From 6632cb1e217df5704a8bf3f7059c1d2ef9c65d48 Mon Sep 17 00:00:00 2001 From: Dony Unardi Date: Tue, 20 Sep 2022 16:39:15 -0700 Subject: [PATCH] update more modules --- R/arm_ref_comp.R | 2 +- R/tm_g_forest_tte.R | 18 ++++++----- R/tm_g_lineplot.R | 20 ++++++------ R/tm_g_pp_adverse_events.R | 15 ++++++--- R/tm_g_pp_patient_timeline.R | 12 +++---- R/tm_g_pp_therapy.R | 34 ++++++++++---------- R/tm_g_pp_vitals.R | 14 ++++++--- R/tm_t_abnormality.R | 15 +++++---- R/tm_t_abnormality_by_worst_grade.R | 16 +++++----- R/tm_t_coxreg.R | 14 ++++++--- R/tm_t_exposure.R | 4 ++- R/tm_t_logistic.R | 17 ++++++---- R/tm_t_pp_laboratory.R | 14 ++++++--- R/tm_t_pp_medical_history.R | 19 +++++++----- R/tm_t_pp_prior_medication.R | 43 ++++++++++++++------------ R/tm_t_shift_by_arm.R | 15 +++++---- R/tm_t_shift_by_arm_by_worst.R | 14 ++++++--- R/tm_t_shift_by_grade.R | 15 +++++---- R/tm_t_smq.R | 14 ++++----- R/tm_t_tte.R | 15 +++++---- man/arm_ref_comp_observer.Rd | 2 +- man/tm_g_forest_tte.Rd | 18 ++++++----- man/tm_g_lineplot.Rd | 20 ++++++------ man/tm_g_pp_adverse_events.Rd | 15 ++++++--- man/tm_g_pp_patient_timeline.Rd | 38 +++++++++++------------ man/tm_g_pp_therapy.Rd | 34 ++++++++++---------- man/tm_g_pp_vitals.Rd | 14 ++++++--- man/tm_t_abnormality.Rd | 15 +++++---- man/tm_t_abnormality_by_worst_grade.Rd | 16 +++++----- man/tm_t_coxreg.Rd | 14 ++++++--- man/tm_t_exposure.Rd | 16 +++++----- man/tm_t_logistic.Rd | 17 ++++++---- man/tm_t_pp_laboratory.Rd | 14 ++++++--- man/tm_t_pp_medical_history.Rd | 19 +++++++----- man/tm_t_pp_prior_medication.Rd | 43 ++++++++++++++------------ man/tm_t_shift_by_arm.Rd | 15 +++++---- man/tm_t_shift_by_arm_by_worst.Rd | 14 ++++++--- man/tm_t_shift_by_grade.Rd | 15 +++++---- man/tm_t_smq.Rd | 14 ++++----- man/tm_t_tte.Rd | 15 +++++---- 40 files changed, 406 insertions(+), 292 deletions(-) diff --git a/R/arm_ref_comp.R b/R/arm_ref_comp.R index 6465fe9df0..60bd28394c 100644 --- a/R/arm_ref_comp.R +++ b/R/arm_ref_comp.R @@ -24,11 +24,11 @@ #' @keywords internal #' #' @examples +#' \dontrun{ #' ds <- teal:::get_dummy_datasets() #' #' arm_ref_comp <- list(ARMCD = list(ref = "ARM A", comp = c("ARM B"))) #' arm_var <- choices_selected(c("ARM", "ARMCD"), "ARM") -#' \dontrun{ #' shinyApp( #' ui = fluidPage( #' teal.widgets::optionalSelectInput( diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R index 911180cc93..2ae15823fe 100644 --- a/R/tm_g_forest_tte.R +++ b/R/tm_g_forest_tte.R @@ -227,8 +227,10 @@ template_forest_tte <- function(dataname = "ANL", #' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADTTE <- synthetic_cdisc_data("latest")$adtte +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADTTE <- synthetic_cdisc_data_latest$adtte #' #' ADSL$RACE <- droplevels(ADSL$RACE) #' @@ -246,13 +248,15 @@ template_forest_tte <- function(dataname = "ANL", #' app <- init( #' data = cdisc_data( #' cdisc_dataset( -#' "ADSL", -#' ADSL, -#' code = "ADSL <- synthetic_cdisc_data('latest')$adsl +#' "ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl #' ADSL$RACE <- droplevels(ADSL$RACE)" #' ), -#' cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), -#' check = TRUE +#' cdisc_dataset( +#' "ADTTE", ADTTE, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADTTE <- synthetic_cdisc_data_latest$adtte") #' ), #' modules = modules( #' tm_g_forest_tte( diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R index 75a5319586..6d7024d056 100644 --- a/R/tm_g_lineplot.R +++ b/R/tm_g_lineplot.R @@ -207,20 +207,22 @@ template_g_lineplot <- function(dataname = "ANL", #' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADLB <- synthetic_cdisc_data("latest")$adlb +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADLB <- synthetic_cdisc_data_latest$adlb #' #' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min)) #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), -#' cdisc_dataset( -#' "ADLB", ADLB, -#' code = "ADLB <- synthetic_cdisc_data('latest')$adlb -#' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))" -#' ), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADLB", ADLB, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data_latest$adlb +#' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))" +#' ) #' ), #' modules = modules( #' tm_g_lineplot( diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R index 97993e5cb3..b3178ceedf 100644 --- a/R/tm_g_pp_adverse_events.R +++ b/R/tm_g_pp_adverse_events.R @@ -182,14 +182,19 @@ template_adverse_events <- function(dataname = "ANL", #' @examples #' library(scda) #' library(nestcolor) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADAE <- synthetic_cdisc_data("latest")$adae +#' +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADAE <- synthetic_cdisc_data_latest$adae #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), -#' cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data('latest')$adae"), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADAE", ADAE, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADAE <- synthetic_cdisc_data_latest$adae") #' ), #' modules = modules( #' tm_g_pp_adverse_events( diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R index c2d5e4d720..621ab7b329 100644 --- a/R/tm_g_pp_patient_timeline.R +++ b/R/tm_g_pp_patient_timeline.R @@ -400,21 +400,21 @@ template_patient_timeline <- function(dataname = "ANL", #' cdisc_dataset("ADCM", ADCM, #' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') #' ADCM <- synthetic_cdisc_data_latest$adcm -#' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) +#' ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) #' ADCM$CMDOSE <- 1 #' ADCM$CMDOSU <- 'U' #' ADCM$CMROUTE <- 'CMROUTE' #' ADCM$CMDOSFRQ <- 'CMDOSFRQ' #' ADCM$CMSTDY <- 1 -#' ADCM[ADCM$CMCAT == "medcl B", ]$CMSTDY <- 20 -#' ADCM[ADCM$CMCAT == "medcl C", ]$CMSTDY <- 150 +#' ADCM[ADCM$CMCAT == 'medcl B', ]$CMSTDY <- 20 +#' ADCM[ADCM$CMCAT == 'medcl C', ]$CMSTDY <- 150 #' ADCM$CMENDY <- 500 -#' ADCM[ADCM$CMCAT == "medcl B", ]$CMENDY <- 700 -#' ADCM[ADCM$CMCAT == "medcl C", ]$CMENDY <- 1000 +#' ADCM[ADCM$CMCAT == 'medcl B', ]$CMENDY <- 700 +#' ADCM[ADCM$CMCAT == 'medcl C', ]$CMENDY <- 1000 #' ADCM$CMASTDTM <- ADCM$ASTDTM #' ADCM$CMAENDTM <- ADCM$AENDTM #' formatters::var_labels( -#' ADCM[c("CMINDC", "CMDECOD", "CMSTDY", "CMENDY")]) <- c( +#' ADCM[c('CMINDC', 'CMDECOD', 'CMSTDY', 'CMENDY')]) <- c( #' 'Indication', #' 'Reported Name of Drug, Med, or Therapy', #' 'Study Day of Start of Medication', diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R index 426d5ef636..30156821b8 100644 --- a/R/tm_g_pp_therapy.R +++ b/R/tm_g_pp_therapy.R @@ -256,8 +256,9 @@ template_therapy <- function(dataname = "ANL", #' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADCM <- synthetic_cdisc_data("latest")$adcm +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <-synthetic_cdisc_data_latest$adsl +#' ADCM <- synthetic_cdisc_data_latest$adcm #' #' #' Modify ADCM #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -280,27 +281,28 @@ template_therapy <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADCM", ADCM, -#' code = 'ADCM <- synthetic_cdisc_data("latest")$adcm -#' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) +#' code = "ADCM <- synthetic_cdisc_data('latest')$adcm +#' ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) #' ADCM$CMDOSE <- 1 #' ADCM$CMTRT <- ADCM$CMCAT -#' ADCM$CMDOSU <- "U" -#' ADCM$CMROUTE <- "CMROUTE" -#' ADCM$CMDOSFRQ <- "CMDOSFRQ" +#' ADCM$CMDOSU <- 'U' +#' ADCM$CMROUTE <- 'CMROUTE' +#' ADCM$CMDOSFRQ <- 'CMDOSFRQ' #' ADCM$CMASTDTM <- ADCM$ASTDTM #' ADCM$CMAENDTM <- ADCM$AENDTM #' formatters::var_labels( -#' ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c( -#' "Indication", -#' "Reported Name of Drug, Med, or Therapy", -#' "Study Day of Start of Medication", -#' "Study Day of End of Medication") -#' ADCM', +#' ADCM[c('CMINDC', 'CMTRT', 'ASTDY', 'AENDY')]) <- c( +#' 'Indication', +#' 'Reported Name of Drug, Med, or Therapy', +#' 'Study Day of Start of Medication', +#' 'Study Day of End of Medication') +#' ADCM", #' keys = adcm_keys -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_g_pp_therapy( diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R index 6e95d202f3..5a506dbb0a 100644 --- a/R/tm_g_pp_vitals.R +++ b/R/tm_g_pp_vitals.R @@ -194,14 +194,18 @@ template_vitals <- function(dataname = "ANL", #' @examples #' library(scda) #' library(nestcolor) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADVS <- synthetic_cdisc_data("latest")$advs +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADVS <- synthetic_cdisc_data_latest$advs #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADVS", ADVS, code = 'ADVS <- synthetic_cdisc_data("latest")$advs'), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADVS", ADVS, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADVS <- synthetic_cdisc_data_latest$advs") #' ), #' modules = modules( #' tm_g_pp_vitals( diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R index 8645728183..60e3a94fb6 100644 --- a/R/tm_t_abnormality.R +++ b/R/tm_t_abnormality.R @@ -235,8 +235,9 @@ template_abnormality <- function(parentname, #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adlb <- synthetic_cdisc_data("latest")$adlb %>% +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adlb <- synthetic_cdisc_data_latest$adlb %>% #' mutate( #' ONTRTFL = case_when( #' AVISIT %in% c("SCREENING", "BASELINE") ~ "", @@ -247,9 +248,12 @@ template_abnormality <- function(parentname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADLB", adlb, -#' code = "ADLB <- synthetic_cdisc_data('latest')$adlb %>% +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data_latest$adlb %>% #' mutate( #' ONTRTFL = case_when( #' AVISIT %in% c('SCREENING', 'BASELINE') ~ '', @@ -258,8 +262,7 @@ template_abnormality <- function(parentname, #' ) #' attr(ADLB[['ONTRTFL']], 'label') <- 'On Treatment Record Flag' #' ADLB" -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_t_abnormality( diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R index 1b64b7652c..e19cfbb2b4 100644 --- a/R/tm_t_abnormality_by_worst_grade.R +++ b/R/tm_t_abnormality_by_worst_grade.R @@ -230,18 +230,20 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adlb <- synthetic_cdisc_data("latest")$adlb %>% +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adlb <- synthetic_cdisc_data_latest$adlb %>% #' filter(!AVISIT %in% c("SCREENING", "BASELINE")) #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADLB", adlb, -#' code = "ADLB <- synthetic_cdisc_data('latest')$adlb %>% -#' filter(!AVISIT %in% c('SCREENING', 'BASELINE'))" -#' ), -#' check = TRUE +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data('latest')$adlb %>% +#' filter(!AVISIT %in% c('SCREENING', 'BASELINE'))") #' ), #' modules = modules( #' tm_t_abnormality_by_worst_grade( diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index 3fe5856b2e..d02fe0501a 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -382,8 +382,9 @@ template_coxreg_m <- function(dataname, #' #' library(scda) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADTTE <- synthetic_cdisc_data("latest")$adtte +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADTTE <- synthetic_cdisc_data_latest$adtte #' arm_ref_comp <- list( #' ACTARMCD = list( #' ref = "ARM B", @@ -397,9 +398,12 @@ template_coxreg_m <- function(dataname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADTTE", ADTTE, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADTTE <- synthetic_cdisc_data_latest$adtte") #' ), #' modules = modules( #' tm_t_coxreg( diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R index 9a62231ee0..256613a185 100644 --- a/R/tm_t_exposure.R +++ b/R/tm_t_exposure.R @@ -77,7 +77,9 @@ template_exposure <- function(parentname, parsed_basic_table_args <- teal.widgets::parse_basic_table_args( teal.widgets::resolve_basic_table_args( user_table = basic_table_args, - module_table = teal.widgets::basic_table_args(main_footer = paste0("* Patient time is the sum of ", paramcd_label)) + module_table = teal.widgets::basic_table_args( + main_footer = paste0("* Patient time is the sum of ", paramcd_label) + ) ) ) diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index 7b6da4e77e..6d524f0f7b 100644 --- a/R/tm_t_logistic.R +++ b/R/tm_t_logistic.R @@ -232,8 +232,10 @@ template_logistic <- function(dataname, #' #' library(scda) #' library(dplyr) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADRS <- synthetic_cdisc_data("latest")$adrs %>% +#' +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADRS <- synthetic_cdisc_data_latest$adrs %>% #' filter(PARAMCD %in% c("BESRSPI", "INVET")) #' #' arm_ref_comp <- list( @@ -249,10 +251,13 @@ template_logistic <- function(dataname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADRS", ADRS, code = 'ADRS <- synthetic_cdisc_data("latest")$adrs %>% -#' filter(PARAMCD %in% c("BESRSPI", "INVET"))'), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADRS", ADRS, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADRS <- synthetic_cdisc_data_latest$adrs %>% +#' filter(PARAMCD %in% c('BESRSPI', 'INVET'))") #' ), #' modules = modules( #' tm_t_logistic( diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R index 072ac90b57..9097f8ab66 100644 --- a/R/tm_t_pp_laboratory.R +++ b/R/tm_t_pp_laboratory.R @@ -109,14 +109,18 @@ template_laboratory <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADLB <- synthetic_cdisc_data("latest")$adlb +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADLB <- synthetic_cdisc_data_latest$adlb #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), -#' cdisc_dataset("ADLB", ADLB, code = 'ADLB <- synthetic_cdisc_data("latest")$adlb'), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADLB", ADLB, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data_latest$adlb") #' ), #' modules = modules( #' tm_t_pp_laboratory( diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R index ffc3a1931d..af43e658ca 100644 --- a/R/tm_t_pp_medical_history.R +++ b/R/tm_t_pp_medical_history.R @@ -86,18 +86,23 @@ template_medical_history <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADMH <- synthetic_cdisc_data("latest")$admh +#' +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADMH <- synthetic_cdisc_data_latest$admh #' ADMH[["MHDISTAT"]] <- "ONGOING" #' formatters::var_labels(ADMH[c("MHDISTAT")]) <- c("Status of Disease") #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADMH", ADMH, code = "ADMH <- synthetic_cdisc_data('latest')$admh -#' ADMH[['MHDISTAT']] <- 'ONGOING' -#' formatters::var_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')"), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADMH", ADMH, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADMH <- synthetic_cdisc_data_latest$admh +#' ADMH[['MHDISTAT']] <- 'ONGOING' +#' formatters::var_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')") #' ), #' modules = modules( #' tm_t_pp_medical_history( diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R index 3a5ba90fd0..724de23c14 100644 --- a/R/tm_t_pp_prior_medication.R +++ b/R/tm_t_pp_prior_medication.R @@ -73,8 +73,9 @@ template_prior_medication <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADCM <- synthetic_cdisc_data("latest")$adcm +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADCM <- synthetic_cdisc_data_latest$adcm #' #' #' Modify ADCM #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -96,26 +97,28 @@ template_prior_medication <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADCM", ADCM, -#' code = 'ADCM <- synthetic_cdisc_data("latest")$adcm -#' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) -#' ADCM$CMDOSE <- 1 -#' ADCM$CMTRT <- ADCM$CMCAT -#' ADCM$CMDOSU <- "U" -#' ADCM$CMROUTE <- "CMROUTE" -#' ADCM$CMDOSFRQ <- "CMDOSFRQ" -#' ADCM$CMASTDTM <- ADCM$ASTDTM -#' ADCM$CMAENDTM <- ADCM$AENDTM -#' formatters::var_labels( -#' ADCM[c("CMINDC", "CMTRT", "ASTDY")]) <- c( -#' "Indication", -#' "Reported Name of Drug, Med, or Therapy", -#' "Study Day of Start of Medication" -#' )', +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADCM <- synthetic_cdisc_data_latest$adcm +#' ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) +#' ADCM$CMDOSE <- 1 +#' ADCM$CMTRT <- ADCM$CMCAT +#' ADCM$CMDOSU <- 'U' +#' ADCM$CMROUTE <- 'CMROUTE' +#' ADCM$CMDOSFRQ <- 'CMDOSFRQ' +#' ADCM$CMASTDTM <- ADCM$ASTDTM +#' ADCM$CMAENDTM <- ADCM$AENDTM +#' formatters::var_labels( +#' ADCM[c('CMINDC', 'CMTRT', 'ASTDY')]) <- c( +#' 'Indication', +#' 'Reported Name of Drug, Med, or Therapy', +#' 'Study Day of Start of Medication' +#' )", #' keys = adcm_keys -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_t_pp_prior_medication( diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R index 0acc0d3534..06b25c0b40 100644 --- a/R/tm_t_shift_by_arm.R +++ b/R/tm_t_shift_by_arm.R @@ -169,15 +169,18 @@ template_shift_by_arm <- function(dataname, #' library(dplyr) #' library(tern) #' library(scda) -#' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adeg <- synthetic_cdisc_data("latest")$adeg +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adeg <- synthetic_cdisc_data_latest$adeg #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADEG", adeg, code = 'ADEG <- synthetic_cdisc_data("latest")$adeg'), -#' check = TRUE +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADEG", adeg, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADEG <- synthetic_cdisc_data_latest$adeg") #' ), #' modules = modules( #' tm_t_shift_by_arm( diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R index 3d368feeb9..6907bc6888 100644 --- a/R/tm_t_shift_by_arm_by_worst.R +++ b/R/tm_t_shift_by_arm_by_worst.R @@ -175,14 +175,18 @@ template_shift_by_arm_by_worst <- function(dataname, #' library(tern) #' library(scda) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adeg <- synthetic_cdisc_data("latest")$adeg +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adeg <- synthetic_cdisc_data_latest$adeg #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADEG", adeg, code = 'ADEG <- synthetic_cdisc_data("latest")$adeg'), -#' check = TRUE +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADEG", adeg, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADEG <- synthetic_cdisc_data_latest$adeg") #' ), #' modules = modules( #' tm_t_shift_by_arm_by_worst( diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index e0c0306c2e..2a5538f4db 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -473,16 +473,19 @@ template_shift_by_grade <- function(parentname, #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adlb <- synthetic_cdisc_data("latest")$adlb +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adlb <- synthetic_cdisc_data_latest$adlb #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADLB", adlb, -#' code = 'ADLB <- synthetic_cdisc_data("latest")$adlb' -#' ), -#' check = TRUE +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data_latest$adlb" +#' ) #' ), #' modules = modules( #' tm_t_shift_by_grade( diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index 44d34e9fa1..3ae73239df 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -317,8 +317,9 @@ template_smq <- function(dataname, #' @examples #' library(scda) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adae <- synthetic_cdisc_data("latest")$adae +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adae <- synthetic_cdisc_data_latest$adae #' #' names_baskets <- grep("^(SMQ|CQ).*NAM$", names(adae), value = TRUE) #' names_scopes <- grep("^SMQ.*SC$", names(adae), value = TRUE) @@ -337,12 +338,11 @@ template_smq <- function(dataname, #' app <- init( #' data = cdisc_data( #' cdisc_dataset("ADSL", adsl, -#' code = "ADSL <- synthetic_cdisc_data('latest')$adsl" -#' ), +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), #' cdisc_dataset("ADAE", adae, -#' code = "ADAE <- synthetic_cdisc_data('latest')$adae" -#' ), -#' check = TRUE +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADAE <- synthetic_cdisc_data_latest$adae") #' ), #' modules = modules( #' tm_t_smq( diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index 0464139f48..959c708ed6 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -371,9 +371,9 @@ template_tte <- function(dataname = "ANL", #' @examples #' #' library(scda) -#' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADTTE <- synthetic_cdisc_data("latest")$adtte +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADTTE <- synthetic_cdisc_data_latest$adtte #' #' arm_ref_comp <- list( #' ACTARMCD = list( @@ -388,9 +388,12 @@ template_tte <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), -#' check = TRUE +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl"), +#' cdisc_dataset("ADTTE", ADTTE, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADTTE <- synthetic_cdisc_data_latest$adtte") #' ), #' modules = modules( #' tm_t_tte( diff --git a/man/arm_ref_comp_observer.Rd b/man/arm_ref_comp_observer.Rd index 4a4be61936..317e55e6af 100644 --- a/man/arm_ref_comp_observer.Rd +++ b/man/arm_ref_comp_observer.Rd @@ -56,11 +56,11 @@ stop the whole observer if FALSE.} Updates the reference and comparison Treatments when the selected Treatment variable changes } \examples{ +\dontrun{ ds <- teal:::get_dummy_datasets() arm_ref_comp <- list(ARMCD = list(ref = "ARM A", comp = c("ARM B"))) arm_var <- choices_selected(c("ARM", "ARMCD"), "ARM") -\dontrun{ shinyApp( ui = fluidPage( teal.widgets::optionalSelectInput( diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index fd1471196d..a981f5ed4d 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -119,8 +119,10 @@ with ADaM structure library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADTTE <- synthetic_cdisc_data("latest")$adtte +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + +ADSL <- synthetic_cdisc_data_latest$adsl +ADTTE <- synthetic_cdisc_data_latest$adtte ADSL$RACE <- droplevels(ADSL$RACE) @@ -138,13 +140,15 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( cdisc_dataset( - "ADSL", - ADSL, - code = "ADSL <- synthetic_cdisc_data('latest')$adsl + "ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl ADSL$RACE <- droplevels(ADSL$RACE)" ), - cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), - check = TRUE + cdisc_dataset( + "ADTTE", ADTTE, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADTTE <- synthetic_cdisc_data_latest$adtte") ), modules = modules( tm_g_forest_tte( diff --git a/man/tm_g_lineplot.Rd b/man/tm_g_lineplot.Rd index 84b88617a0..b7bf97c054 100644 --- a/man/tm_g_lineplot.Rd +++ b/man/tm_g_lineplot.Rd @@ -127,20 +127,22 @@ ADaM structure. library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADLB <- synthetic_cdisc_data("latest")$adlb +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADLB <- synthetic_cdisc_data_latest$adlb ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min)) app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), - cdisc_dataset( - "ADLB", ADLB, - code = "ADLB <- synthetic_cdisc_data('latest')$adlb - ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))" - ), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADLB", ADLB, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data_latest$adlb + ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))" + ) ), modules = modules( tm_g_lineplot( diff --git a/man/tm_g_pp_adverse_events.Rd b/man/tm_g_pp_adverse_events.Rd index eefea228fa..d5a74d41db 100644 --- a/man/tm_g_pp_adverse_events.Rd +++ b/man/tm_g_pp_adverse_events.Rd @@ -90,14 +90,19 @@ This teal module produces a patient profile adverse events table and plot using \examples{ library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADAE <- synthetic_cdisc_data("latest")$adae + +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADAE <- synthetic_cdisc_data_latest$adae app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), - cdisc_dataset("ADAE", ADAE, code = "ADAE <- synthetic_cdisc_data('latest')$adae"), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADAE", ADAE, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADAE <- synthetic_cdisc_data_latest$adae") ), modules = modules( tm_g_pp_adverse_events( diff --git a/man/tm_g_pp_patient_timeline.Rd b/man/tm_g_pp_patient_timeline.Rd index 1a61715902..11d7df8eb4 100644 --- a/man/tm_g_pp_patient_timeline.Rd +++ b/man/tm_g_pp_patient_timeline.Rd @@ -138,35 +138,35 @@ adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", app <- init( data = cdisc_data( cdisc_dataset("ADSL", ADSL, - code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") - ADSL <- synthetic_cdisc_data_latest$adsl' + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl" ), cdisc_dataset("ADAE", ADAE, - code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") - ADAE <- synthetic_cdisc_data_latest$adae' + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADAE <- synthetic_cdisc_data_latest$adae" ), cdisc_dataset("ADCM", ADCM, - code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") - ADCM <- synthetic_cdisc_data("latest")$adcm - ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADCM <- synthetic_cdisc_data_latest$adcm + ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) ADCM$CMDOSE <- 1 - ADCM$CMDOSU <- "U" - ADCM$CMROUTE <- "CMROUTE" - ADCM$CMDOSFRQ <- "CMDOSFRQ" + ADCM$CMDOSU <- 'U' + ADCM$CMROUTE <- 'CMROUTE' + ADCM$CMDOSFRQ <- 'CMDOSFRQ' ADCM$CMSTDY <- 1 - ADCM[ADCM$CMCAT == "medcl B", ]$CMSTDY <- 20 - ADCM[ADCM$CMCAT == "medcl C", ]$CMSTDY <- 150 + ADCM[ADCM$CMCAT == 'medcl B', ]$CMSTDY <- 20 + ADCM[ADCM$CMCAT == 'medcl C', ]$CMSTDY <- 150 ADCM$CMENDY <- 500 - ADCM[ADCM$CMCAT == "medcl B", ]$CMENDY <- 700 - ADCM[ADCM$CMCAT == "medcl C", ]$CMENDY <- 1000 + ADCM[ADCM$CMCAT == 'medcl B', ]$CMENDY <- 700 + ADCM[ADCM$CMCAT == 'medcl C', ]$CMENDY <- 1000 ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM formatters::var_labels( - ADCM[c("CMINDC", "CMDECOD", "CMSTDY", "CMENDY")]) <- c( - "Indication", - "Reported Name of Drug, Med, or Therapy", - "Study Day of Start of Medication", - "Study Day of End of Medication")', + ADCM[c('CMINDC', 'CMDECOD', 'CMSTDY', 'CMENDY')]) <- c( + 'Indication', + 'Reported Name of Drug, Med, or Therapy', + 'Study Day of Start of Medication', + 'Study Day of End of Medication')", keys = adcm_keys ) ), diff --git a/man/tm_g_pp_therapy.Rd b/man/tm_g_pp_therapy.Rd index cbce92939e..da48f1baf7 100644 --- a/man/tm_g_pp_therapy.Rd +++ b/man/tm_g_pp_therapy.Rd @@ -103,8 +103,9 @@ This teal module produces a patient profile therapy plot using ADaM datasets. library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADCM <- synthetic_cdisc_data("latest")$adcm +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <-synthetic_cdisc_data_latest$adsl +ADCM <- synthetic_cdisc_data_latest$adcm #' Modify ADCM ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -127,27 +128,28 @@ adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADCM", ADCM, - code = 'ADCM <- synthetic_cdisc_data("latest")$adcm - ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) + code = "ADCM <- synthetic_cdisc_data('latest')$adcm + ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) ADCM$CMDOSE <- 1 ADCM$CMTRT <- ADCM$CMCAT - ADCM$CMDOSU <- "U" - ADCM$CMROUTE <- "CMROUTE" - ADCM$CMDOSFRQ <- "CMDOSFRQ" + ADCM$CMDOSU <- 'U' + ADCM$CMROUTE <- 'CMROUTE' + ADCM$CMDOSFRQ <- 'CMDOSFRQ' ADCM$CMASTDTM <- ADCM$ASTDTM ADCM$CMAENDTM <- ADCM$AENDTM formatters::var_labels( - ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c( - "Indication", - "Reported Name of Drug, Med, or Therapy", - "Study Day of Start of Medication", - "Study Day of End of Medication") - ADCM', + ADCM[c('CMINDC', 'CMTRT', 'ASTDY', 'AENDY')]) <- c( + 'Indication', + 'Reported Name of Drug, Med, or Therapy', + 'Study Day of Start of Medication', + 'Study Day of End of Medication') + ADCM", keys = adcm_keys - ), - check = TRUE + ) ), modules = modules( tm_g_pp_therapy( diff --git a/man/tm_g_pp_vitals.Rd b/man/tm_g_pp_vitals.Rd index 2d34aadf47..b7c7356692 100644 --- a/man/tm_g_pp_vitals.Rd +++ b/man/tm_g_pp_vitals.Rd @@ -78,14 +78,18 @@ This teal module produces a patient profile vitals plot using ADaM datasets. \examples{ library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADVS <- synthetic_cdisc_data("latest")$advs +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADVS <- synthetic_cdisc_data_latest$advs app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADVS", ADVS, code = 'ADVS <- synthetic_cdisc_data("latest")$advs'), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADVS", ADVS, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADVS <- synthetic_cdisc_data_latest$advs") ), modules = modules( tm_g_pp_vitals( diff --git a/man/tm_t_abnormality.Rd b/man/tm_t_abnormality.Rd index e8e54c9218..4b6acb586b 100644 --- a/man/tm_t_abnormality.Rd +++ b/man/tm_t_abnormality.Rd @@ -107,8 +107,9 @@ excluded in accordance with GDSR specifications by using \code{exclude_base_abn} library(scda) library(dplyr) -adsl <- synthetic_cdisc_data("latest")$adsl -adlb <- synthetic_cdisc_data("latest")$adlb \%>\% +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adlb <- synthetic_cdisc_data_latest$adlb \%>\% mutate( ONTRTFL = case_when( AVISIT \%in\% c("SCREENING", "BASELINE") ~ "", @@ -119,9 +120,12 @@ attr(adlb[["ONTRTFL"]], "label") <- "On Treatment Record Flag" app <- init( data = cdisc_data( - cdisc_dataset("ADSL", adsl, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADLB", adlb, - code = "ADLB <- synthetic_cdisc_data('latest')$adlb \%>\% + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data_latest$adlb \%>\% mutate( ONTRTFL = case_when( AVISIT \%in\% c('SCREENING', 'BASELINE') ~ '', @@ -130,8 +134,7 @@ app <- init( ) attr(ADLB[['ONTRTFL']], 'label') <- 'On Treatment Record Flag' ADLB" - ), - check = TRUE + ) ), modules = modules( tm_t_abnormality( diff --git a/man/tm_t_abnormality_by_worst_grade.Rd b/man/tm_t_abnormality_by_worst_grade.Rd index 79f49bed41..61c04bb276 100644 --- a/man/tm_t_abnormality_by_worst_grade.Rd +++ b/man/tm_t_abnormality_by_worst_grade.Rd @@ -98,18 +98,20 @@ Teal Module: Laboratory test results with highest grade post-baseline library(scda) library(dplyr) -adsl <- synthetic_cdisc_data("latest")$adsl -adlb <- synthetic_cdisc_data("latest")$adlb \%>\% +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adlb <- synthetic_cdisc_data_latest$adlb \%>\% filter(!AVISIT \%in\% c("SCREENING", "BASELINE")) app <- init( data = cdisc_data( - cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADLB", adlb, - code = "ADLB <- synthetic_cdisc_data('latest')$adlb \%>\% - filter(!AVISIT \%in\% c('SCREENING', 'BASELINE'))" - ), - check = TRUE + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data('latest')$adlb \%>\% + filter(!AVISIT \%in\% c('SCREENING', 'BASELINE'))") ), modules = modules( tm_t_abnormality_by_worst_grade( diff --git a/man/tm_t_coxreg.Rd b/man/tm_t_coxreg.Rd index 56f33e43af..43a36fef54 100644 --- a/man/tm_t_coxreg.Rd +++ b/man/tm_t_coxreg.Rd @@ -134,8 +134,9 @@ Wald test will be substituted. library(scda) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADTTE <- synthetic_cdisc_data("latest")$adtte +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADTTE <- synthetic_cdisc_data_latest$adtte arm_ref_comp <- list( ACTARMCD = list( ref = "ARM B", @@ -149,9 +150,12 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADTTE", ADTTE, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADTTE <- synthetic_cdisc_data_latest$adtte") ), modules = modules( tm_t_coxreg( diff --git a/man/tm_t_exposure.Rd b/man/tm_t_exposure.Rd index b9b6e8af1d..886eef19b7 100644 --- a/man/tm_t_exposure.Rd +++ b/man/tm_t_exposure.Rd @@ -114,22 +114,22 @@ formatters::var_labels(adex) <- labels app <- init( data = cdisc_data( cdisc_dataset("ADSL", adsl, - code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") - ADSL <- synthetic_cdisc_data_latest$adsl' + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl" ), cdisc_dataset("ADEX", adex, - code = 'set.seed(1, kind = "Mersenne-Twister") - synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") + code = "set.seed(1, kind = 'Mersenne-Twister') + synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') ADEX <- synthetic_cdisc_data_latest$adex labels <- formatters::var_labels(ADEX, fill = FALSE) ADEX <- ADEX \%>\% distinct(USUBJID, .keep_all = TRUE) \%>\% - mutate(PARAMCD = "TDURD", - PARAM = "Overall duration (days)", + mutate(PARAMCD = 'TDURD', + PARAM = 'Overall duration (days)', AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE), - AVALU = "Days") \%>\% + AVALU = 'Days') \%>\% bind_rows(ADEX) - formatters::var_labels(ADEX) <- labels' # nolint + formatters::var_labels(ADEX) <- labels" # nolint ) ), modules = modules( diff --git a/man/tm_t_logistic.Rd b/man/tm_t_logistic.Rd index 41a5a14df0..6e0c97a21f 100644 --- a/man/tm_t_logistic.Rd +++ b/man/tm_t_logistic.Rd @@ -83,8 +83,10 @@ STREAM template \code{lgrt02}. library(scda) library(dplyr) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADRS <- synthetic_cdisc_data("latest")$adrs \%>\% + +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADRS <- synthetic_cdisc_data_latest$adrs \%>\% filter(PARAMCD \%in\% c("BESRSPI", "INVET")) arm_ref_comp <- list( @@ -100,10 +102,13 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADRS", ADRS, code = 'ADRS <- synthetic_cdisc_data("latest")$adrs \%>\% - filter(PARAMCD \%in\% c("BESRSPI", "INVET"))'), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADRS", ADRS, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADRS <- synthetic_cdisc_data_latest$adrs \%>\% + filter(PARAMCD \%in\% c('BESRSPI', 'INVET'))") ), modules = modules( tm_t_logistic( diff --git a/man/tm_t_pp_laboratory.Rd b/man/tm_t_pp_laboratory.Rd index c2238cc1d5..3d472b97b9 100644 --- a/man/tm_t_pp_laboratory.Rd +++ b/man/tm_t_pp_laboratory.Rd @@ -62,14 +62,18 @@ This teal module produces a patient profile laboratory table using ADaM datasets } \examples{ library(scda) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADLB <- synthetic_cdisc_data("latest")$adlb +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADLB <- synthetic_cdisc_data_latest$adlb app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), - cdisc_dataset("ADLB", ADLB, code = 'ADLB <- synthetic_cdisc_data("latest")$adlb'), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADLB", ADLB, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data_latest$adlb") ), modules = modules( tm_t_pp_laboratory( diff --git a/man/tm_t_pp_medical_history.Rd b/man/tm_t_pp_medical_history.Rd index a5a2edb1b8..ac093544bc 100644 --- a/man/tm_t_pp_medical_history.Rd +++ b/man/tm_t_pp_medical_history.Rd @@ -50,18 +50,23 @@ This teal module produces a patient medical history report using ADaM datasets. } \examples{ library(scda) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADMH <- synthetic_cdisc_data("latest")$admh + +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADMH <- synthetic_cdisc_data_latest$admh ADMH[["MHDISTAT"]] <- "ONGOING" formatters::var_labels(ADMH[c("MHDISTAT")]) <- c("Status of Disease") app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADMH", ADMH, code = "ADMH <- synthetic_cdisc_data('latest')$admh - ADMH[['MHDISTAT']] <- 'ONGOING' - formatters::var_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')"), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADMH", ADMH, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADMH <- synthetic_cdisc_data_latest$admh + ADMH[['MHDISTAT']] <- 'ONGOING' + formatters::var_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')") ), modules = modules( tm_t_pp_medical_history( diff --git a/man/tm_t_pp_prior_medication.Rd b/man/tm_t_pp_prior_medication.Rd index b5c41de67c..e3081a73dd 100644 --- a/man/tm_t_pp_prior_medication.Rd +++ b/man/tm_t_pp_prior_medication.Rd @@ -54,8 +54,9 @@ This teal module produces a patient prior medication report using ADaM datasets. } \examples{ library(scda) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADCM <- synthetic_cdisc_data("latest")$adcm +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADCM <- synthetic_cdisc_data_latest$adcm #' Modify ADCM ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -77,26 +78,28 @@ adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADCM", ADCM, - code = 'ADCM <- synthetic_cdisc_data("latest")$adcm - ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) - ADCM$CMDOSE <- 1 - ADCM$CMTRT <- ADCM$CMCAT - ADCM$CMDOSU <- "U" - ADCM$CMROUTE <- "CMROUTE" - ADCM$CMDOSFRQ <- "CMDOSFRQ" - ADCM$CMASTDTM <- ADCM$ASTDTM - ADCM$CMAENDTM <- ADCM$AENDTM - formatters::var_labels( - ADCM[c("CMINDC", "CMTRT", "ASTDY")]) <- c( - "Indication", - "Reported Name of Drug, Med, or Therapy", - "Study Day of Start of Medication" - )', + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADCM <- synthetic_cdisc_data_latest$adcm + ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD)) + ADCM$CMDOSE <- 1 + ADCM$CMTRT <- ADCM$CMCAT + ADCM$CMDOSU <- 'U' + ADCM$CMROUTE <- 'CMROUTE' + ADCM$CMDOSFRQ <- 'CMDOSFRQ' + ADCM$CMASTDTM <- ADCM$ASTDTM + ADCM$CMAENDTM <- ADCM$AENDTM + formatters::var_labels( + ADCM[c('CMINDC', 'CMTRT', 'ASTDY')]) <- c( + 'Indication', + 'Reported Name of Drug, Med, or Therapy', + 'Study Day of Start of Medication' + )", keys = adcm_keys - ), - check = TRUE + ) ), modules = modules( tm_t_pp_prior_medication( diff --git a/man/tm_t_shift_by_arm.Rd b/man/tm_t_shift_by_arm.Rd index f3fc34d60a..ffad82945d 100644 --- a/man/tm_t_shift_by_arm.Rd +++ b/man/tm_t_shift_by_arm.Rd @@ -95,15 +95,18 @@ Teal Module: Shift by Arm library(dplyr) library(tern) library(scda) - -adsl <- synthetic_cdisc_data("latest")$adsl -adeg <- synthetic_cdisc_data("latest")$adeg +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adeg <- synthetic_cdisc_data_latest$adeg app <- init( data = cdisc_data( - cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADEG", adeg, code = 'ADEG <- synthetic_cdisc_data("latest")$adeg'), - check = TRUE + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADEG", adeg, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADEG <- synthetic_cdisc_data_latest$adeg") ), modules = modules( tm_t_shift_by_arm( diff --git a/man/tm_t_shift_by_arm_by_worst.Rd b/man/tm_t_shift_by_arm_by_worst.Rd index 65c7c6c1af..c86247a156 100644 --- a/man/tm_t_shift_by_arm_by_worst.Rd +++ b/man/tm_t_shift_by_arm_by_worst.Rd @@ -96,14 +96,18 @@ library(dplyr) library(tern) library(scda) -adsl <- synthetic_cdisc_data("latest")$adsl -adeg <- synthetic_cdisc_data("latest")$adeg +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adeg <- synthetic_cdisc_data_latest$adeg app <- init( data = cdisc_data( - cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADEG", adeg, code = 'ADEG <- synthetic_cdisc_data("latest")$adeg'), - check = TRUE + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADEG", adeg, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADEG <- synthetic_cdisc_data_latest$adeg") ), modules = modules( tm_t_shift_by_arm_by_worst( diff --git a/man/tm_t_shift_by_grade.Rd b/man/tm_t_shift_by_grade.Rd index 8e1b0287dd..457cce5670 100644 --- a/man/tm_t_shift_by_grade.Rd +++ b/man/tm_t_shift_by_grade.Rd @@ -108,16 +108,19 @@ Teal Module: Grade Summary Table library(scda) library(dplyr) -adsl <- synthetic_cdisc_data("latest")$adsl -adlb <- synthetic_cdisc_data("latest")$adlb +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adlb <- synthetic_cdisc_data_latest$adlb app <- init( data = cdisc_data( - cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADLB", adlb, - code = 'ADLB <- synthetic_cdisc_data("latest")$adlb' - ), - check = TRUE + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data_latest$adlb" + ) ), modules = modules( tm_t_shift_by_grade( diff --git a/man/tm_t_smq.Rd b/man/tm_t_smq.Rd index 922f23be85..200f6d4006 100644 --- a/man/tm_t_smq.Rd +++ b/man/tm_t_smq.Rd @@ -91,8 +91,9 @@ Adverse Events Table by Standardized \code{MedDRA} Query. \examples{ library(scda) -adsl <- synthetic_cdisc_data("latest")$adsl -adae <- synthetic_cdisc_data("latest")$adae +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +adsl <- synthetic_cdisc_data_latest$adsl +adae <- synthetic_cdisc_data_latest$adae names_baskets <- grep("^(SMQ|CQ).*NAM$", names(adae), value = TRUE) names_scopes <- grep("^SMQ.*SC$", names(adae), value = TRUE) @@ -111,12 +112,11 @@ cs_scopes <- choices_selected( app <- init( data = cdisc_data( cdisc_dataset("ADSL", adsl, - code = "ADSL <- synthetic_cdisc_data('latest')$adsl" - ), + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), cdisc_dataset("ADAE", adae, - code = "ADAE <- synthetic_cdisc_data('latest')$adae" - ), - check = TRUE + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADAE <- synthetic_cdisc_data_latest$adae") ), modules = modules( tm_t_smq( diff --git a/man/tm_t_tte.Rd b/man/tm_t_tte.Rd index 04a4a7576b..ea073a9792 100644 --- a/man/tm_t_tte.Rd +++ b/man/tm_t_tte.Rd @@ -125,9 +125,9 @@ The arm and stratification variables and taken from the \code{parentname} data. \examples{ library(scda) - -ADSL <- synthetic_cdisc_data("latest")$adsl -ADTTE <- synthetic_cdisc_data("latest")$adtte +synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +ADSL <- synthetic_cdisc_data_latest$adsl +ADTTE <- synthetic_cdisc_data_latest$adtte arm_ref_comp <- list( ACTARMCD = list( @@ -142,9 +142,12 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), - check = TRUE + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl"), + cdisc_dataset("ADTTE", ADTTE, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADTTE <- synthetic_cdisc_data_latest$adtte") ), modules = modules( tm_t_tte(