Create minimal test data for examples and initialize the substitution (…

…#721)
insightsengineering · Feb 23, 2023 · 2ebf50c · 2ebf50c
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diff --git a/NEWS.md b/NEWS.md
@@ -1,7 +1,6 @@
 # teal.modules.clinical 0.8.14.9020
 
 ### Breaking changes
-
 * Replaced `chunks` with simpler `qenv` class.
 * Replaced `datasets` argument containing `FilteredData` with the new arguments `data` (`tdata` object) and `filter_panel_api` (`FilterPanelAPI`).
 
@@ -13,10 +12,13 @@
 * Added adjustment method choice to `tm_a_mmrm` to allow for Kenward-Roger adjustment of standard errors and p-values.
 
 ### Miscellaneous
-* Package now uses `scda.2022` rather than `scda.2021` in SUGGESTS. 
+* Package now uses `scda.2022` rather than `scda.2021` in SUGGESTS.
 * 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.
+* 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
@@ -0,0 +1,29 @@
+#' Simulated CDISC Data for Examples
+#'
+#' @format `rds` (`data.frame`)
+#'
+#' @name ex_data
+NULL
+
+#' @describeIn ex_data ADSL data
+#'
+"tmc_ex_adsl"
+
+#' @describeIn ex_data ADAE data
+#'
+"tmc_ex_adae"
+
+#' @describeIn ex_data ADLB data
+#'
+"tmc_ex_adlb"
+
+#' @describeIn ex_data ADRS data
+#'
+"tmc_ex_adrs"
+
+#' @describeIn ex_data ADTTE data
+#'
+"tmc_ex_adtte"
+#' @describeIn ex_data ADCM data
+#'
+"tmc_ex_adcm"
diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -145,9 +145,7 @@ template_a_gee <- function(output_table,
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = 'synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
+#'     cdisc_dataset("ADSL", ADSL),
 #'     cdisc_dataset("ADQS", ADQS,
 #'       code = 'ADQS <- synthetic_cdisc_dataset("latest", "adqs") %>%
 #'               dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -451,7 +451,6 @@ template_mmrm_plots <- function(fit_name,
 #' numerical precision.
 #'
 #' @examples
-#'
 #' library(scda)
 #'
 #' ADSL <- synthetic_cdisc_dataset("latest", "adsl")

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -15,11 +15,11 @@
 #'
 #' @examples
 #' library(dplyr)
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
+#' ADSL <- tmc_ex_adsl %>%
+#'   dplyr::mutate(ITTFL = factor("Y"))
+#' ADAE <- tmc_ex_adae
 #'
 #' adae_labels <- formatters::var_labels(ADAE, fill = FALSE)
 #' ADAE <- ADAE %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
@@ -29,15 +29,8 @@
 #'
 #' 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")
-#'               adae_labels <- formatters::var_labels(ADAE, fill = FALSE)
-#'               ADAE <- ADAE %>%
-#'                 dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
-#'               formatters::var_labels(ADAE) <- adae_labels
-#'               ADAE'
-#'     )
+#'     cdisc_dataset("ADSL", ADSL),
+#'     cdisc_dataset("ADAE", ADAE)
 #'   ),
 #'   modules = modules(
 #'     tm_g_barchart_simple(

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -188,19 +188,17 @@ template_g_ci <- function(dataname, # nolint
 #'   and point shape).
 #'
 #' @export
-#' @examples
 #'
-#' library(scda)
+#' @examples
 #' library(nestcolor)
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+#'
+#' ADSL <- tmc_ex_adsl
+#' ADLB <- tmc_ex_adlb
 #'
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL),
-#'     cdisc_dataset("ADLB", ADLB),
-#'     code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#'     ADLB <- synthetic_cdisc_dataset("latest", "adlb")' # nolint
+#'     cdisc_dataset("ADLB", ADLB)
 #'   ),
 #'   modules = modules(
 #'     tm_g_ci(

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -215,14 +215,12 @@ template_forest_rsp <- function(dataname = "ANL",
 #' @template author_song24
 #'
 #' @examples
-#'
-#' library(scda)
 #' library(dplyr)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADRS <- synthetic_cdisc_dataset("latest", "adrs") %>%
-#'   mutate(AVALC = d_onco_rsp_label(AVALC)) %>%
+#' ADSL <- tmc_ex_adsl
+#' ADRS <- tmc_ex_adrs %>%
+#'   mutate(AVALC = tern::d_onco_rsp_label(AVALC)) %>%
 #'   filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
 #'
 #' arm_ref_comp <- list(
@@ -239,12 +237,7 @@ template_forest_rsp <- function(dataname = "ANL",
 #' app <- init(
 #'   data = cdisc_data(
 #'     cdisc_dataset("ADSL", ADSL),
-#'     cdisc_dataset("ADRS", ADRS),
-#'     code =
-#'       '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")' # nolint
+#'     cdisc_dataset("ADRS", ADRS)
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_rsp(

diff --git a/R/tm_g_forest_tte.R b/R/tm_g_forest_tte.R
@@ -224,11 +224,10 @@ template_forest_tte <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
+#' ADSL <- tmc_ex_adsl
+#' ADTTE <- tmc_ex_adtte
 #'
 #' ADSL$RACE <- droplevels(ADSL$RACE)
 #'
@@ -245,15 +244,8 @@ template_forest_tte <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset(
-#'       "ADSL", ADSL,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#'         ADSL$RACE <- droplevels(ADSL$RACE)' # nolint
-#'     ),
-#'     cdisc_dataset(
-#'       "ADTTE", ADTTE,
-#'       code = 'ADTTE <- synthetic_cdisc_dataset("latest", "adtte")'
-#'     )
+#'     cdisc_dataset("ADSL", ADSL),
+#'     cdisc_dataset("ADTTE", ADTTE)
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_tte(

diff --git a/R/tm_g_ipp.R b/R/tm_g_ipp.R
@@ -187,11 +187,10 @@ template_g_ipp <- function(dataname = "ANL",
 #'
 #' @examples
 #' library(dplyr)
-#' library(scda)
 #' library(nestcolor)
 #'
-#' adsl <- synthetic_cdisc_dataset("latest", "adsl") %>% slice(1:20)
-#' adlb <- synthetic_cdisc_dataset("latest", "adlb")
+#' adsl <- tmc_ex_adsl %>% slice(1:20)
+#' adlb <- tmc_ex_adlb
 #' adlb <- adlb %>% filter(USUBJID %in% adsl$USUBJID)
 #'
 #' adsl <- df_explicit_na(adsl)
@@ -202,16 +201,11 @@ template_g_ipp <- function(dataname = "ANL",
 #'   data = cdisc_data(
 #'     cdisc_dataset(
 #'       "ADSL",
-#'       adsl,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl") %>% slice(1:20)
-#'       ADSL <- df_explicit_na(ADSL)' # nolint
+#'       adsl
 #'     ),
 #'     cdisc_dataset(
 #'       "ADLB",
-#'       adlb,
-#'       code = 'ADLB <- synthetic_cdisc_dataset("latest", "adlb")
-#'       ADLB <- df_explicit_na(ADLB) %>%
-#'       dplyr::filter(AVISIT != "SCREENING")' # nolint
+#'       adlb
 #'     )
 #'   ),
 #'   modules = modules(

diff --git a/R/tm_g_km.R b/R/tm_g_km.R
@@ -239,11 +239,10 @@ template_g_km <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADTTE <- synthetic_cdisc_dataset("latest", "adtte")
+#' ADSL <- tmc_ex_adsl
+#' ADTTE <- tmc_ex_adtte
 #'
 #' arm_ref_comp <- list(
 #'   ACTARMCD = list(
@@ -258,8 +257,8 @@ template_g_km <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL, code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'),
-#'     cdisc_dataset("ADTTE", ADTTE, code = 'ADTTE <- synthetic_cdisc_dataset("latest", "adtte")')
+#'     cdisc_dataset("ADSL", ADSL),
+#'     cdisc_dataset("ADTTE", ADTTE)
 #'   ),
 #'   modules = modules(
 #'     tm_g_km(

diff --git a/R/tm_g_lineplot.R b/R/tm_g_lineplot.R
@@ -203,23 +203,17 @@ template_g_lineplot <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADLB <- synthetic_cdisc_dataset("latest", "adlb")
+#' ADSL <- tmc_ex_adsl
+#' ADLB <- tmc_ex_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_dataset("latest", "adsl")'
-#'     ),
-#'     cdisc_dataset("ADLB", ADLB,
-#'       code = 'ADLB <- synthetic_cdisc_dataset("latest", "adlb")
-#'         ADLB <- dplyr::mutate(ADLB, AVISIT == forcats::fct_reorder(AVISIT, AVISITN, min))' # nolint
-#'     )
+#'     cdisc_dataset("ADSL", ADSL),
+#'     cdisc_dataset("ADLB", ADLB)
 #'   ),
 #'   modules = modules(
 #'     tm_g_lineplot(

diff --git a/R/tm_g_pp_adverse_events.R b/R/tm_g_pp_adverse_events.R
@@ -180,20 +180,15 @@ template_adverse_events <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
+#' ADSL <- tmc_ex_adsl
+#' ADAE <- tmc_ex_adae
 #'
 #' 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("ADSL", ADSL),
+#'     cdisc_dataset("ADAE", 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
@@ -354,14 +354,13 @@ template_patient_timeline <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADAE <- synthetic_cdisc_dataset("latest", "adae")
-#' ADCM <- synthetic_cdisc_dataset("latest", "adcm")
+#' ADSL <- tmc_ex_adsl
+#' ADAE <- tmc_ex_adae
+#' ADCM <- tmc_ex_adcm
 #'
-#' #' Modify ADCM
+#' # Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
 #' ADCM$CMDOSE <- 1
 #' ADCM$CMDOSU <- "U"

diff --git a/R/tm_g_pp_therapy.R b/R/tm_g_pp_therapy.R
@@ -253,13 +253,12 @@ template_therapy <- function(dataname = "ANL",
 #' @export
 #'
 #' @examples
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
-#' ADCM <- synthetic_cdisc_dataset("latest", "adcm")
+#' ADSL <- tmc_ex_adsl
+#' ADCM <- tmc_ex_adcm
 #'
-#' #' Modify ADCM
+#' # Modify ADCM
 #' ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
 #' ADCM$CMDOSE <- 1
 #' ADCM$CMTRT <- ADCM$CMCAT
@@ -280,26 +279,8 @@ template_therapy <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", ADSL,
-#'       code = 'ADSL <- synthetic_cdisc_dataset("latest", "adsl")'
-#'     ),
+#'     cdisc_dataset("ADSL", ADSL),
 #'     cdisc_dataset("ADCM", ADCM,
-#'       code = 'ADCM <- synthetic_cdisc_dataset("latest", "adcm")
-#'         ADCM$CMINDC <- paste0("Indication_", as.numeric(ADCM$CMDECOD))
-#'         ADCM$CMDOSE <- 1
-#'         ADCM$CMTRT <- ADCM$CMCAT
-#'         ADCM$CMDOSU <- "U"
-#'         ADCM$CMROUTE <- "CMROUTE"
-#'         ADCM$CMDOSFRQ <- "CMDOSFRQ"
-#'         ADCM$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',
 #'       keys = adcm_keys
 #'     )
 #'   ),

diff --git a/R/tm_g_pp_vitals.R b/R/tm_g_pp_vitals.R
@@ -191,6 +191,7 @@ template_vitals <- function(dataname = "ANL",
 #' @examples
 #' library(scda)
 #' library(nestcolor)
+#'
 #' ADSL <- synthetic_cdisc_dataset("latest", "adsl")
 #' ADVS <- synthetic_cdisc_dataset("latest", "advs")
 #'