Update scda data (#658)

* Update all data loads

* Update documentation

* Update NEWS

* Update to 2022_10_13 release

* Update test data version

* Fix lint

This reverts commit 172877b.

Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: teal.modules.clinical
 Title: Teal Modules for Standard Clinical Outputs
-Version: 0.8.14
+Version: 0.8.14.9000
 Date: 2022-10-14
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),

NEWS.md

@@ -1,3 +1,8 @@
+# teal.modules.clinical 0.8.14.9000
+
+### Enhancements
+* Replaced `synthetic_cdisc_data` with refactored `synthetic_cdisc_dataset` function to speed up dataset loading in tests/examples.
+
 # teal.modules.clinical 0.8.14
 
 ### Enhancements

R/labels.R

@@ -13,7 +13,7 @@
 #' column_annotation_label(data, "cyl")
 #' column_annotation_label(data, "cyl", omit_raw_name = TRUE)
 #' \dontrun{
-#' ANL <- scda::synthetic_cdisc_data("latest")$adsl
+#' ANL <- synthetic_cdisc_dataset("latest", "adsl")
 #' column_annotation_label(ANL, "ACTARM")
 #' }
 #' @export

R/tm_a_mmrm.R

@@ -454,9 +454,8 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' library(scda)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADQS <- synthetic_cdisc_data_latest$adqs %>%
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADQS <- synthetic_cdisc_dataset("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(
@@ -477,12 +476,10 @@ template_mmrm_plots <- function(fit_name,
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'               ADSL <- synthetic_cdisc_data_latest$adsl"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
 #'     ),
 #'     cdisc_dataset("ADQS", ADQS,
-#'       code = 'synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#'               ADQS <- synthetic_cdisc_data("latest")$adqs %>%
+#'       code = 'ADQS <- synthetic_cdisc_dataset("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(

R/tm_g_barchart_simple.R

@@ -18,26 +18,25 @@
 #' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADAE <- synthetic_cdisc_data("latest")$adae
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
 #'
 #' adae_labels <- formatters::var_labels(ADAE, fill = FALSE)
 #' ADAE <- ADAE %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'
 #' # reinstate labels
 #' formatters::var_labels(ADAE) <- adae_labels
 #'
-#'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = "ADSL <- synthetic_cdisc_data('latest')$adsl"),
+#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'),
 #'     cdisc_dataset("ADAE", ADAE,
-#'       code = "ADAE <- synthetic_cdisc_data('latest')$adae
+#'       code = 'ADAE <- synthetic_cdisc_dataset("latest", "adae")
 #'               adae_labels <- formatters::var_labels(ADAE, fill = FALSE)
 #'               ADAE <- ADAE %>%
-#'                 dplyr::filter(!((AETOXGR == 1) & (AESEV == 'MILD') & (ARM == 'A: Drug X')))
+#'                 dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'               formatters::var_labels(ADAE) <- adae_labels
-#'               ADAE"
+#'               ADAE'
 #'     )
 #'   ),
 #'   modules = modules(

R/tm_g_ci.R

@@ -192,15 +192,15 @@ template_g_ci <- function(dataname, # nolint
 #'
 #' library(scda)
 #' library(nestcolor)
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADLB <- synthetic_cdisc_dataset("latest", "adlb")
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL),
 #'     cdisc_dataset("ADLB", ADLB),
-#'     code = "ADSL <- synthetic_cdisc_data('latest')$adsl
-#'     ADLB <- synthetic_cdisc_data('latest')$adlb"
+#'     code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#'     ADLB <- synthetic_cdisc_dataset("latest", "adlb")' # nolint
 #'   ),
 #'   modules = modules(
 #'     tm_g_ci(

R/tm_g_forest_rsp.R

@@ -220,9 +220,8 @@ template_forest_rsp <- function(dataname = "ANL",
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADRS <- synthetic_cdisc_data_latest$adrs %>%
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADRS <- synthetic_cdisc_dataset("latest", "adrs") %>%
 #'   mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
 #'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #'
@@ -242,11 +241,10 @@ template_forest_rsp <- function(dataname = "ANL",
 #'     cdisc_dataset("ADSL", ADSL),
 #'     cdisc_dataset("ADRS", ADRS),
 #'     code =
-#'       "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'        ADSL <- synthetic_cdisc_data_latest$adsl
-#'        ADRS <- synthetic_cdisc_data_latest$adrs %>%
+#'       'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#'        ADRS <- synthetic_cdisc_dataset("latest", "adrs") %>%
 #'        mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
-#'        filter(PARAMCD != 'OVRINV' | AVISIT == 'FOLLOW UP')"
+#'        filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")' # nolint
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_rsp(

R/tm_g_forest_tte.R

@@ -227,10 +227,8 @@ template_forest_tte <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#'
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADTTE <- synthetic_cdisc_data_latest$adtte
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
 #'
 #' ADSL$RACE <- droplevels(ADSL$RACE)
 #'
@@ -249,14 +247,12 @@ template_forest_tte <- function(dataname = "ANL",
 #'   data = cdisc_data(
 #'     cdisc_dataset(
 #'       "ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADSL <- synthetic_cdisc_data_latest$adsl
-#'         ADSL$RACE <- droplevels(ADSL$RACE)"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#'         ADSL$RACE <- droplevels(ADSL$RACE)' # nolint
 #'     ),
 #'     cdisc_dataset(
 #'       "ADTTE", ADTTE,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADTTE <- synthetic_cdisc_data_latest$adtte"
+#'       code = 'ADTTE <- synthetic_cdisc_dataset("latest", "adtte")'
 #'     )
 #'   ),
 #'   modules = modules(

R/tm_g_ipp.R

@@ -190,8 +190,8 @@ template_g_ipp <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' adsl <- synthetic_cdisc_data("latest")$adsl %>% slice(1:20)
-#' adlb <- synthetic_cdisc_data("latest")$adlb
+#' adsl <- synthetic_cdisc_dataset("latest", "adsl") %>% slice(1:20)
+#' adlb <- synthetic_cdisc_dataset("latest", "adlb")
 #' adlb <- adlb %>% filter(USUBJID %in% adsl$USUBJID)
 #'
 #' adsl <- df_explicit_na(adsl)
@@ -203,15 +203,15 @@ template_g_ipp <- function(dataname = "ANL",
 #'     cdisc_dataset(
 #'       "ADSL",
 #'       adsl,
-#'       code = "ADSL <- synthetic_cdisc_data('latest')$adsl %>% slice(1:20)
-#'       ADSL <- df_explicit_na(ADSL)"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl") %>% slice(1:20)
+#'       ADSL <- df_explicit_na(ADSL)' # nolint
 #'     ),
 #'     cdisc_dataset(
 #'       "ADLB",
 #'       adlb,
-#'       code = "ADLB <- synthetic_cdisc_data('latest')$adlb
+#'       code = 'ADLB <- synthetic_cdisc_dataset("latest", "adlb")
 #'       ADLB <- df_explicit_na(ADLB) %>%
-#'       dplyr::filter(AVISIT != 'SCREENING')"
+#'       dplyr::filter(AVISIT != "SCREENING")' # nolint
 #'     )
 #'   ),
 #'   modules = modules(

R/tm_g_km.R

@@ -293,12 +293,11 @@ template_g_km <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#'
 #' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl
-#' ADTTE <- synthetic_cdisc_data("latest")$adtte
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
 #'
 #' arm_ref_comp <- list(
 #'   ACTARMCD = list(
@@ -313,8 +312,8 @@ 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')
+#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'),
+#'     cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_dataset("latest", "adtte")')
 #'   ),
 #'   modules = modules(
 #'     tm_g_km(

R/tm_g_lineplot.R

@@ -203,26 +203,22 @@ template_g_lineplot <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#'
 #' library(scda)
 #' library(nestcolor)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADLB <- synthetic_cdisc_data_latest$adlb
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADLB <- synthetic_cdisc_dataset("latest", "adlb")
 #'
 #' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
 #'     ),
 #'     cdisc_dataset("ADLB", ADLB,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADLB <- synthetic_cdisc_data_latest$adlb
-#'         ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))"
+#'       code = 'ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+#'         ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))' # nolint
 #'     )
 #'   ),
 #'   modules = modules(

R/tm_g_pp_adverse_events.R

@@ -183,19 +183,16 @@ template_adverse_events <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADAE <- synthetic_cdisc_data_latest$adae
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
 #'     ),
 #'     cdisc_dataset("ADAE", ADAE,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADAE <- synthetic_cdisc_data_latest$adae"
+#'       code = 'ADAE <- synthetic_cdisc_dataset("latest", "adae")'
 #'     )
 #'   ),
 #'   modules = modules(

R/tm_g_pp_patient_timeline.R

@@ -357,11 +357,9 @@ template_patient_timeline <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' 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$adcm
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
+#' ADCM <- synthetic_cdisc_dataset("latest", "adcm")
 #'
 #' #' Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
@@ -390,35 +388,32 @@ template_patient_timeline <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
 #'     ),
 #'     cdisc_dataset("ADAE", ADAE,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADAE <- synthetic_cdisc_data_latest$adae"
+#'       code = 'ADAE <- synthetic_cdisc_dataset("latest", "adae")'
 #'     ),
 #'     cdisc_dataset("ADCM", ADCM,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADCM <- synthetic_cdisc_data_latest$adcm
-#'         ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
+#'       code = 'ADCM <- synthetic_cdisc_dataset("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
 #'     )
 #'   ),

R/tm_g_pp_therapy.R

@@ -256,9 +256,8 @@ template_therapy <- function(dataname = "ANL",
 #' library(scda)
 #' library(nestcolor)
 #'
-#' synthetic_cdisc_data_latest <- synthetic_cdisc_data("latest")
-#' ADSL <- synthetic_cdisc_data_latest$adsl
-#' ADCM <- synthetic_cdisc_data_latest$adcm
+#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
+#' ADCM <- synthetic_cdisc_dataset("latest", "adcm")
 #'
 #' #' Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
@@ -282,26 +281,25 @@ template_therapy <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL,
-#'       code = "synthetic_cdisc_data_latest <- synthetic_cdisc_data('latest')
-#'         ADSL <- synthetic_cdisc_data_latest$adsl"
+#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
 #'     ),
 #'     cdisc_dataset("ADCM", ADCM,
-#'       code = "ADCM <- synthetic_cdisc_data('latest')$adcm
-#'         ADCM$CMINDC <- paste0('Indication_', as.numeric(ADCM$CMDECOD))
+#'       code = 'ADCM <- synthetic_cdisc_dataset("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
 #'     )
 #'   ),