merge main

Merge branch 'main' into 105_table_09_tplyr

# Conflicts:
#	R/argument_convention.R
#	man/argument_convention.Rd

Author: ayogasekaram

NAMESPACE

@@ -34,6 +34,7 @@ export(make_table_32_gtsum)
 export(make_table_33)
 export(make_table_34)
 export(make_table_35)
+export(make_table_38)
 export(split_cols_by_arm)
 import(Tplyr)
 import(checkmate)

R/argument_convention.R

@@ -64,9 +64,11 @@
 #'      `"Risk Difference (%) (95% CI)"`. For more than one risk difference column, `"arm x vs. arm y"` text will also
 #'      be included in the column labels by default. The length of `col_label` must be equal to the length of `arm_y`.
 #'    * `pct`: (optional) whether the output should be returned as percentages. Defaults to `TRUE`.
+#' @param saffl_var (`character`)\cr flag variable used to indicate inclusion in safety population.
 #' @param sex_scope (`character`)\cr Level of `SEX` to output in table.
-#' @param trtsdtm_var (`character`)\cr treatment start datetime variable.
 #' @param trtedtm_var (`character`)\cr treatment end datetime variable.
+#' @param trtemfl_var (`character`)\cr flag variable used to identify Treatment-emergent AE.
+#' @param trtsdtm_var (`character`)\cr treatment start datetime variable.
 #' @param u_trtdur (`character`)\cr unit for duration of treatment. Options are `"days"`, `"weeks"`, `"months"`,
 #'   and `"years"`.
 #' @param xticks (`vector` of `numeric`)\cr x-axis tick positions. If `NA` (default), tick mark positions are

R/fda-table_35.R

@@ -1,4 +1,4 @@
-#' Table 35. Patients With Adverse Events1 by System Organ Class,
+#' Table 35. Patients With Adverse Events by System Organ Class,
 #'   Safety Population, Pooled Analysis (or Trial X)
 #'
 #' @details

R/fda-table_38.R

@@ -0,0 +1,96 @@
+#' FDA Table 38: Patients With Adverse Events by System Organ Class, FDA Medical Query (Broad) and Preferred Term,
+#'  Safety Population, Pooled Analysis (or Trial X)
+#'
+#' @details
+#' * `adae` must contain the variables `AEBODSYS`, `AESER`, and the variables specified by
+#'   `arm_var`, `id_var`, `saffl_var`, `trtemfl_var`, `fmqsc_var`, `fmqnam_var`, and `pref_var`.
+#' * If specified, `alt_counts_df` must contain the variables specified by `arm_var`, `id_var`, and `saffl_var`.
+#' * Flag variables (i.e. `XXXFL`) are expected to have two levels: `"Y"` (true) and `"N"` (false). Missing values in
+#'   flag variables are treated as `"N"`.
+#' * Columns are split by arm. Overall population column is excluded by default (see `lbl_overall` argument).
+#' * Numbers in table represent the absolute numbers of patients and fraction of `N`.
+#' * All-zero rows are removed by default (see `prune_0` argument).
+#'
+#' @inheritParams argument_convention
+#'
+#' @examples
+#' library(dplyr)
+#'
+#' adae <- random.cdisc.data::cadae
+#' adsl <- random.cdisc.data::cadsl
+#'
+#' set.seed(1)
+#' adae <- adae %>%
+#'   rename(FMQ01SC = SMQ01SC) %>%
+#'   mutate(
+#'     AESER = sample(c("Y", "N"), size = nrow(adae), replace = TRUE),
+#'     FMQ01NAM = sample(c("FMQ1", "FMQ2", "FMQ3"), size = nrow(adae), replace = TRUE)
+#'   )
+#' adae$FMQ01SC[is.na(adae$FMQ01SC)] <- "Broad"
+#'
+#' tbl <- make_table_38(adae = adae, alt_counts_df = adsl)
+#' tbl
+#'
+#' @export
+make_table_38 <- function(adae,
+                          alt_counts_df = NULL,
+                          show_colcounts = TRUE,
+                          id_var = "USUBJID",
+                          arm_var = "ARM",
+                          saffl_var = "SAFFL",
+                          trtemfl_var = "TRTEMFL",
+                          fmqsc_var = "FMQ01SC",
+                          fmqnam_var = "FMQ01NAM",
+                          fmq_scope = "BROAD",
+                          pref_var = "AEDECOD",
+                          lbl_overall = NULL,
+                          lbl_pref_var = formatters::var_labels(adae, fill = TRUE)[pref_var],
+                          risk_diff = NULL,
+                          prune_0 = TRUE,
+                          na_level = "<Missing>",
+                          annotations = NULL) {
+  checkmate::assert_subset(c(
+    "AEBODSYS", arm_var, id_var, saffl_var, trtemfl_var, fmqsc_var,
+    fmqnam_var, pref_var
+  ), names(adae))
+  assert_flag_variables(adae, saffl_var, trtemfl_var)
+  checkmate::assert_subset(toupper(fmq_scope), c("NARROW", "BROAD"))
+
+  adae <- adae %>%
+    filter(.data[[saffl_var]] == "Y", .data[[trtemfl_var]] == "Y", .data[[fmqsc_var]] == fmq_scope) %>%
+    df_explicit_na(na_level = na_level)
+  adae[[fmqnam_var]] <- with_label(adae[[fmqnam_var]], paste0("FMQ (", tools::toTitleCase(tolower(fmq_scope)), ")"))
+
+  alt_counts_df <- alt_counts_df_preproc(alt_counts_df, id_var, arm_var, saffl_var)
+
+  lyt <- basic_table_annot(show_colcounts, annotations) %>%
+    split_cols_by_arm(arm_var, lbl_overall, risk_diff) %>%
+    split_rows_by(
+      var = "AEBODSYS",
+      split_fun = drop_split_levels,
+      split_label = obj_label(adae$AEBODSYS),
+      label_pos = "topleft"
+    ) %>%
+    split_rows_by(
+      fmqnam_var,
+      child_labels = "hidden",
+      label_pos = "topleft",
+      split_label = obj_label(adae[[fmqnam_var]])
+    ) %>%
+    summarize_num_patients(
+      var = id_var,
+      .stats = "unique",
+      .labels = c(unique = NULL),
+      riskdiff = !is.null(risk_diff)
+    ) %>%
+    count_occurrences(
+      vars = pref_var,
+      riskdiff = !is.null(risk_diff)
+    ) %>%
+    append_topleft(paste("   ", lbl_pref_var))
+
+  tbl <- build_table(lyt, df = adae, alt_counts_df = alt_counts_df)
+  if (prune_0) tbl <- prune_table(tbl)
+
+  tbl
+}