Merge c85816d into 27dd15e

DESCRIPTION

@@ -66,15 +66,11 @@ Suggests:
     forcats,
     knitr,
     nestcolor (>= 0.1.0),
-    scda (>= 0.1.5),
-    scda.2022 (>= 0.1.3),
     teal.data (>= 0.1.2),
-    testthat (>= 2.0)
+    testthat (>= 3.0)
 VignetteBuilder:
     knitr
 Remotes:
-    insightsengineering/scda.2022@*release,
-    insightsengineering/scda@*release,
     insightsengineering/teal.code@*release,
     insightsengineering/teal.data@*release,
     insightsengineering/teal.logger@*release,
@@ -86,6 +82,7 @@ Remotes:
     insightsengineering/tern.mmrm@*release,
     insightsengineering/tern@*release
 Config/Needs/website: insightsengineering/nesttemplate
+Config/testthat/edition: 3
 Encoding: UTF-8
 Language: en-US
 LazyData: true

NEWS.md

@@ -18,7 +18,8 @@
   automatically determined optimizer.
 * Creation of internal data for `adsl`, `adae`, `adaette`, `adcm`, `adeg`, `adex`, `adlb`, `admh`, `adqs`, `adrs`, `adtte`, and `advs`. 
   They are accessible via `tmc_ex_*` prefix.
-* Partial substitution of `scda` data with internal data in examples.
+* Updated all examples and tests to use datasets from the `teal.modules.clinical` package instead of `scda` datasets.
+* Updated tests to use `testthat` 3rd edition and replaced all applicable tests with snapshot testing.
 
 # teal.modules.clinical 0.8.14
 

R/teal.modules.clinical.R

@@ -6,25 +6,20 @@
 #' @import teal
 #' @import tern
 #' @importFrom magrittr %>%
-#' @importFrom rlang :=
+#' @importFrom methods is
+#' @importFrom rlang := .data
+#' @importFrom tern.gee lsmeans
 #'
 #' @docType package
 #' @name teal.modules.clinical
 #' @keywords internal
 NULL
 
 # We need this to avoid R CMD check warning about missing global definitions.
-if (getRversion() >= "2.15.1") {
-  utils::globalVariables(c(
-    "new_arm_ref_comp",
-    "new_comp_arm",
-    "usubjid"
-  ))
-}
-
-#' Avoiding R CMD check notes
-#' @importFrom methods is
-#' @importFrom rlang .data
-#' @importFrom tern.gee lsmeans
-#' @noRd
-NULL
+utils::globalVariables(c(
+  "column_name",
+  "n_column_name",
+  "new_arm_ref_comp",
+  "new_comp_arm",
+  "usubjid"
+))

R/tm_g_pp_patient_timeline.R

@@ -356,27 +356,24 @@ template_patient_timeline <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADAE <- tmc_ex_adae
-#' ADCM <- tmc_ex_adcm
+#' adsl <- tmc_ex_adsl
+#' adae <- tmc_ex_adae
+#' adcm <- tmc_ex_adcm
 #'
 #' # Modify ADCM
-#' 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", ]$CMSTDY <- 150
-#' ADCM$CMENDY <- 500
-#' 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$CMDOSE <- 1
+#' adcm$CMDOSU <- "U"
+#' adcm$CMROUTE <- "CMROUTE"
+#' adcm$CMDOSFRQ <- "CMDOSFRQ"
+#' adcm$CMSTDY <- 1
+#' adcm[adcm$CMCAT == "medcl B", ]$CMSTDY <- 20
+#' adcm[adcm$CMCAT == "medcl C", ]$CMSTDY <- 150
+#' adcm$CMENDY <- 500
+#' 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",
@@ -386,35 +383,9 @@ template_patient_timeline <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
-#'     cdisc_dataset("ADAE", ADAE,
-#'       code = 'ADAE <- synthetic_cdisc_dataset("latest", "adae")'
-#'     ),
-#'     cdisc_dataset("ADCM", ADCM,
-#'       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$CMSTDY <- 1
-#'         ADCM[ADCM$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$CMASTDTM <- ADCM$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")',
-#'       keys = adcm_keys
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADAE", adae),
+#'     cdisc_dataset("ADCM", adcm, keys = adcm_keys)
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_patient_timeline(
@@ -425,43 +396,43 @@ template_patient_timeline <- function(dataname = "ANL",
 #'       patient_col = "USUBJID",
 #'       plot_height = c(600L, 200L, 2000L),
 #'       cmdecod = choices_selected(
-#'         choices = variable_choices(ADCM, "CMDECOD"),
+#'         choices = variable_choices(adcm, "CMDECOD"),
 #'         selected = "CMDECOD",
 #'       ),
 #'       aeterm = choices_selected(
-#'         choices = variable_choices(ADAE, "AETERM"),
+#'         choices = variable_choices(adae, "AETERM"),
 #'         selected = c("AETERM")
 #'       ),
 #'       aetime_start = choices_selected(
-#'         choices = variable_choices(ADAE, "ASTDTM"),
+#'         choices = variable_choices(adae, "ASTDTM"),
 #'         selected = c("ASTDTM")
 #'       ),
 #'       aetime_end = choices_selected(
-#'         choices = variable_choices(ADAE, "AENDTM"),
+#'         choices = variable_choices(adae, "AENDTM"),
 #'         selected = c("AENDTM")
 #'       ),
 #'       dstime_start = choices_selected(
-#'         choices = variable_choices(ADCM, "CMASTDTM"),
+#'         choices = variable_choices(adcm, "CMASTDTM"),
 #'         selected = c("CMASTDTM")
 #'       ),
 #'       dstime_end = choices_selected(
-#'         choices = variable_choices(ADCM, "CMAENDTM"),
+#'         choices = variable_choices(adcm, "CMAENDTM"),
 #'         selected = c("CMAENDTM")
 #'       ),
 #'       aerelday_start = choices_selected(
-#'         choices = variable_choices(ADAE, "ASTDY"),
+#'         choices = variable_choices(adae, "ASTDY"),
 #'         selected = c("ASTDY")
 #'       ),
 #'       aerelday_end = choices_selected(
-#'         choices = variable_choices(ADAE, "AENDY"),
+#'         choices = variable_choices(adae, "AENDY"),
 #'         selected = c("AENDY")
 #'       ),
 #'       dsrelday_start = choices_selected(
-#'         choices = variable_choices(ADCM, "ASTDY"),
+#'         choices = variable_choices(adcm, "ASTDY"),
 #'         selected = c("ASTDY")
 #'       ),
 #'       dsrelday_end = choices_selected(
-#'         choices = variable_choices(ADCM, "AENDY"),
+#'         choices = variable_choices(adcm, "AENDY"),
 #'         selected = c("AENDY")
 #'       )
 #'     )