From e3ecbf902551a9ec043891bca9a9241955d868db Mon Sep 17 00:00:00 2001 From: Dony Unardi Date: Wed, 28 Sep 2022 07:53:54 -0700 Subject: [PATCH] fix package --as-cran (#602) * update link and examples * [skip actions] Restyle files * update examples * [skip actions] Restyle files * update example as pointed out by lint * [skip actions] Roxygen Man Pages Auto Update * update per lint findings * update more modules * [skip actions] Restyle files * [skip actions] Roxygen Man Pages Auto Update * lintr * capitalize time Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: Mahmoud Hallal <86970066+mhallal1@users.noreply.github.com> Co-authored-by: Mahmoud Hallal --- R/arm_ref_comp.R | 2 +- R/tm_a_mmrm.R | 16 +++++--- R/tm_g_barchart_simple.R | 3 +- R/tm_g_forest_rsp.R | 13 ++++--- R/tm_g_forest_tte.R | 19 ++++++---- R/tm_g_km.R | 3 +- R/tm_g_lineplot.R | 18 ++++++--- R/tm_g_pp_adverse_events.R | 17 ++++++--- R/tm_g_pp_patient_timeline.R | 51 +++++++++++++++----------- R/tm_g_pp_therapy.R | 35 ++++++++++-------- R/tm_g_pp_vitals.R | 16 +++++--- R/tm_t_abnormality.R | 16 +++++--- R/tm_t_abnormality_by_worst_grade.R | 16 +++++--- R/tm_t_binary_outcome.R | 21 +++++++---- R/tm_t_coxreg.R | 16 +++++--- R/tm_t_exposure.R | 27 ++++++++------ R/tm_t_logistic.R | 19 +++++++--- R/tm_t_pp_laboratory.R | 16 +++++--- R/tm_t_pp_medical_history.R | 21 +++++++---- R/tm_t_pp_prior_medication.R | 44 ++++++++++++---------- R/tm_t_shift_by_arm.R | 17 ++++++--- R/tm_t_shift_by_arm_by_worst.R | 16 +++++--- R/tm_t_shift_by_grade.R | 16 +++++--- R/tm_t_smq.R | 14 ++++--- R/tm_t_summary_by.R | 13 ++++--- R/tm_t_tte.R | 17 ++++++--- R/utils.R | 14 +++++-- README.md | 2 +- man/arm_ref_comp_observer.Rd | 2 +- man/call_concatenate.Rd | 10 ++++- man/template_binary_outcome.Rd | 7 +++- man/tm_a_mmrm.Rd | 16 +++++--- man/tm_g_barchart_simple.Rd | 3 +- man/tm_g_forest_rsp.Rd | 13 ++++--- man/tm_g_forest_tte.Rd | 19 ++++++---- man/tm_g_km.Rd | 3 +- man/tm_g_lineplot.Rd | 18 ++++++--- man/tm_g_pp_adverse_events.Rd | 17 ++++++--- man/tm_g_pp_patient_timeline.Rd | 51 +++++++++++++++----------- man/tm_g_pp_therapy.Rd | 35 ++++++++++-------- man/tm_g_pp_vitals.Rd | 16 +++++--- man/tm_t_abnormality.Rd | 16 +++++--- man/tm_t_abnormality_by_worst_grade.Rd | 16 +++++--- man/tm_t_binary_outcome.Rd | 14 ++++--- man/tm_t_coxreg.Rd | 16 +++++--- man/tm_t_exposure.Rd | 27 ++++++++------ man/tm_t_logistic.Rd | 19 +++++++--- man/tm_t_pp_laboratory.Rd | 16 +++++--- man/tm_t_pp_medical_history.Rd | 21 +++++++---- man/tm_t_pp_prior_medication.Rd | 44 ++++++++++++---------- man/tm_t_shift_by_arm.Rd | 17 ++++++--- man/tm_t_shift_by_arm_by_worst.Rd | 16 +++++--- man/tm_t_shift_by_grade.Rd | 16 +++++--- man/tm_t_smq.Rd | 14 ++++--- man/tm_t_summary_by.Rd | 13 ++++--- man/tm_t_tte.Rd | 17 ++++++--- 56 files changed, 611 insertions(+), 379 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_a_mmrm.R b/R/tm_a_mmrm.R index 03d060f4f1..4769015301 100644 --- a/R/tm_a_mmrm.R +++ b/R/tm_a_mmrm.R @@ -454,8 +454,9 @@ template_mmrm_plots <- function(fit_name, #' #' library(scda) #' -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADQS <- synthetic_cdisc_data("latest")$adqs %>% +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADQS <- synthetic_cdisc_data_latest$adqs %>% #' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>% #' dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>% #' dplyr::mutate( @@ -475,9 +476,13 @@ template_mmrm_plots <- function(fit_name, #' #' 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("ADQS", ADQS, -#' code = 'ADQS <- synthetic_cdisc_data("latest")$adqs %>% +#' code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +#' ADQS <- synthetic_cdisc_data("latest")$adqs %>% #' dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>% #' dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>% #' dplyr::mutate( @@ -487,8 +492,7 @@ template_mmrm_plots <- function(fit_name, #' as.numeric() %>% #' as.factor() # making consecutive numeric factor #' )' -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_a_mmrm( diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R index afa4b79d98..75c6a24ac7 100644 --- a/R/tm_g_barchart_simple.R +++ b/R/tm_g_barchart_simple.R @@ -38,8 +38,7 @@ #' dplyr::filter(!((AETOXGR == 1) & (AESEV == 'MILD') & (ARM == 'A: Drug X'))) #' formatters::var_labels(ADAE) <- adae_labels #' ADAE" -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_g_barchart_simple( diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R index b2190943a4..e4fdd88e5a 100644 --- a/R/tm_g_forest_rsp.R +++ b/R/tm_g_forest_rsp.R @@ -220,8 +220,9 @@ template_forest_rsp <- function(dataname = "ANL", #' library(dplyr) #' library(nestcolor) #' -#' 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 %>% #' mutate(AVALC = d_onco_rsp_label(AVALC)) %>% #' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP") #' @@ -241,11 +242,11 @@ template_forest_rsp <- function(dataname = "ANL", #' cdisc_dataset("ADSL", ADSL), #' cdisc_dataset("ADRS", ADRS), #' code = -#' "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 %>% #' mutate(AVALC = d_onco_rsp_label(AVALC)) %>% -#' filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')", -#' check = TRUE +#' filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')" #' ), #' modules = modules( #' tm_g_forest_rsp( diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R index 911180cc93..980672f654 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 +248,16 @@ 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_km.R b/R/tm_g_km.R index 3bd3830829..b409a09bfb 100644 --- a/R/tm_g_km.R +++ b/R/tm_g_km.R @@ -287,8 +287,7 @@ template_g_km <- 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("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte') #' ), #' modules = modules( #' tm_g_km( diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R index b704745d1b..cca736456a 100644 --- a/R/tm_g_lineplot.R +++ b/R/tm_g_lineplot.R @@ -207,17 +207,23 @@ template_g_lineplot <- function(dataname = "ANL", #' library(scda) #' library(nestcolor) #' -#' ADSL <- synthetic_cdisc_data("latest")$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$adlb +#' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))" +#' ) #' ), #' modules = modules( #' tm_g_lineplot( diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R index 97993e5cb3..5f59e470af 100644 --- a/R/tm_g_pp_adverse_events.R +++ b/R/tm_g_pp_adverse_events.R @@ -182,14 +182,21 @@ template_adverse_events <- function(dataname = "ANL", #' @examples #' library(scda) #' library(nestcolor) -#' ADSL <- synthetic_cdisc_data("latest")$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$adae" +#' ) #' ), #' modules = modules( #' tm_g_pp_adverse_events( diff --git a/R/tm_g_pp_patient_timeline.R b/R/tm_g_pp_patient_timeline.R index 01e04057f5..621ab7b329 100644 --- a/R/tm_g_pp_patient_timeline.R +++ b/R/tm_g_pp_patient_timeline.R @@ -356,9 +356,12 @@ template_patient_timeline <- function(dataname = "ANL", #' @examples #' library(scda) #' library(nestcolor) -#' ADSL <- synthetic_cdisc_data("latest")$adsl -#' ADAE <- synthetic_cdisc_data("latest")$adae -#' ADCM <- synthetic_cdisc_data("latest")$adcm +#' +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +#' +#' ADSL <- synthetic_cdisc_data_latest$adsl +#' ADAE <- synthetic_cdisc_data_latest$adae +#' ADCM <- synthetic_cdisc_data_latest$adcm #' #' #' Modify ADCM #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -386,32 +389,38 @@ template_patient_timeline <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), -#' cdisc_dataset("ADAE", ADAE, code = 'ADAE <- synthetic_cdisc_data("latest")$adae'), +#' cdisc_dataset("ADSL", ADSL, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl" +#' ), +#' cdisc_dataset("ADAE", ADAE, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADAE <- synthetic_cdisc_data_latest$adae" +#' ), #' cdisc_dataset("ADCM", ADCM, -#' code = 'ADCM <- synthetic_cdisc_data("latest")$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 -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_g_pp_patient_timeline( diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R index 426d5ef636..65cb9c4051 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 +281,29 @@ 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$AENDTM #' formatters::var_labels( -#' ADCM[c("CMINDC", "CMTRT", "ASTDY", "AENDY")]) <- c( -#' "Indication", -#' "Reported Name of Drug, Med, or Therapy", -#' "Study Day of Start of Medication", -#' "Study Day of End of Medication") -#' ADCM', +#' ADCM[c('CMINDC', 'CMTRT', 'ASTDY', 'AENDY')]) <- c( +#' 'Indication', +#' 'Reported Name of Drug, Med, or Therapy', +#' 'Study Day of Start of Medication', +#' 'Study Day of End of Medication') +#' ADCM", #' keys = adcm_keys -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_g_pp_therapy( diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R index 6e95d202f3..2a2a5c2fcc 100644 --- a/R/tm_g_pp_vitals.R +++ b/R/tm_g_pp_vitals.R @@ -194,14 +194,20 @@ template_vitals <- function(dataname = "ANL", #' @examples #' library(scda) #' library(nestcolor) -#' ADSL <- synthetic_cdisc_data("latest")$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$advs" +#' ) #' ), #' modules = modules( #' tm_g_pp_vitals( diff --git a/R/tm_t_abnormality.R b/R/tm_t_abnormality.R index 8645728183..48223d806b 100644 --- a/R/tm_t_abnormality.R +++ b/R/tm_t_abnormality.R @@ -235,8 +235,9 @@ template_abnormality <- function(parentname, #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$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$adlb %>% #' mutate( #' ONTRTFL = case_when( #' AVISIT %in% c("SCREENING", "BASELINE") ~ "", @@ -247,9 +248,13 @@ template_abnormality <- function(parentname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = "ADSL <- synthetic_cdisc_data('latest')$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$adlb %>% #' mutate( #' ONTRTFL = case_when( #' AVISIT %in% c('SCREENING', 'BASELINE') ~ '', @@ -258,8 +263,7 @@ template_abnormality <- function(parentname, #' ) #' attr(ADLB[['ONTRTFL']], 'label') <- 'On Treatment Record Flag' #' ADLB" -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_t_abnormality( diff --git a/R/tm_t_abnormality_by_worst_grade.R b/R/tm_t_abnormality_by_worst_grade.R index 1b64b7652c..d5dcbac92f 100644 --- a/R/tm_t_abnormality_by_worst_grade.R +++ b/R/tm_t_abnormality_by_worst_grade.R @@ -230,18 +230,22 @@ template_abnormality_by_worst_grade <- function(parentname, # nolint #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$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 %>% +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data('latest')$adlb %>% #' filter(!AVISIT %in% c('SCREENING', 'BASELINE'))" -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_t_abnormality_by_worst_grade( diff --git a/R/tm_t_binary_outcome.R b/R/tm_t_binary_outcome.R index 8e33834c73..ac7bf45f1b 100644 --- a/R/tm_t_binary_outcome.R +++ b/R/tm_t_binary_outcome.R @@ -19,8 +19,11 @@ #' library(dplyr) #' library(scda) #' library(tern) -#' adsl <- synthetic_cdisc_data("latest")$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$adrs #' #' # Generate an expression for the analysis of responders. #' a <- template_binary_outcome( @@ -396,8 +399,10 @@ template_binary_outcome <- function(dataname, #' @examples #' library(dplyr) #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$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$adrs %>% #' mutate(AVALC = d_onco_rsp_label(AVALC)) %>% #' filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP") #' arm_ref_comp <- list( @@ -409,11 +414,11 @@ template_binary_outcome <- function(dataname, #' cdisc_dataset("ADSL", ADSL), #' cdisc_dataset("ADRS", ADRS), #' code = -#' "ADSL <- synthetic_cdisc_data('latest')$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$adrs %>% #' mutate(AVALC = d_onco_rsp_label(AVALC)) %>% -#' filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')", -#' check = TRUE +#' filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')" #' ), #' modules = modules( #' tm_t_binary_outcome( diff --git a/R/tm_t_coxreg.R b/R/tm_t_coxreg.R index e8fb8b74b8..7c9f4dff6b 100644 --- a/R/tm_t_coxreg.R +++ b/R/tm_t_coxreg.R @@ -410,8 +410,9 @@ template_coxreg_m <- function(dataname, #' #' library(scda) #' -#' ADSL <- synthetic_cdisc_data("latest")$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$adtte #' arm_ref_comp <- list( #' ACTARMCD = list( #' ref = "ARM B", @@ -425,9 +426,14 @@ template_coxreg_m <- function(dataname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$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$adtte" +#' ) #' ), #' modules = modules( #' tm_t_coxreg( diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R index 6669a0152e..d7659d597a 100644 --- a/R/tm_t_exposure.R +++ b/R/tm_t_exposure.R @@ -229,12 +229,12 @@ template_exposure <- function(parentname, #' @export #' #' @examples -#' #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$adsl -#' adex <- synthetic_cdisc_data("latest")$adex +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adex <- synthetic_cdisc_data_latest$adex #' #' set.seed(1, kind = "Mersenne-Twister") #' labels <- formatters::var_labels(adex, fill = FALSE) @@ -251,21 +251,24 @@ template_exposure <- function(parentname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", adsl, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl" +#' ), #' cdisc_dataset("ADEX", adex, -#' code = 'set.seed(1, kind = "Mersenne-Twister") -#' ADEX <- synthetic_cdisc_data("latest")$adex +#' code = "set.seed(1, kind = 'Mersenne-Twister') +#' synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADEX <- synthetic_cdisc_data_latest$adex #' labels <- formatters::var_labels(ADEX, fill = FALSE) #' ADEX <- ADEX %>% #' distinct(USUBJID, .keep_all = TRUE) %>% -#' mutate(PARAMCD = "TDURD", -#' PARAM = "Overall duration (days)", +#' mutate(PARAMCD = 'TDURD', +#' PARAM = 'Overall duration (days)', #' AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE), -#' AVALU = "Days") %>% +#' AVALU = 'Days') %>% #' bind_rows(ADEX) -#' formatters::var_labels(ADEX) <- labels' # nolint -#' ), -#' check = TRUE +#' formatters::var_labels(ADEX) <- labels" # nolint +#' ) #' ), #' modules = modules( #' tm_t_exposure( diff --git a/R/tm_t_logistic.R b/R/tm_t_logistic.R index 7b6da4e77e..7ac08ac752 100644 --- a/R/tm_t_logistic.R +++ b/R/tm_t_logistic.R @@ -232,8 +232,10 @@ template_logistic <- function(dataname, #' #' library(scda) #' library(dplyr) -#' ADSL <- synthetic_cdisc_data("latest")$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$adrs %>% #' filter(PARAMCD %in% c("BESRSPI", "INVET")) #' #' arm_ref_comp <- list( @@ -249,10 +251,15 @@ template_logistic <- function(dataname, #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$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$adrs %>% +#' filter(PARAMCD %in% c('BESRSPI', 'INVET'))" +#' ) #' ), #' modules = modules( #' tm_t_logistic( diff --git a/R/tm_t_pp_laboratory.R b/R/tm_t_pp_laboratory.R index 072ac90b57..6aff8ae187 100644 --- a/R/tm_t_pp_laboratory.R +++ b/R/tm_t_pp_laboratory.R @@ -109,14 +109,20 @@ template_laboratory <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$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$adlb" +#' ) #' ), #' modules = modules( #' tm_t_pp_laboratory( diff --git a/R/tm_t_pp_medical_history.R b/R/tm_t_pp_medical_history.R index ffc3a1931d..a5280417e7 100644 --- a/R/tm_t_pp_medical_history.R +++ b/R/tm_t_pp_medical_history.R @@ -86,18 +86,25 @@ template_medical_history <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$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$admh +#' ADMH[['MHDISTAT']] <- 'ONGOING' +#' formatters::var_labels(ADMH[c('MHDISTAT')]) <- c('Status of Disease')" +#' ) #' ), #' modules = modules( #' tm_t_pp_medical_history( diff --git a/R/tm_t_pp_prior_medication.R b/R/tm_t_pp_prior_medication.R index 3a5ba90fd0..9a42bfe8d9 100644 --- a/R/tm_t_pp_prior_medication.R +++ b/R/tm_t_pp_prior_medication.R @@ -73,8 +73,9 @@ template_prior_medication <- function(dataname = "ANL", #' #' @examples #' library(scda) -#' ADSL <- synthetic_cdisc_data("latest")$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$CMDECOD)) @@ -96,26 +97,29 @@ template_prior_medication <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$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$AENDTM +#' formatters::var_labels( +#' ADCM[c('CMINDC', 'CMTRT', 'ASTDY')]) <- c( +#' 'Indication', +#' 'Reported Name of Drug, Med, or Therapy', +#' 'Study Day of Start of Medication' +#' )", #' keys = adcm_keys -#' ), -#' check = TRUE +#' ) #' ), #' modules = modules( #' tm_t_pp_prior_medication( diff --git a/R/tm_t_shift_by_arm.R b/R/tm_t_shift_by_arm.R index 0acc0d3534..4132fe4565 100644 --- a/R/tm_t_shift_by_arm.R +++ b/R/tm_t_shift_by_arm.R @@ -169,15 +169,20 @@ template_shift_by_arm <- function(dataname, #' library(dplyr) #' library(tern) #' library(scda) -#' -#' adsl <- synthetic_cdisc_data("latest")$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$adeg" +#' ) #' ), #' modules = modules( #' tm_t_shift_by_arm( diff --git a/R/tm_t_shift_by_arm_by_worst.R b/R/tm_t_shift_by_arm_by_worst.R index 4406e9d7f9..be8bbb3f66 100644 --- a/R/tm_t_shift_by_arm_by_worst.R +++ b/R/tm_t_shift_by_arm_by_worst.R @@ -177,14 +177,20 @@ template_shift_by_arm_by_worst <- function(dataname, #' library(tern) #' library(scda) #' -#' adsl <- synthetic_cdisc_data("latest")$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$adeg" +#' ) #' ), #' modules = modules( #' tm_t_shift_by_arm_by_worst( diff --git a/R/tm_t_shift_by_grade.R b/R/tm_t_shift_by_grade.R index fc7cbff64a..91c0c782ba 100644 --- a/R/tm_t_shift_by_grade.R +++ b/R/tm_t_shift_by_grade.R @@ -475,16 +475,20 @@ template_shift_by_grade <- function(parentname, #' library(scda) #' library(dplyr) #' -#' adsl <- synthetic_cdisc_data("latest")$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("ADLB", adlb, -#' code = 'ADLB <- synthetic_cdisc_data("latest")$adlb' +#' cdisc_dataset("ADSL", adsl, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADSL <- synthetic_cdisc_data_latest$adsl" #' ), -#' check = TRUE +#' cdisc_dataset("ADLB", adlb, +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' ADLB <- synthetic_cdisc_data_latest$adlb" +#' ) #' ), #' modules = modules( #' tm_t_shift_by_grade( diff --git a/R/tm_t_smq.R b/R/tm_t_smq.R index 23f9ed20c7..3d80a4f0d6 100644 --- a/R/tm_t_smq.R +++ b/R/tm_t_smq.R @@ -317,8 +317,9 @@ template_smq <- function(dataname, #' @examples #' library(scda) #' -#' adsl <- synthetic_cdisc_data("latest")$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$", names(adae), value = TRUE) @@ -337,12 +338,13 @@ template_smq <- function(dataname, #' app <- init( #' data = cdisc_data( #' cdisc_dataset("ADSL", adsl, -#' code = "ADSL <- synthetic_cdisc_data('latest')$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$adae" +#' ) #' ), #' modules = modules( #' tm_t_smq( diff --git a/R/tm_t_summary_by.R b/R/tm_t_summary_by.R index a58463342f..a3dc923aeb 100644 --- a/R/tm_t_summary_by.R +++ b/R/tm_t_summary_by.R @@ -328,14 +328,17 @@ template_summary_by <- function(parentname, #' @examples #' # Preparation of the test case. #' library(scda) -#' adsl <- synthetic_cdisc_data("latest")$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")$adlb'), -#' check = TRUE +#' cdisc_dataset("ADSL", adsl), +#' cdisc_dataset("ADLB", adlb), +#' code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') +#' adsl <- synthetic_cdisc_data_latest$adsl +#' adlb <- synthetic_cdisc_data_latest$adlb" #' ), #' modules = modules( #' tm_t_summary_by( diff --git a/R/tm_t_tte.R b/R/tm_t_tte.R index b67338fd83..972ac30784 100644 --- a/R/tm_t_tte.R +++ b/R/tm_t_tte.R @@ -377,9 +377,9 @@ template_tte <- function(dataname = "ANL", #' @examples #' #' library(scda) -#' -#' ADSL <- synthetic_cdisc_data("latest")$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$adtte #' #' arm_ref_comp <- list( #' ACTARMCD = list( @@ -394,9 +394,14 @@ template_tte <- function(dataname = "ANL", #' #' app <- init( #' data = cdisc_data( -#' cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$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/R/utils.R b/R/utils.R index 9caa961ac4..ea36c329a4 100644 --- a/R/utils.R +++ b/R/utils.R @@ -19,9 +19,15 @@ #' call_concatenate(list(quote(f), quote(g), quote(h))) #' call_concatenate(list(quote(f))) #' call_concatenate(list()) -#' call_concatenate(list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg))))) +#' call_concatenate( +#' list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))) +#' ) #' -#' eval(call_concatenate(list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))))) +#' eval( +#' call_concatenate( +#' list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))) +#' ) +#' ) #' } call_concatenate <- function(args, bin_op = "+") { checkmate::assert_string(bin_op) @@ -400,7 +406,7 @@ is.cs_or_des <- function(x) { # nolint #' #' @export split_col_expr <- function(compare, combine, ref, arm_var) { - if (compare & combine) { + if (compare && combine) { substitute( expr = split_cols_by_groups( var = arm_var, @@ -411,7 +417,7 @@ split_col_expr <- function(compare, combine, ref, arm_var) { arm_var = arm_var ) ) - } else if (compare & !combine) { + } else if (compare && !combine) { substitute( expr = rtables::split_cols_by( var = arm_var, diff --git a/README.md b/README.md index 45d9639cab..5768c4d14d 100644 --- a/README.md +++ b/README.md @@ -25,7 +25,7 @@ These modules include, but are not limited to: - `tm_g_pp_patient_timeline`: general timeline for individual patients - ... -Most of the modules in `teal.modules.clinical` use functions from the R package [tern](https://insightsengineering.github.io/tern) in order to produce their output. +Most of the modules in `teal.modules.clinical` use functions from the R package [tern](https://insightsengineering.github.io/tern/) in order to produce their output. ## Installation 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/call_concatenate.Rd b/man/call_concatenate.Rd index bd25f3b5c4..82b419ffca 100644 --- a/man/call_concatenate.Rd +++ b/man/call_concatenate.Rd @@ -26,8 +26,14 @@ Reduce(function(existing, new) call("+", existing, new), list(quote(f), quote(g) call_concatenate(list(quote(f), quote(g), quote(h))) call_concatenate(list(quote(f))) call_concatenate(list()) -call_concatenate(list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg))))) +call_concatenate( + list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))) +) -eval(call_concatenate(list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))))) +eval( + call_concatenate( + list(quote(ggplot2::ggplot(mtcars)), quote(ggplot2::geom_point(ggplot2::aes(wt, mpg)))) + ) +) } } diff --git a/man/template_binary_outcome.Rd b/man/template_binary_outcome.Rd index a15c1f0144..6cdd89b568 100644 --- a/man/template_binary_outcome.Rd +++ b/man/template_binary_outcome.Rd @@ -80,8 +80,11 @@ Creates a valid expression for binary outcome analysis. library(dplyr) library(scda) library(tern) -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$adrs # Generate an expression for the analysis of responders. a <- template_binary_outcome( diff --git a/man/tm_a_mmrm.Rd b/man/tm_a_mmrm.Rd index c290760ed2..f9bd265ff0 100644 --- a/man/tm_a_mmrm.Rd +++ b/man/tm_a_mmrm.Rd @@ -117,8 +117,9 @@ numerical precision. library(scda) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADQS <- synthetic_cdisc_data("latest")$adqs \%>\% +synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +ADSL <- synthetic_cdisc_data_latest$adsl +ADQS <- synthetic_cdisc_data_latest$adqs \%>\% dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") \%>\% dplyr::filter(AVISIT \%in\% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) \%>\% dplyr::mutate( @@ -138,9 +139,13 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"), + cdisc_dataset("ADSL", ADSL, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl" + ), cdisc_dataset("ADQS", ADQS, - code = 'ADQS <- synthetic_cdisc_data("latest")$adqs \%>\% + code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") + ADQS <- synthetic_cdisc_data("latest")$adqs \%>\% dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") \%>\% dplyr::filter(AVISIT \%in\% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) \%>\% dplyr::mutate( @@ -150,8 +155,7 @@ app <- init( as.numeric() \%>\% as.factor() # making consecutive numeric factor )' - ), - check = TRUE + ) ), modules = modules( tm_a_mmrm( diff --git a/man/tm_g_barchart_simple.Rd b/man/tm_g_barchart_simple.Rd index 5340420bed..cb3004128e 100644 --- a/man/tm_g_barchart_simple.Rd +++ b/man/tm_g_barchart_simple.Rd @@ -87,8 +87,7 @@ app <- init( dplyr::filter(!((AETOXGR == 1) & (AESEV == 'MILD') & (ARM == 'A: Drug X'))) formatters::var_labels(ADAE) <- adae_labels ADAE" - ), - check = TRUE + ) ), modules = modules( tm_g_barchart_simple( diff --git a/man/tm_g_forest_rsp.Rd b/man/tm_g_forest_rsp.Rd index 3d520670da..376827dbb0 100644 --- a/man/tm_g_forest_rsp.Rd +++ b/man/tm_g_forest_rsp.Rd @@ -116,8 +116,9 @@ library(scda) library(dplyr) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$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$adrs \%>\% mutate(AVALC = d_onco_rsp_label(AVALC)) \%>\% filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP") @@ -137,11 +138,11 @@ app <- init( cdisc_dataset("ADSL", ADSL), cdisc_dataset("ADRS", ADRS), code = - "ADSL <- synthetic_cdisc_data('latest')$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$adrs \%>\% mutate(AVALC = d_onco_rsp_label(AVALC)) \%>\% - filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')", - check = TRUE + filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')" ), modules = modules( tm_g_forest_rsp( diff --git a/man/tm_g_forest_tte.Rd b/man/tm_g_forest_tte.Rd index fd1471196d..ea075b9111 100644 --- a/man/tm_g_forest_tte.Rd +++ b/man/tm_g_forest_tte.Rd @@ -119,8 +119,10 @@ with ADaM structure library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$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$RACE) @@ -138,13 +140,16 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( cdisc_dataset( - "ADSL", - ADSL, - code = "ADSL <- synthetic_cdisc_data('latest')$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$adtte" + ) ), modules = modules( tm_g_forest_tte( diff --git a/man/tm_g_km.Rd b/man/tm_g_km.Rd index 0b289676e8..b5a366f722 100644 --- a/man/tm_g_km.Rd +++ b/man/tm_g_km.Rd @@ -122,8 +122,7 @@ arm_ref_comp <- list( app <- init( data = cdisc_data( cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$adsl'), - cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte'), - check = TRUE + cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_data("latest")$adtte') ), modules = modules( tm_g_km( diff --git a/man/tm_g_lineplot.Rd b/man/tm_g_lineplot.Rd index 7de7bc9b81..a5e5a647f6 100644 --- a/man/tm_g_lineplot.Rd +++ b/man/tm_g_lineplot.Rd @@ -127,17 +127,23 @@ 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..f73d9161ea 100644 --- a/man/tm_g_pp_adverse_events.Rd +++ b/man/tm_g_pp_adverse_events.Rd @@ -90,14 +90,21 @@ 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 99e7eb1994..11d7df8eb4 100644 --- a/man/tm_g_pp_patient_timeline.Rd +++ b/man/tm_g_pp_patient_timeline.Rd @@ -104,9 +104,12 @@ This teal module produces a patient profile timeline plot using ADaM datasets. \examples{ library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$adsl -ADAE <- synthetic_cdisc_data("latest")$adae -ADCM <- synthetic_cdisc_data("latest")$adcm + +synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") + +ADSL <- synthetic_cdisc_data_latest$adsl +ADAE <- synthetic_cdisc_data_latest$adae +ADCM <- synthetic_cdisc_data_latest$adcm #' Modify ADCM ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD)) @@ -134,32 +137,38 @@ 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")$adsl'), - cdisc_dataset("ADAE", ADAE, code = 'ADAE <- synthetic_cdisc_data("latest")$adae'), + 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" + ), cdisc_dataset("ADCM", ADCM, - code = '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$AENDTM formatters::var_labels( - ADCM[c("CMINDC", "CMDECOD", "CMSTDY", "CMENDY")]) <- c( - "Indication", - "Reported Name of Drug, Med, or Therapy", - "Study Day of Start of Medication", - "Study Day of End of Medication")', + ADCM[c('CMINDC', 'CMDECOD', 'CMSTDY', 'CMENDY')]) <- c( + 'Indication', + 'Reported Name of Drug, Med, or Therapy', + 'Study Day of Start of Medication', + 'Study Day of End of Medication')", keys = adcm_keys - ), - check = TRUE + ) ), modules = modules( tm_g_pp_patient_timeline( diff --git a/man/tm_g_pp_therapy.Rd b/man/tm_g_pp_therapy.Rd index cbce92939e..7fab9b1cec 100644 --- a/man/tm_g_pp_therapy.Rd +++ b/man/tm_g_pp_therapy.Rd @@ -103,8 +103,9 @@ This teal module produces a patient profile therapy plot using ADaM datasets. library(scda) library(nestcolor) -ADSL <- synthetic_cdisc_data("latest")$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$CMDECOD)) @@ -127,27 +128,29 @@ adcm_keys <- c("STUDYID", "USUBJID", "ASTDTM", "CMSEQ", "ATC1", "ATC2", "ATC3", app <- init( data = cdisc_data( - cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_data("latest")$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..f863c8a19b 100644 --- a/man/tm_g_pp_vitals.Rd +++ b/man/tm_g_pp_vitals.Rd @@ -78,14 +78,20 @@ 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..4991118588 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 +120,13 @@ 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 +135,7 @@ 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..40c96f1663 100644 --- a/man/tm_t_abnormality_by_worst_grade.Rd +++ b/man/tm_t_abnormality_by_worst_grade.Rd @@ -98,18 +98,22 @@ 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')$adlb \%>\% + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data('latest')$adlb \%>\% filter(!AVISIT \%in\% c('SCREENING', 'BASELINE'))" - ), - check = TRUE + ) ), modules = modules( tm_t_abnormality_by_worst_grade( diff --git a/man/tm_t_binary_outcome.Rd b/man/tm_t_binary_outcome.Rd index ca68793a54..7e915911c8 100644 --- a/man/tm_t_binary_outcome.Rd +++ b/man/tm_t_binary_outcome.Rd @@ -121,8 +121,10 @@ reference group. \examples{ library(dplyr) library(scda) -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 \%>\% mutate(AVALC = d_onco_rsp_label(AVALC)) \%>\% filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP") arm_ref_comp <- list( @@ -134,11 +136,11 @@ app <- init( cdisc_dataset("ADSL", ADSL), cdisc_dataset("ADRS", ADRS), code = - "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 \%>\% mutate(AVALC = d_onco_rsp_label(AVALC)) \%>\% - filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')", - check = TRUE + filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')" ), modules = modules( tm_t_binary_outcome( diff --git a/man/tm_t_coxreg.Rd b/man/tm_t_coxreg.Rd index 56f33e43af..234b07fe20 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 +150,14 @@ 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 2fdd144517..886eef19b7 100644 --- a/man/tm_t_exposure.Rd +++ b/man/tm_t_exposure.Rd @@ -91,12 +91,12 @@ For more details, see the vignette: \code{vignette("custom-basic-table-arguments Teal module: Exposure Table for Risk management plan } \examples{ - library(scda) library(dplyr) -adsl <- synthetic_cdisc_data("latest")$adsl -adex <- synthetic_cdisc_data("latest")$adex +synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest") +adsl <- synthetic_cdisc_data_latest$adsl +adex <- synthetic_cdisc_data_latest$adex set.seed(1, kind = "Mersenne-Twister") labels <- formatters::var_labels(adex, fill = FALSE) @@ -113,21 +113,24 @@ formatters::var_labels(adex) <- labels 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("ADEX", adex, - code = 'set.seed(1, kind = "Mersenne-Twister") - ADEX <- synthetic_cdisc_data("latest")$adex + code = "set.seed(1, kind = 'Mersenne-Twister') + synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADEX <- synthetic_cdisc_data_latest$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 - ), - check = TRUE + formatters::var_labels(ADEX) <- labels" # nolint + ) ), modules = modules( tm_t_exposure( diff --git a/man/tm_t_logistic.Rd b/man/tm_t_logistic.Rd index 41a5a14df0..dee4601922 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 +102,15 @@ 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..b55ed271ff 100644 --- a/man/tm_t_pp_laboratory.Rd +++ b/man/tm_t_pp_laboratory.Rd @@ -62,14 +62,20 @@ 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..999014d578 100644 --- a/man/tm_t_pp_medical_history.Rd +++ b/man/tm_t_pp_medical_history.Rd @@ -50,18 +50,25 @@ 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..82832afce9 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 +78,29 @@ 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..52cfc24139 100644 --- a/man/tm_t_shift_by_arm.Rd +++ b/man/tm_t_shift_by_arm.Rd @@ -95,15 +95,20 @@ 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 87ba1dce0c..ccf12a90d7 100644 --- a/man/tm_t_shift_by_arm_by_worst.Rd +++ b/man/tm_t_shift_by_arm_by_worst.Rd @@ -96,14 +96,20 @@ 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..8f7a10d0e5 100644 --- a/man/tm_t_shift_by_grade.Rd +++ b/man/tm_t_shift_by_grade.Rd @@ -108,16 +108,20 @@ 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")$adsl'), - cdisc_dataset("ADLB", adlb, - code = 'ADLB <- synthetic_cdisc_data("latest")$adlb' + cdisc_dataset("ADSL", adsl, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADSL <- synthetic_cdisc_data_latest$adsl" ), - check = TRUE + cdisc_dataset("ADLB", adlb, + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + ADLB <- synthetic_cdisc_data_latest$adlb" + ) ), modules = modules( tm_t_shift_by_grade( diff --git a/man/tm_t_smq.Rd b/man/tm_t_smq.Rd index 922f23be85..c659423405 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 +112,13 @@ 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_summary_by.Rd b/man/tm_t_summary_by.Rd index dff34c369d..6c2a367978 100644 --- a/man/tm_t_summary_by.Rd +++ b/man/tm_t_summary_by.Rd @@ -113,14 +113,17 @@ Teal Module: Summarize Variables by Row Groups Module \examples{ # Preparation of the test case. 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), + cdisc_dataset("ADLB", adlb), + code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest') + adsl <- synthetic_cdisc_data_latest$adsl + adlb <- synthetic_cdisc_data_latest$adlb" ), modules = modules( tm_t_summary_by( diff --git a/man/tm_t_tte.Rd b/man/tm_t_tte.Rd index 04a4a7576b..62e31a1139 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 +142,14 @@ 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(