Add TMC example data (#731)

Closes #729 --------- Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com>
insightsengineering · Mar 1, 2023 · 327fd66 · 327fd66
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diff --git a/NEWS.md b/NEWS.md
@@ -16,8 +16,8 @@
 * Removed unused argument `param` from `tm_g_pp_vitals`.
 * Removed optimizer choice from `tm_a_mmrm` since we can just always use the 
   automatically determined optimizer.
-* Creation of internal data for `adsl`, `adae`, `adlb`, `adcm`, `adrs`, and `adtte`. They are accessible
-  via `tmc_ex_*` prefix.
+* 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.
 
 # teal.modules.clinical 0.8.14

diff --git a/R/data.R b/R/data.R
@@ -13,17 +13,42 @@ NULL
 #'
 "tmc_ex_adae"
 
+#' @describeIn ex_data ADAETTE data
+#'
+"tmc_ex_adaette"
+
+#' @describeIn ex_data ADCM data
+#'
+"tmc_ex_adcm"
+
+#' @describeIn ex_data ADEG data
+#'
+"tmc_ex_adeg"
+
+#' @describeIn ex_data ADEX data
+#'
+"tmc_ex_adex"
+
 #' @describeIn ex_data ADLB data
 #'
 "tmc_ex_adlb"
 
+#' @describeIn ex_data ADMH data
+#'
+"tmc_ex_admh"
+
+#' @describeIn ex_data ADQS data
+#'
+"tmc_ex_adqs"
+
 #' @describeIn ex_data ADRS data
 #'
 "tmc_ex_adrs"
 
 #' @describeIn ex_data ADTTE data
 #'
 "tmc_ex_adtte"
-#' @describeIn ex_data ADCM data
+
+#' @describeIn ex_data ADVS data
 #'
-"tmc_ex_adcm"
+"tmc_ex_advs"
diff --git a/R/labels.R b/R/labels.R
@@ -13,8 +13,7 @@
 #' column_annotation_label(data, "cyl")
 #' column_annotation_label(data, "cyl", omit_raw_name = TRUE)
 #' \dontrun{
-#' ANL <- synthetic_cdisc_dataset("latest", "adsl")
-#' column_annotation_label(ANL, "ACTARM")
+#' column_annotation_label(tmc_ex_adsl, "ACTARM")
 #' }
 #' @export
 column_annotation_label <- function(dataset, column, omit_raw_name = FALSE) {

diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -128,10 +128,8 @@ template_a_gee <- function(output_table,
 #' @export
 #'
 #' @examples
-#' library(scda)
-#'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADQS <- synthetic_cdisc_dataset("latest", "adqs") %>%
+#' adsl <- tmc_ex_adsl
+#' adqs <- tmc_ex_adqs %>%
 #'   dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
 #'   dplyr::mutate(
 #'     AVISIT = as.factor(AVISIT),
@@ -145,21 +143,8 @@ template_a_gee <- function(output_table,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL),
-#'     cdisc_dataset("ADQS", ADQS,
-#'       code = 'ADQS <- synthetic_cdisc_dataset("latest", "adqs") %>%
-#'               dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
-#'               dplyr::mutate(
-#'                 AVISIT = as.factor(AVISIT),
-#'                 AVISITN = rank(AVISITN) %>%
-#'                   as.factor() %>%
-#'                   as.numeric() %>%
-#'                   as.factor(),
-#'                 AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
-#'               ) %>%
-#'               droplevels()
-#'              '
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADQS", adqs)
 #'   ),
 #'   modules = modules(
 #'     tm_a_gee(
@@ -170,7 +155,7 @@ template_a_gee <- function(output_table,
 #'       arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
 #'       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
 #'       paramcd = choices_selected(
-#'         choices = value_choices(ADQS, "PARAMCD", "PARAM"),
+#'         choices = value_choices(adqs, "PARAMCD", "PARAM"),
 #'         selected = "FKSI-FWB"
 #'       ),
 #'       cov_var = choices_selected(c("BASE", "AGE", "SEX"), NULL)

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -451,10 +451,8 @@ template_mmrm_plots <- function(fit_name,
 #' numerical precision.
 #'
 #' @examples
-#' library(scda)
-#'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADQS <- synthetic_cdisc_dataset("latest", "adqs") %>%
+#' adsl <- tmc_ex_adsl
+#' adqs <- tmc_ex_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(
@@ -474,21 +472,8 @@ template_mmrm_plots <- function(fit_name,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
-#'     cdisc_dataset("ADQS", 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(
-#'                 AVISIT = as.factor(AVISIT),
-#'                 AVISITN = rank(AVISITN) %>%
-#'                   as.factor() %>%
-#'                   as.numeric() %>%
-#'                   as.factor() # making consecutive numeric factor
-#'               )'
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADQS", adqs)
 #'   ),
 #'   modules = modules(
 #'     tm_a_mmrm(
@@ -500,7 +485,7 @@ template_mmrm_plots <- function(fit_name,
 #'       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
 #'       arm_ref_comp = arm_ref_comp,
 #'       paramcd = choices_selected(
-#'         choices = value_choices(ADQS, "PARAMCD", "PARAM"),
+#'         choices = value_choices(adqs, "PARAMCD", "PARAM"),
 #'         selected = "FKSI-FWB"
 #'       ),
 #'       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
@@ -1110,8 +1095,8 @@ srv_mmrm <- function(id,
     state_has_changed <- shiny::reactive({
       shiny::req(state$input)
       displayed_state <- mmrm_inputs_reactive()
-      equal_ADSL <- dplyr::all_equal(state$input$adsl_filtered, displayed_state$adsl_filtered) # nolint
-      equal_dataname <- dplyr::all_equal(state$input$anl_filtered, displayed_state$anl_filtered)
+      equal_ADSL <- all.equal(state$input$adsl_filtered, displayed_state$adsl_filtered) # nolint
+      equal_dataname <- all.equal(state$input$anl_filtered, displayed_state$anl_filtered)
       true_means_change <- vapply(
         sync_inputs,
         FUN = function(x) {
@@ -1132,7 +1117,7 @@ srv_mmrm <- function(id,
         FUN.VALUE = logical(1)
       )
 
-      # all_equal function either returns TRUE or a character scalar to describe where there is inequality
+      # all.equal function either returns TRUE or a character scalar to describe where there is inequality
       any(c(is.character(equal_ADSL), is.character(equal_dataname), true_means_change))
     })
 

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -205,30 +205,28 @@ template_g_lineplot <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' ADSL <- tmc_ex_adsl
-#' ADLB <- tmc_ex_adlb
-#'
-#' ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))
+#' adsl <- tmc_ex_adsl
+#' adlb <- tmc_ex_adlb %>% dplyr::mutate(AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL),
-#'     cdisc_dataset("ADLB", ADLB)
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADLB", adlb)
 #'   ),
 #'   modules = modules(
 #'     tm_g_lineplot(
 #'       label = "Line Plot",
 #'       dataname = "ADLB",
 #'       strata = choices_selected(
-#'         variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
+#'         variable_choices(adsl, c("ARM", "ARMCD", "ACTARMCD")),
 #'         "ARM"
 #'       ),
 #'       y = choices_selected(
-#'         variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
+#'         variable_choices(adlb, c("AVAL", "BASE", "CHG", "PCHG")),
 #'         "AVAL"
 #'       ),
 #'       param = choices_selected(
-#'         value_choices(ADLB, "PARAMCD", "PARAM"),
+#'         value_choices(adlb, "PARAMCD", "PARAM"),
 #'         "ALT"
 #'       )
 #'     )

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -189,20 +189,15 @@ template_vitals <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADVS <- synthetic_cdisc_dataset("latest", "advs")
+#' adsl <- tmc_ex_adsl
+#' advs <- tmc_ex_advs
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
-#'     cdisc_dataset("ADVS", ADVS,
-#'       code = 'ADVS <- synthetic_cdisc_dataset("latest", "advs")'
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADVS", advs)
 #'   ),
 #'   modules = modules(
 #'     tm_g_pp_vitals(
@@ -212,15 +207,15 @@ template_vitals <- function(dataname = "ANL",
 #'       patient_col = "USUBJID",
 #'       plot_height = c(600L, 200L, 2000L),
 #'       paramcd = choices_selected(
-#'         choices = variable_choices(ADVS, "PARAMCD"),
+#'         choices = variable_choices(advs, "PARAMCD"),
 #'         selected = "PARAMCD"
 #'       ),
 #'       xaxis = choices_selected(
-#'         choices = variable_choices(ADVS, "ADY"),
+#'         choices = variable_choices(advs, "ADY"),
 #'         selected = "ADY"
 #'       ),
 #'       aval = choices_selected(
-#'         choices = variable_choices(ADVS, "AVAL"),
+#'         choices = variable_choices(advs, "AVAL"),
 #'         selected = "AVAL"
 #'       )
 #'     )

diff --git a/R/tm_t_ancova.R b/R/tm_t_ancova.R
@@ -429,12 +429,8 @@ template_ancova <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' # Preparation of the test case.
-#' library(dplyr)
-#' library(scda)
-#'
-#' adsl <- synthetic_cdisc_dataset("latest", "adsl")
-#' adqs <- synthetic_cdisc_dataset("latest", "adqs")
+#' adsl <- tmc_ex_adsl
+#' adqs <- tmc_ex_adqs
 #'
 #' arm_ref_comp <- list(
 #'   ARM = list(
@@ -450,12 +446,7 @@ template_ancova <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADQS", adqs),
-#'     code =
-#'       '
-#'       ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#'       ADQS <- synthetic_cdisc_dataset("latest", "adqs")
-#'       '
+#'     cdisc_dataset("ADQS", adqs)
 #'   ),
 #'   modules = modules(
 #'     tm_t_ancova(

diff --git a/R/tm_t_events_patyear.R b/R/tm_t_events_patyear.R
@@ -150,28 +150,16 @@ template_events_patyear <- function(dataname,
 #'
 #' @export
 #' @examples
-#' # Preparation of the test case.
-#' library(dplyr)
-#' library(scda)
-#'
-#' adsl <- synthetic_cdisc_dataset("latest", "adsl")
-#' adaette <- synthetic_cdisc_dataset("latest", "adaette")
-#' adaette <- adaette %>%
+#' adsl <- tmc_ex_adsl
+#' adaette <- tmc_ex_adaette %>%
 #'   dplyr::filter(PARAMCD %in% c("AETTE1", "AETTE2", "AETTE3")) %>%
 #'   dplyr::mutate(is_event = CNSR == 0) %>%
 #'   dplyr::mutate(n_events = as.integer(is_event))
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADAETTE", adaette),
-#'     code =
-#'       'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#'       ADAETTE <- synthetic_cdisc_dataset("latest", "adaette")
-#'       ADAETTE <- ADAETTE %>%
-#'         dplyr::filter(PARAMCD %in% c("AETTE1", "AETTE2", "AETTE3")) %>%
-#'         dplyr::mutate(is_event = CNSR == 0) %>%
-#'         dplyr::mutate(n_events = as.integer(is_event))' # nolint
+#'     cdisc_dataset("ADAETTE", adaette)
 #'   ),
 #'   modules = modules(
 #'     tm_t_events_patyear(

diff --git a/R/tm_t_exposure.R b/R/tm_t_exposure.R
@@ -1,4 +1,3 @@
-
 #' Template: Exposure Table for Risk management plan
 #'
 #' @inheritParams template_arguments
@@ -233,43 +232,26 @@ template_exposure <- function(parentname,
 #' @export
 #'
 #' @examples
-#' library(scda)
-#' library(dplyr)
-#'
-#' adsl <- synthetic_cdisc_dataset("latest", "adsl")
-#' adex <- synthetic_cdisc_dataset("latest", "adex")
+#' adsl <- tmc_ex_adsl
+#' adex <- tmc_ex_adex
 #'
 #' set.seed(1, kind = "Mersenne-Twister")
 #' labels <- formatters::var_labels(adex, fill = FALSE)
 #' adex <- adex %>%
-#'   distinct(USUBJID, .keep_all = TRUE) %>%
-#'   mutate(
+#'   dplyr::distinct(USUBJID, .keep_all = TRUE) %>%
+#'   dplyr::mutate(
 #'     PARAMCD = "TDURD",
 #'     PARAM = "Overall duration (days)",
-#'     AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
+#'     AVAL = sample(x = seq(1, 200), size = dplyr::n(), replace = TRUE),
 #'     AVALU = "Days"
 #'   ) %>%
-#'   bind_rows(adex)
+#'   dplyr::bind_rows(adex)
 #' formatters::var_labels(adex) <- labels
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
-#'     cdisc_dataset("ADEX", adex,
-#'       code = 'set.seed(1, kind = "Mersenne-Twister")
-#'       ADEX <- synthetic_cdisc_dataset("latest", "adsl")
-#'       labels <- formatters::var_labels(ADEX, fill = FALSE)
-#'       ADEX <- ADEX %>%
-#'        distinct(USUBJID, .keep_all = TRUE) %>%
-#'        mutate(PARAMCD = "TDURD",
-#'               PARAM = "Overall duration (days)",
-#'               AVAL = sample(x = seq(1, 200), size = n(), replace = TRUE),
-#'               AVALU = "Days") %>%
-#'               bind_rows(ADEX)
-#'       formatters::var_labels(ADEX) <- labels' # nolint
-#'     )
+#'     cdisc_dataset("ADSL", adsl),
+#'     cdisc_dataset("ADEX", adex)
 #'   ),
 #'   modules = modules(
 #'     tm_t_exposure(