.000000}<LSEP>[argument 1; litteral](real){0.000000}<LSEP>[argument 2; litteral](real){0.000000}<LSEP>[argument 3; litteral](real){0.200000}<LEND>[call](){}<LSEP>[](symbol){data}<LSEP>[argument 0; litteral](str){NBAPlayerStatistics0910}<LEND>[assign](){<-}<LSEP>[](symbol){dat}<LEND>[call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){NBAPlayerStatistics0910}<LEND>[argument 1; 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litteral](str){TotalMinutesPlayed}<LSEP>[argument 6; litteral](str){FieldGoalsMade}<LSEP>[argument 7; litteral](str){FieldGoalsAttempted}<LSEP>[argument 8; litteral](str){ThreesMade}<LSEP>[argument 9; litteral](str){ThreesAttempted}<LSEP>[argument 10; litteral](str){FreeThrowsMade}<LSEP>[argument 11; litteral](str){FreeThrowsAttempted}<LSEP>[argument 12; litteral](str){OffensiveRebounds}<LSEP>[argument 13; litteral](str){TotalRebounds}<LSEP>[argument 14; litteral](str){Assists}<LSEP>[argument 15; litteral](str){Steals}<LSEP>[argument 16; litteral](str){Turnovers}<LSEP>[argument 17; litteral](str){Blocks}<LSEP>[argument 18; litteral](str){PersonalFouls}<LSEP>[argument 19; litteral](str){Disqualifications}<LSEP>[argument 20; litteral](str){TotalPoints}<LSEP>[argument 21; litteral](str){Technicals}<LSEP>[argument 22; litteral](str){Ejections}<LSEP>[argument 23; litteral](str){FlagrantFouls}<LSEP>[argument 24; litteral](str){GamesStarted}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){herfindahl}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){^}<LEND>[argument 0; call](){}<LSEP>[](symbol){sumex}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){x}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){y}<LEND>[](symbol){y}<LEND>[assign](){<-}<LSEP>[](symbol){rosenbluth}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sumex}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LSEP>[](symbol){x}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[](symbol){y}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[assign](){<-}<LSEP>[](symbol){exogeny}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ex}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){n}<LEND>[call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){x}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sumex}<LSEP>[](symbol){x}<LSEP>[](symbol){ex}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){n}<LEND>[](symbol){y}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){}<LSEP>[argument 0; litteral](real){2.000000}<LSEP>[](symbol){y}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){y}<LEND>[assign](){<-}<LSEP>[](symbol){concentration_ratio}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){g}<LSEP>[](symbol){ex}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sumex}<LSEP>[](symbol){x}<LSEP>[](symbol){ex}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){y}<LEND>[call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){y}<LEND>[argument 1; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[](symbol){g}<LEND>[](symbol){y}<LEND>[assign](){<-}<LSEP>[](symbol){sumex}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){ex}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){x}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){x}<LSEP>[](symbol){ex}<LEND>[statement 1; call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LSEP>[](symbol){x}
[](){expression}<LSEP>[control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){requireNamespace}<LSEP>[argument 0; litteral](str){spelling}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){spelling}<LSEP>[](symbol){spell_check_test}<LEND>[argument 0; litteral](logical){TRUE}<LSEP>[argument 1; litteral](logical){TRUE}<LSEP>[argument 2; litteral](logical){TRUE}
[](){expression}<LSEP>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){testthat}<LEND>[call](){}<LSEP>[](symbol){library}<LSEP>[](symbol){rwhatsapp}<LEND>[call](){}<LSEP>[](symbol){test_check}<LSEP>[argument 0; litteral](str){rwhatsapp}
[](){expression}<LSEP>[call](){}<LSEP>[](symbol){context}<LSEP>[argument 0; litteral](str){test-rwhatsapp}<LEND>[assign](){<-}<LSEP>[](symbol){history}<LEND>[call](){}<LSEP>[](symbol){system.file}<LSEP>[argument 0; litteral](str){extdata}<LSEP>[argument 1; litteral](str){sample.txt}<LSEP>[argument 2; litteral](str){rwhatsapp}<LEND>[assign](){<-}<LSEP>[](symbol){converted}<LEND>[call](){}<LSEP>[](symbol){structure}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){1499898922.226000}<LSEP>[argument 1; litteral](real){1499937164.226000}<LEND>[argument 1; litteral](str){GMT}<LEND>[argument 2; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){POSIXct}<LSEP>[argument 1; litteral](str){POSIXt}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){rwa_read structure}<LEND>[argument 1; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){df}<LEND>[call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.2017, 10:35:22 PM - Joha...}<LSEP>[argument 1; litteral](str){13.07.2017, 09:12:44 AM - R: Y...}<LEND>[statement 1; call](){}<LSEP>[](symbol){expect_s3_class}<LSEP>[](symbol){df}<LSEP>[argument 1; litteral](str){tbl_df}<LEND>[statement 2; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){ncol}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](integer){6}<LEND>[statement 3; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){df}<LEND>[argument 1; litteral](integer){2}<LEND>[statement 4; call](){}<LSEP>[](symbol){expect_s3_class}<LEND>[argument 0; call](){}<LSEP>[](symbol){lookup_emoji}<LEND>[argument 0; call](){}<LSEP>[](symbol){subset}<LSEP>[](symbol){df}<LSEP>[](symbol){text}<LEND>[argument 1; litteral](str){tbl_df}<LEND>[call](){}<LSEP>[](symbol){test_that}<LSEP>[argument 0; litteral](str){time is converted correctly}<LEND>[argument 1; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){skip_on_cran}<LEND>[statement 1; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.2017, 10:35:22 PM - Joha...}<LSEP>[argument 1; litteral](str){13.07.2017, 09:12:44 AM - R: Y...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 2; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.2017, 10:35 PM - Johanne...}<LSEP>[argument 1; litteral](str){13.07.2017, 09:12 AM - R: Yes,...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 3; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.2017, 22:35:22 - Johanne...}<LSEP>[argument 1; litteral](str){13.07.2017, 09:12:44 - R: Yes,...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 4; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.2017, 22:35 - Johannes G...}<LSEP>[argument 1; litteral](str){13.07.2017, 09:12 - R: Yes, it...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 5; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.2017, 10:35:22 PM - Joha...}<LSEP>[argument 1; litteral](str){07.13.2017, 09:12:44 AM - R: Y...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 6; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.2017, 10:35 PM - Johanne...}<LSEP>[argument 1; litteral](str){07.13.2017, 09:12 AM - R: Yes,...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 7; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.2017, 22:35:22 - Johanne...}<LSEP>[argument 1; litteral](str){07.13.2017, 09:12:44 - R: Yes,...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 8; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.2017, 22:35 - Johannes G...}<LSEP>[argument 1; litteral](str){07.13.2017, 09:12 - R: Yes, it...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 9; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.17, 10:35:22 PM - Johann...}<LSEP>[argument 1; litteral](str){13.07.17, 09:12:44 AM - R: Yes...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 10; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.17, 10:35 PM - Johannes ...}<LSEP>[argument 1; litteral](str){13.07.17, 09:12 AM - R: Yes, i...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 11; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.17, 22:35:22 - Johannes ...}<LSEP>[argument 1; litteral](str){13.07.17, 09:12:44 - R: Yes, i...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 12; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){12.07.17, 22:35 - Johannes Gru...}<LSEP>[argument 1; litteral](str){13.07.17, 09:12 - R: Yes, it was}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 13; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.17, 10:35:22 PM - Johann...}<LSEP>[argument 1; litteral](str){07.13.17, 09:12:44 AM - R: Yes...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 14; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.17, 10:35 PM - Johannes ...}<LSEP>[argument 1; litteral](str){07.13.17, 09:12 AM - R: Yes, i...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){60.000000}<LEND>[statement 15; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){07.12.17, 22:35:22 - Johannes ...}<LSEP>[argument 1; litteral](str){07.13.17, 09:12:44 - R: Yes, i...}<LEND>[argument 1; litteral](str){GMT}<LEND>[](symbol){time}<LEND>[](symbol){converted}<LSEP>[argument 2; litteral](real){5.000000}<LEND>[statement 16; call](){}<LSEP>[](symbol){expect_equal}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){rwa_read}<LEND>[argument 0; 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litteral](str){SYNEQFF}<LSEP>[argument 5; litteral](str){SYEQYF}<LSEP>[argument 6; litteral](str){F}<LEND>[false branch; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){species}<LSEP>[argument 1; litteral](str){mm}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){receptor}<LSEP>[argument 1; litteral](str){tr}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){common_frameshifts}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){AVF}<LSEP>[argument 1; litteral](str){LVL}<LSEP>[argument 2; litteral](str){PVL}<LSEP>[argument 3; litteral](str){ALF}<LSEP>[argument 4; litteral](str){IIF}<LSEP>[argument 5; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){check_within_cdr3}<LSEP>[litteral](str){\\\\}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jct_correction}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){QNTLYF}<LSEP>[argument 1; litteral](str){GSYEQYF}<LSEP>[argument 2; litteral](str){TEVFF}<LSEP>[argument 3; litteral](str){YAEQFF}<LSEP>[argument 4; litteral](str){DTQYF}<LSEP>[argument 5; litteral](str){EQYF}<LSEP>[argument 6; litteral](str){NYAEQFF}<LSEP>[argument 7; litteral](str){SYEQYF}<LSEP>[argument 8; litteral](str){YEQYF}<LSEP>[argument 9; litteral](str){F}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){common_frameshifts}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){check_within_cdr3}<LSEP>[litteral](str){\\\\}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){jct_correction}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){count}<LSEP>[](symbol){number_of_simulated_seqs}<LEND>[statement 14; control flow](){while}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){0.000000}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){count}<LSEP>[](symbol){number_of_seqs}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){number_of_seqs}<LSEP>[](symbol){count}<LEND>[](symbol){freq_update_time}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){VDJ_used}<LSEP>[](symbol){vdj_used}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){vdj_list}<LEND>[call](){}<LSEP>[](symbol){.update_vdj_freqs}<LSEP>[](symbol){vdj_list_ref}<LSEP>[](symbol){vdj_used}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sample_insertions_and_deletion_lengths}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){insertions_and_deletion_lengths}<LEND>[argument 1; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){nrow}<LSEP>[](symbol){insertions_and_deletion_lengths}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){sample_insertions}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sample_insertions_and_deletion_lengths}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){n1}<LSEP>[argument 1; litteral](str){n2}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){sample_deletions}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){sample_insertions_and_deletion_lengths}<LEND>[argument 1; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){del_v}<LSEP>[argument 1; litteral](str){del_d_5}<LSEP>[argument 2; litteral](str){del_d_3}<LSEP>[argument 3; litteral](str){del_j}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){sampled_v_name}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){vdj_list}<LSEP>[](symbol){V}<LEND>[](symbol){gene}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](logical){TRUE}<LEND>[argument 3; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){vdj_list}<LSEP>[](symbol){V}<LEND>[](symbol){frequency}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){sampled_v_seq_raw}<LEND>[call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){vdj_list}<LSEP>[](symbol){V}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){vdj_list}<LSEP>[](symbol){V}<LEND>[](symbol){gene}<LEND>[](symbol){sampled_v_name}<LEND>[argument 2; litteral](str){sequence}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; 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call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){sequencesim}<LEND>[argument 1; litteral](real){3.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){sequencesim}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){sequencesim}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){sequencesim}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){sequencesim_aa}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){Biostrings}<LSEP>[](symbol){translate}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){Biostrings}<LSEP>[](symbol){DNAStringSet}<LEND>[](symbol){sequencesim}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){p}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){curr_seq}<LSEP>[](symbol){sequencesim_aa}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){curr_seq_nt}<LSEP>[](symbol){sequencesim}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){curr_jct}<LEND>[call](){}<LSEP>[](symbol){tryCatch}<LEND>[argument 0; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){Biostrings}<LSEP>[](symbol){translate}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){Biostrings}<LSEP>[](symbol){DNAStringSet}<LEND>[](symbol){cdr3_found_tmp}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){e}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){p}<LSEP>[litteral](str){}<LEND>[statement 1; call](){}<LSEP>[](symbol){return}<LSEP>[](symbol){p}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){anchor_end}<LEND>[call](){}<LSEP>[](symbol){sample}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){W}<LSEP>[argument 1; litteral](str){F}<LEND>[statement 6; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){%in%}<LSEP>[argument 0; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){strsplit}<LEND>[](symbol){sequencesim_aa}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){locations_beg}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_locate_all}<LEND>[](symbol){curr_seq_nt}<LSEP>[](symbol){cdr3_found_tmp}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){locations_beg_aa}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_locate_all}<LEND>[](symbol){curr_seq}<LSEP>[](symbol){curr_jct}<LEND>[statement 2; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){locations_beg_aa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){cdr3_to_end}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){curr_seq_nt}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){locations_beg}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){start}<LEND>[argument 2; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){curr_seq_nt}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){cdr3_to_end_aa}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){curr_seq}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){locations_beg_aa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](str){start}<LEND>[argument 2; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){curr_seq}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){res}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){anchor_end}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){stringr}<LSEP>[](symbol){str_match}<LEND>[](symbol){cdr3_to_end_aa}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){cdr3_to_end_aa}<LSEP>[argument 1; litteral](real){1.000000}<LSEP>[argument 2; litteral](real){3.000000}<LEND>[argument 1; litteral](str){(.?)}<LEND>[argument 2; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){anchor_end}<LSEP>[](symbol){x}<LEND>[argument 3; litteral](str){}<LEND>[argument 1; litteral](real){1.000000}<LSEP>[](symbol){}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){cdr3_found_aa}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){res}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){res}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 4; assign](){<-}<LSEP>[](symbol){end_cdr3_to_end_aa}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){strsplit}<LEND>[](symbol){cdr3_to_end_aa}<LSEP>[](symbol){cdr3_found_aa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){find_jct_correction}<LEND>[call](){}<LSEP>[](symbol){sapply}<LEND>[argument 0; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){jct_correction}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LEND>[body; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){end_cdr3_to_end_aa}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){jct_correction}<LSEP>[](symbol){x}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){jct_correction}<LSEP>[](symbol){x}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){add_jct_corr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){jct_correction}<LSEP>[](symbol){find_jct_correction}<LEND>[statement 7; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){>}<LEND>[argument 0; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){add_jct_corr}<LEND>[argument 1; litteral](real){1.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){corr_ordered_by_length}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){add_jct_corr}<LEND>[argument 1; call](){}<LSEP>[](symbol){order}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){add_jct_corr}<LEND>[](symbol){add_jct_corr}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){add_jct_corr}<LEND>[call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){corr_ordered_by_length}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){corr_ordered_by_length}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){cdr3_found_aa}<LEND>[call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){cdr3_found_aa}<LSEP>[](symbol){add_jct_corr}<LSEP>[argument 2; litteral](str){}<LEND>[statement 9; assign](){<-}<LSEP>[](symbol){cdr3_found_nt}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){substr}<LEND>[](symbol){cdr3_to_end}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[](symbol){*}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){cdr3_found_aa}<LEND>[argument 1; litteral](real){3.000000}<LEND>[statement 10; assign](){<-}<LSEP>[](symbol){post_cdr3_j}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){strsplit}<LEND>[](symbol){curr_seq}<LSEP>[](symbol){cdr3_found_aa}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 1; litteral](real){2.000000}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){frameshifted_cdr3}<LSEP>[litteral](logical){FALSE}<LEND>[statement 12; control flow](){for}<LSEP>[](symbol){y}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){check_within_cdr3}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){\|}<LEND>[argument 0; call](){}<LSEP>[](symbol){grepl}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){check_within_cdr3}<LSEP>[](symbol){y}<LEND>[](symbol){cdr3_found_aa}<LEND>[argument 1; call](){}<LSEP>[](symbol){grepl}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){check_within_cdr3}<LSEP>[](symbol){y}<LEND>[](symbol){post_cdr3_j}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){frameshifted_cdr3}<LSEP>[litteral](logical){TRUE}<LEND>[statement 13; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){&}<LEND>[argument 0; call](){}<LSEP>[](symbol){!}<LEND>[argument 0; call](){}<LSEP>[](symbol){is.na}<LSEP>[](symbol){cdr3_found_aa}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){>=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){cdr3_found_aa}<LEND>[](symbol){min_cdr3_length}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){<=}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){cdr3_found_aa}<LEND>[](symbol){max_cdr3_length}<LEND>[argument 1; call](){}<LSEP>[](symbol){!}<LSEP>[](symbol){frameshifted_cdr3}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){!=}<LSEP>[](symbol){cat_threshold}<LSEP>[argument 1; litteral](real){inf}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){%%}<LEND>[argument 0; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){number_of_seqs}<LSEP>[](symbol){count}<LEND>[argument 1; litteral](real){1.000000}<LEND>[](symbol){cat_threshold}<LEND>[argument 1; litteral](real){0.000000}<LEND>[true branch; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){simulated sequences:}<LEND>[argument 1; call](){}<LSEP>[](symbol){(}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){number_of_seqs}<LSEP>[](symbol){count}<LEND>[argument 1; litteral](real){1.000000}<LEND>[argument 2; litteral](str){\n}<LEND>[statement 1; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){simulated_seqs}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){sequencesim}<LSEP>[](symbol){sequencesim_aa}<LSEP>[](symbol){cdr3_found_nt}<LSEP>[](symbol){cdr3_found_aa}<LSEP>[](symbol){sampled_v_name}<LSEP>[](symbol){sampled_d_name}<LSEP>[](symbol){sampled_j_name}<LSEP>[](symbol){sampled_n1}<LSEP>[](symbol){sampled_n2}<LEND>[argument 9; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sample_deletions}<LSEP>[](symbol){del_v}<LEND>[argument 10; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sample_deletions}<LSEP>[](symbol){del_d_5}<LEND>[argument 11; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sample_deletions}<LSEP>[](symbol){del_d_3}<LEND>[argument 12; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){sample_deletions}<LSEP>[](symbol){del_j}<LEND>[argument 13; call](){}<LSEP>[](symbol){substr}<LSEP>[](symbol){sampled_v_seq}<LEND>[argument 1; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){pos_start_end_v}<LSEP>[argument 1; litteral](str){start}<LEND>[argument 2; call](){}<LSEP>[](symbol){nchar}<LSEP>[](symbol){sampled_v_seq}<LEND>[](symbol){sampled_d_seq}<LEND>[argument 15; call](){}<LSEP>[](symbol){paste}<LSEP>[](symbol){sampled_j_seq_pre_anchor}<LSEP>[](symbol){chosen_anchor_j}<LSEP>[argument 2; litteral](str){}<LEND>[argument 16; litteral](logical){NA}<LSEP>[argument 17; litteral](logical){NA}<LSEP>[](symbol){shm_record_out}<LSEP>[](symbol){name_repertoire}<LEND>[statement 2; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){vdj_used}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){data.frame}<LSEP>[](symbol){sampled_v_name}<LSEP>[](symbol){sampled_d_name}<LSEP>[](symbol){sampled_j_name}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){count}<LEND>[call](){}<LSEP>[](symbol){-}<LSEP>[](symbol){count}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 15; assign](){<-}<LSEP>[](symbol){simulated_seqs_datatable}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){data.table}<LSEP>[](symbol){rbindlist}<LEND>[](symbol){simulated_seqs}<LEND>[statement 16; assign](){<-}<LSEP>[](symbol){simulated_seqs_df}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){data.table}<LSEP>[](symbol){setDF}<LEND>[](symbol){simulated_seqs_datatable}<LEND>[](symbol){simulated_seqs_df}
[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){.plot_report_repertoire_AA_freq_comparative}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repertoire_seqs}<LSEP>[](symbol){repertoire_name}<LSEP>[](symbol){freqs_input}<LSEP>[](symbol){reference_name}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){darken_color}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){color}<LSEP>[](symbol){factor}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){col2rgb}<LEND>[](symbol){color}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){col}<LSEP>[](symbol){factor}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){rgb}<LEND>[argument 0; call](){}<LSEP>[](symbol){t}<LSEP>[](symbol){col}<LEND>[argument 1; litteral](real){255.000000}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){colorset}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){#a6cee3}<LSEP>[argument 1; litteral](str){#1f78b4}<LSEP>[argument 2; litteral](str){#b2df8a}<LSEP>[argument 3; litteral](str){#33a02c}<LSEP>[argument 4; litteral](str){#fb9a99}<LSEP>[argument 5; litteral](str){#e31a1c}<LSEP>[argument 6; litteral](str){#fdbf6f}<LSEP>[argument 7; litteral](str){#ff7f00}<LSEP>[argument 8; litteral](str){#cab2d6}<LSEP>[argument 9; litteral](str){#6a3d9a}<LSEP>[argument 10; litteral](str){#8dd3c7}<LSEP>[argument 11; litteral](str){#ffffb3}<LSEP>[argument 12; litteral](str){#bebada}<LSEP>[argument 13; litteral](str){#fb8072}<LSEP>[argument 14; litteral](str){#80b1d3}<LSEP>[argument 15; litteral](str){#fdb462}<LSEP>[argument 16; litteral](str){#b3de69}<LSEP>[argument 17; litteral](str){#fccde5}<LSEP>[argument 18; litteral](str){#d9d9d9}<LSEP>[argument 19; litteral](str){#bc80bd}<LSEP>[argument 20; litteral](str){black}<LEND>[statement 2; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){hub_seqs_exclusion}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){top_x}<LSEP>[](symbol){report}<LSEP>[](symbol){output_dir}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){output_dir}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wd}<LEND>[call](){}<LSEP>[](symbol){tempdir}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wd}<LSEP>[](symbol){output_dir}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){CDR3s}<LEND>[call](){}<LSEP>[](symbol){unique}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){junction_aa}<LEND>[statement 2; assign](){<-}<LSEP>[](symbol){similarity}<LSEP>[litteral](real){1.000000}<LEND>[statement 3; 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[](){expression}<LSEP>[assign](){<-}<LSEP>[](symbol){plot_report_repertoire}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){output_dir}<LSEP>[](symbol){verbose}<LEND>[body; block](){}<LSEP>[statement 0; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){output_dir}<LSEP>[argument 1; litteral](str){}<LEND>[true branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wd}<LEND>[call](){}<LSEP>[](symbol){tempdir}<LEND>[false branch; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){wd}<LSEP>[](symbol){output_dir}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){darken_color}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){color}<LSEP>[](symbol){factor}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){col2rgb}<LEND>[](symbol){color}<LEND>[statement 1; assign](){<-}<LSEP>[](symbol){col}<LEND>[call](){}<LSEP>[](symbol){/}<LSEP>[](symbol){col}<LSEP>[](symbol){factor}<LEND>[statement 2; 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litteral](str){#fdb462}<LSEP>[argument 16; litteral](str){#b3de69}<LSEP>[argument 17; litteral](str){#fccde5}<LSEP>[argument 18; litteral](str){#d9d9d9}<LSEP>[argument 19; litteral](str){#bc80bd}<LSEP>[argument 20; litteral](str){black}<LEND>[statement 3; assign](){<-}<LSEP>[](symbol){color_list}<LEND>[call](){}<LSEP>[](symbol){list}<LEND>[statement 4; control flow](){for}<LSEP>[](symbol){i}<LEND>[range; call](){}<LSEP>[](symbol){:}<LSEP>[argument 0; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){length}<LSEP>[](symbol){colorset}<LEND>[body; block](){}<LSEP>[statement 0; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){color_list}<LSEP>[](symbol){i}<LEND>[call](){}<LSEP>[](symbol){darken_color}<LEND>[argument 0; call](){}<LSEP>[](symbol){[}<LSEP>[](symbol){colorset}<LSEP>[](symbol){i}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 5; assign](){<-}<LSEP>[](symbol){darkened_colors}<LEND>[call](){}<LSEP>[](symbol){unlist}<LSEP>[](symbol){color_list}<LEND>[statement 6; assign](){<-}<LSEP>[](symbol){name_rep}<LEND>[call](){}<LSEP>[](symbol){[[}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){name_repertoire}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 7; assign](){<-}<LSEP>[](symbol){lengths_rep}<LEND>[call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){sequence_aa}<LEND>[statement 8; assign](){<-}<LSEP>[](symbol){lengths_rep_df}<LEND>[call](){}<LSEP>[](symbol){as.data.frame}<LEND>[argument 0; call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){lengths_rep}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){lengths_rep}<LEND>[statement 9; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){names}<LSEP>[](symbol){lengths_rep_df}<LEND>[call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){length}<LSEP>[argument 1; litteral](str){freq}<LEND>[statement 10; assign](){<-}<LSEP>[variable; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lengths_rep_df}<LSEP>[](symbol){repertoire_name}<LEND>[](symbol){name_rep}<LEND>[statement 11; assign](){<-}<LSEP>[](symbol){maxlen_gen_in}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){max}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lengths_rep_df}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 12; assign](){<-}<LSEP>[](symbol){minlen_gen_in}<LEND>[call](){}<LSEP>[](symbol){-}<LEND>[argument 0; call](){}<LSEP>[](symbol){min}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.integer}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){lengths_rep_df}<LSEP>[](symbol){length}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 13; assign](){<-}<LSEP>[](symbol){length}<LEND>[assign](){<-}<LSEP>[](symbol){freq}<LEND>[assign](){<-}<LSEP>[](symbol){repertoire_name}<LSEP>[litteral](NULL){NULL}<LEND>[statement 14; assign](){<-}<LSEP>[](symbol){df_seq_length}<LEND>[call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[](symbol){+}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){ggplot}<LEND>[](symbol){lengths_rep_df}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[](symbol){length}<LSEP>[](symbol){freq}<LSEP>[](symbol){repertoire_name}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_bar}<LEND>[argument 0; litteral](str){identity}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){position_dodge}<LEND>[argument 0; litteral](real){0.900000}<LEND>[argument 2; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){geom_text}<LEND>[](symbol){lengths_rep_df}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){aes}<LEND>[argument 0; call](){}<LSEP>[](symbol){round}<LSEP>[](symbol){freq}<LSEP>[argument 1; litteral](real){2.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){-}<LSEP>[argument 0; litteral](real){0.700000}<LEND>[argument 2; litteral](str){black}<LEND>[argument 3; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){position_dodge}<LEND>[argument 0; litteral](real){0.900000}<LEND>[argument 4; litteral](str){bold}<LSEP>[argument 5; litteral](real){2.000000}<LSEP>[argument 6; litteral](logical){FALSE}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){theme_bw}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){labs}<LEND>[argument 0; litteral](str){Full VDJ length (a.a.)}<LSEP>[argument 1; litteral](str){Frequency [%]}<LSEP>[argument 2; litteral](str){}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){ggplot2}<LSEP>[](symbol){scale_fill_manual}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](str){black}<LEND>[argument 1; call](){}<LSEP>[](symbol){.theme.akbar}<LEND>[statement 15; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){pdf}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){wd}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){length_distribution_}<LSEP>[](symbol){name_rep}<LSEP>[argument 2; litteral](str){.pdf}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){Helvetica}<LSEP>[argument 2; litteral](real){8.000000}<LSEP>[argument 3; litteral](real){6.000000}<LEND>[statement 16; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){pushViewport}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){viewport}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.layout}<LEND>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){null}<LEND>[statement 17; assign](){<-}<LSEP>[](symbol){vplayout}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){viewport}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 18; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){print}<LEND>[](symbol){df_seq_length}<LEND>[argument 1; call](){}<LSEP>[](symbol){vplayout}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 19; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.off}<LEND>[statement 20; assign](){<-}<LSEP>[](symbol){lengths_cdr3_aa}<LEND>[call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){junction_aa}<LEND>[statement 21; assign](){<-}<LSEP>[](symbol){lengths_rep_df}<LEND>[call](){}<LSEP>[](symbol){/}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){lengths_cdr3_aa}<LEND>[argument 1; call](){}<LSEP>[](symbol){sum}<LEND>[argument 0; call](){}<LSEP>[](symbol){table}<LSEP>[](symbol){lengths_cdr3_aa}<LEND>[statement 22; assign](){<-}<LSEP>[](symbol){most_common_length}<LEND>[call](){}<LSEP>[](symbol){names}<LEND>[argument 0; call](){}<LSEP>[](symbol){tail}<LEND>[argument 0; call](){}<LSEP>[](symbol){sort}<LSEP>[](symbol){lengths_rep_df}<LEND>[argument 1; litteral](real){1.000000}<LEND>[statement 23; assign](){<-}<LSEP>[](symbol){repertoire_cdr3_len_14}<LEND>[call](){}<LSEP>[](symbol){[}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){junction_aa}<LEND>[argument 1; call](){}<LSEP>[](symbol){==}<LEND>[argument 0; call](){}<LSEP>[](symbol){nchar}<LEND>[argument 0; call](){}<LSEP>[](symbol){as.character}<LEND>[argument 0; call](){}<LSEP>[](symbol){$}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){junction_aa}<LEND>[](symbol){most_common_length}<LEND>[statement 24; assign](){<-}<LSEP>[](symbol){input_aa_freqs}<LEND>[call](){}<LSEP>[](symbol){.get_AA_freq_distribution}<LSEP>[](symbol){repertoire_cdr3_len_14}<LSEP>[](symbol){most_common_length}<LEND>[statement 25; assign](){<-}<LSEP>[](symbol){plots_aa_freq_list_imgt}<LEND>[call](){}<LSEP>[](symbol){.plot_report_repertoire_AA_freq}<LSEP>[](symbol){input_aa_freqs}<LSEP>[](symbol){name_rep}<LEND>[statement 26; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){pdf}<LEND>[argument 0; call](){}<LSEP>[](symbol){file.path}<LSEP>[](symbol){wd}<LEND>[argument 1; call](){}<LSEP>[](symbol){paste}<LSEP>[argument 0; litteral](str){aa_freq_}<LSEP>[](symbol){name_rep}<LSEP>[argument 2; litteral](str){.pdf}<LSEP>[argument 3; litteral](str){}<LEND>[argument 1; litteral](str){Helvetica}<LSEP>[argument 2; litteral](real){13.000000}<LSEP>[argument 3; litteral](real){10.000000}<LEND>[statement 27; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){pushViewport}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){viewport}<LEND>[argument 0; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){grid.layout}<LEND>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 2; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){unit}<LEND>[argument 0; call](){}<LSEP>[](symbol){c}<LSEP>[argument 0; litteral](real){0.500000}<LSEP>[argument 1; litteral](real){4.000000}<LEND>[argument 1; litteral](str){null}<LEND>[statement 28; assign](){<-}<LSEP>[](symbol){vplayout}<LEND>[](){function}<LSEP>[](pairlist){}<LSEP>[](symbol){x}<LSEP>[](symbol){y}<LEND>[body; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grid}<LSEP>[](symbol){viewport}<LEND>[](symbol){x}<LSEP>[](symbol){y}<LEND>[statement 29; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){base}<LSEP>[](symbol){print}<LEND>[argument 0; call](){}<LSEP>[](symbol){[[}<LSEP>[](symbol){plots_aa_freq_list_imgt}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[argument 1; call](){}<LSEP>[](symbol){vplayout}<LSEP>[argument 0; litteral](real){1.000000}<LSEP>[argument 1; litteral](real){1.000000}<LEND>[statement 30; call](){}<LSEP>[call name; call](){}<LSEP>[](symbol){::}<LSEP>[](symbol){grDevices}<LSEP>[](symbol){dev.off}<LEND>[statement 31; call](){}<LSEP>[](symbol){.plot_vdj_occ}<LSEP>[](symbol){repertoire}<LSEP>[](symbol){wd}<LEND>[statement 32; control flow](){if}<LSEP>[condition; call](){}<LSEP>[](symbol){==}<LSEP>[](symbol){verbose}<LSEP>[argument 1; litteral](logical){TRUE}<LEND>[true branch; block](){}<LSEP>[statement 0; call](){}<LSEP>[](symbol){cat}<LSEP>[argument 0; litteral](str){Plots saved in PDF format in: }<LSEP>[](symbol){wd}<LSEP>[argument 2; litteral](str){\n}

Subsets and Splits