108 VST01 and EGT01 (#109)

new tables

Co-authored-by: benoit <benoit.falquet@roche.com>

NAMESPACE

@@ -22,6 +22,8 @@ export(dst01_2)
 export(dst01_2_lyt)
 export(dst01_3)
 export(dst01_3_lyt)
+export(egt01_1)
+export(egt01_1_lyt)
 export(ext01_1)
 export(ext01_1_lyt)
 export(ext01_2)
@@ -40,6 +42,8 @@ export(std_mutate_fun)
 export(std_pmap)
 export(syn_test_data)
 export(var_labels_for)
+export(vst01_1)
+export(vst01_1_lyt)
 import(dm)
 import(dplyr)
 import(rtables)

R/egt01.R

@@ -0,0 +1,127 @@
+#' EGT01 Table 1 (Default) ECG Assessments and Change from Baseline by Visit Table 1
+#'
+#' The `EGT01` table 1 summarizes several electrocardiogram parameters and their evolution throughout the study.
+#'
+#' @inheritParams gen_args
+#' @param summaryvars (`vector of string`) the variables to be analyzed. For this table, `AVAL` and `CHG` by default.
+#' @param summaryvars_lbls (`vector of string`) the label of the variables to be analyzed.
+#' @param visitvar (`string`) typically one of `"AVISIT"` (Default) or `"ATPTN"` depending on the type of time point to
+#'   be displayed
+#'
+#' @details
+#'  * The `Analysis Value` column, displays the number of patients, the mean, standard deviation, median and range of
+#'  the analysis value for each visit.
+#'  * The `Change from Baseline` column, displays the number of patient and the mean, standard deviation,
+#'  median and range of changes relative to the baseline.
+#'  * Remove zero-count rows unless overridden with `prune_0 = FALSE`.
+#'  * Split columns by arm, typically `ACTARM`.
+#'  * Does not include a total column by default.
+#'  * Sorted  based on factor level; first by `PARAM` labels in alphabetic order then by chronological time point given
+#'  by `AVISIT`. Re-level to customize order
+#'
+#' @importFrom dplyr filter
+#'
+#' @export
+#'
+#' @examples
+#' library(dm)
+#'
+#' db <- syn_test_data() %>%
+#'   preprocess_data("egt01_1")
+#'
+#' egt01_1(db)
+#' egt01_1(db, summaryvars_lbls = c("Value at Visit", "Change from Baseline"))
+#'
+egt01_1 <- function(adam_db,
+                    armvar = .study$armvar,
+                    summaryvars = .study$evo_vars,
+                    summaryvars_lbls = var_labels_for(adam_db$adeg, summaryvars),
+                    visitvar = "AVISIT", # or ATPTN
+                    prune_0 = TRUE,
+                    deco = std_deco("EGT01"),
+                    .study = list(
+                      armvar = "ACTARM",
+                      evo_vars = c("AVAL", "CHG")
+                    )) {
+
+  lbl_AVISIT <- var_labels_for(adam_db$adeg, visitvar)
+  lbl_PARAM <- var_labels_for(adam_db$adeg, "PARAM")
+
+  lyt <- egt01_1_lyt(
+    armvar = armvar,
+    summaryvars = summaryvars,
+    summaryvars_lbls = summaryvars_lbls,
+    visitvar = visitvar,
+    lbl_AVISIT = lbl_AVISIT,
+    lbl_PARAM = lbl_PARAM,
+    deco = deco
+  )
+
+  tbl <- build_table(
+    lyt,
+    df = adam_db$adeg
+  )
+
+  if (prune_0) tbl <- tbl %>% prune_table()
+
+  tbl
+
+}
+
+#' EGT01 Layout 1 (Default)
+#'
+#' @describeIn egt01_1
+#'
+#' @inheritParams gen_args
+#'
+#' @param summaryvars (`vector of string`) the variables to be analyzed. For this table, `AVAL` and `CHG` by default.
+#' @param summaryvars_lbls (`vector of string`) the label of the variables to be analyzed.
+#' @param visitvar (`string`) typically one of `"AVISIT"` (Default) or `"ATPTN"` depending on the type of time point to
+#'   be displayed.
+#' @param lbl_AVISIT (`string`) label of the `visitvar` variable.
+#' @param lbl_PARAM (`string`) label of the `PARAM` variable.
+#'
+#' @return
+#' @export
+egt01_1_lyt <- function(armvar = .study$armvar,
+                        summaryvars = .study$evo_vars,
+                        summaryvars_lbls = .study$evo_vars_lbls,
+                        visitvar = .study$visitvar,
+                        lbl_AVISIT = "",
+                        lbl_PARAM = "",
+                        deco = std_deco("EGT01"),
+                        .study = list(
+                          armvar = "ACTARM",
+                          evo_vars = c("AVAL", "CHG"),
+                          evo_vars_lbls = c("Analysis \nValue", "Change from \nBaseline"),
+                          visitvar = "AVISIT"
+                        )
+) {
+
+
+  # TODE solve the problem of the overall column
+  # remove change from baseline in BASELINE
+
+  basic_table_deco(deco) %>%
+    split_cols_by(armvar) %>%
+    split_rows_by(
+      "PARAM",
+      split_fun = drop_split_levels,
+      label_pos = "hidden",
+      split_label = paste(lbl_PARAM)
+    ) %>%
+    split_rows_by(
+      visitvar,
+      split_fun = drop_split_levels,
+      label_pos = "hidden",
+      split_label = lbl_AVISIT
+    ) %>%
+    split_cols_by_multivar(
+      vars = summaryvars,
+      varlabels = summaryvars_lbls,
+      nested = TRUE
+    ) %>%
+    summarize_colvars() %>%
+    append_topleft(paste(lbl_PARAM)) %>%
+    append_topleft(c(paste(" ", lbl_AVISIT), " "))
+}

R/standard_data_preprocessing.R

@@ -11,9 +11,11 @@ std_preprocessing_map <- tibble::tribble(
   "dst01_1", NA, NA, c("adsl"),
   "dst01_2", NA, "mutate_adsl_gp", c("adsl"),
   "dst01_3", NA, "mutate_adsl_gp", c("adsl"),
+  "egt01_1", "filter_adeg_anl01fl", NA, c("adsl", "adeg"),
   "ext01_1", "filter_adex_drug", "reorder_adex_params", c("adsl", "adex"),
   "ext01_2", "filter_adex_drug", "remove_adex_aval", c("adsl", "adex"),
-  "lbt01_1", "filter_adlb_anl01fl", NA, c("adsl", "adlb")
+  "lbt01_1", "filter_adlb_anl01fl", NA, c("adsl", "adlb"),
+  "vst01_1", "filter_advs_anl01fl", NA, c("adsl", "advs")
 )
 
 #' Standard Preprocessing Map
@@ -217,6 +219,30 @@ filter_adlb_anl01fl <- function(adam_db) {
     dm_apply_filters()
 }
 
+#' Filter `adeg` for `ANL01FL`
+#'
+#' @inheritParams gen_args
+#'
+filter_adeg_anl01fl <- function(adam_db) {
+  assert_that(is(adam_db, "dm"))
+
+  adam_db %>%
+    dm_filter(adeg, bol_YN(ANL01FL)) %>%
+    dm_apply_filters()
+}
+
+#' Filter `advs` for `ANL01FL`
+#'
+#' @inheritParams gen_args
+#'
+filter_advs_anl01fl <- function(adam_db) {
+  assert_that(is(adam_db, "dm"))
+
+  adam_db %>%
+    dm_filter(advs, bol_YN(ANL01FL)) %>%
+    dm_apply_filters()
+}
+
 #' Filter `adex` for `PARCAT1`
 #'
 #' @inheritParams gen_args

R/utils.R

@@ -357,6 +357,11 @@ syn_test_data <- function() {
     mutate(ANL01FL = "Y") %>%
     dm_update_zoomed()
 
+  db_m <- db %>%
+    dm_zoom_to(advs) %>%
+    mutate(ANL01FL = "Y") %>%
+    dm_update_zoomed()
+
   db_m
 }
 

R/vst01.R

@@ -0,0 +1,129 @@
+#' VST01 Table 1 (Default) Vital Sign Results and change from Baseline By Visit Table 1
+#'
+#' The `VST01` table provides an overview of the Vital Sign values and its change from baseline of each respective arm
+#' over the course of the trial.
+#'
+#' @inheritParams gen_args
+#' @param summaryvars (`vector of string`) the variables to be analyzed. For this table, `AVAL` and `CHG` by default.
+#' @param summaryvars_lbls (`vector of string`) the label of the variables to be analyzed.
+#' @param visitvar (`string`) typically one of `"AVISIT"` (Default) or `"ATPTN"` depending on the type of time point to
+#'   be displayed
+#'
+#' @details
+#'  * The `Analysis Value` column, displays the number of patients, the mean, standard deviation, median and range of
+#'  the analysis value for each visit.
+#'  * The `Change from Baseline` column, displays the number of patient and the mean, standard deviation,
+#'  median and range of changes relative to the baseline.
+#'  * Remove zero-count rows unless overridden with `prune_0 = FALSE`.
+#'  * Split columns by arm, typically `ACTARM`.
+#'  * Does not include a total column by default.
+#'  * Sorted  based on factor level; first by `PARAM` labels in alphabetic order then by chronological time point given
+#'  by `AVISIT`. Re-level to customize order
+#'
+#' @importFrom dplyr filter
+#'
+#' @export
+#'
+#' @examples
+#' library(dm)
+#'
+#' db <- syn_test_data() %>%
+#'   preprocess_data("vst01_1")
+#'
+#' vst01_1(db)
+#' vst01_1(db, summaryvars_lbls = c("Value at Visit", "Change from Baseline"))
+#'
+vst01_1 <- function(adam_db,
+                    armvar = .study$armvar,
+                    summaryvars = .study$evo_vars,
+                    summaryvars_lbls = var_labels_for(adam_db$advs, summaryvars),
+                    visitvar = "AVISIT", # or ATPTN
+                    prune_0 = TRUE,
+                    deco = std_deco("VST01"),
+                    .study = list(
+                      armvar = "ACTARM",
+                      evo_vars = c("AVAL", "CHG")
+                    )) {
+
+  lbl_AVISIT <- var_labels_for(adam_db$advs, visitvar)
+  lbl_PARAM <- var_labels_for(adam_db$advs, "PARAM")
+
+  lyt <- vst01_1_lyt(
+    armvar = armvar,
+    summaryvars = summaryvars,
+    summaryvars_lbls = summaryvars_lbls,
+    visitvar = visitvar,
+    lbl_AVISIT = lbl_AVISIT,
+    lbl_PARAM = lbl_PARAM,
+    deco = deco
+  )
+
+  tbl <- build_table(
+    lyt,
+    df = adam_db$advs,
+    alt_counts_df = adam_db$adsl
+  )
+
+  if (prune_0) tbl <- tbl %>% trim_rows()
+
+  tbl
+}
+
+#' LBT01 Layout 1 (Default)
+#'
+#' @describeIn vst01_1
+#'
+#' @inheritParams gen_args
+#'
+#' @param summaryvars (`vector of string`) the variables to be analyzed. For this table, `AVAL` and `CHG` by default.
+#' @param summaryvars_lbls (`vector of string`) the label of the variables to be analyzed.
+#' @param visitvar (`string`) typically one of `"AVISIT"` (Default) or `"ATPTN"` depending on the type of time point to
+#'   be displayed.
+#' @param lbl_AVISIT (`string`) label of the `visitvar` variable.
+#' @param lbl_PARAM (`string`) label of the `PARAM` variable.
+#'
+#' @return
+#' @export
+vst01_1_lyt <- function(armvar = .study$armvar,
+                        summaryvars = .study$evo_vars,
+                        summaryvars_lbls = .study$evo_vars_lbls,
+                        visitvar = .study$visitvar,
+                        lbl_AVISIT = "",
+                        lbl_PARAM = "",
+                        deco = std_deco("EGT01"),
+                        .study = list(
+                          armvar = "ACTARM",
+                          evo_vars = c("AVAL", "CHG"),
+                          evo_vars_lbls = c("Analysis \nValue", "Change from \nBaseline"),
+                          visitvar = "AVISIT"
+                        )
+) {
+
+
+  # TODE solve the problem of the overall column
+  # remove change from baseline in BASELINE
+  # problem with the column count
+
+  basic_table_deco(deco) %>%
+    split_cols_by(armvar) %>%
+    split_rows_by(
+      "PARAM",
+      split_fun = drop_split_levels,
+      label_pos = "hidden",
+      split_label = paste(lbl_PARAM)
+    ) %>%
+    split_rows_by(
+      visitvar,
+      split_fun = drop_split_levels,
+      label_pos = "hidden",
+      split_label = lbl_AVISIT
+    ) %>%
+    split_cols_by_multivar(
+      vars = summaryvars,
+      varlabels = summaryvars_lbls,
+      nested = TRUE
+    ) %>%
+    summarize_colvars() %>%
+    append_topleft(paste(lbl_PARAM)) %>%
+    append_topleft(paste(" ", lbl_AVISIT))
+}

_pkgdown.yaml

@@ -36,9 +36,11 @@ reference:
       - dst01_1
       - dst01_2
       - dst01_3
+      - egt01_1
       - ext01_1
       - ext01_2
       - lbt01_1
+      - vst01_1
 
   - title: Data Preprocess Functions
     contents:
@@ -52,7 +54,9 @@ reference:
       - std_mutate_fun
       - filter_adex_drug
       - filter_adae_anl01fl
+      - filter_adeg_anl01fl
       - filter_adlb_anl01fl
+      - filter_advs_anl01fl
       - mutate_adsl_gp
       - remove_adex_aval
       - reorder_adex_params

inst/WORDLIST

@@ -16,6 +16,7 @@ CTACAE
 CTCAE
 DMT
 EORTC
+EGT
 GDSR
 LBT
 NCI
@@ -45,3 +46,4 @@ templating
 tlg
 tlgfunction
 tlgs
+VST