195 new table table 36 (#208)

* Add make_table_36

* Add tests for make_table_36

* Addd quarto page for make_table_36

* [skip actions] Restyle files

* Update NEWS file

* Remove scda from table 22

* Solve lintr marks for table 22

* empty commit

* Update WORDLIST

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Abinaya Yogasekaram <[email protected]>
Co-authored-by: ayogasekaram <[email protected]>
Co-authored-by: Emily de la Rua <[email protected]>

Author: 4 people

NAMESPACE

@@ -33,6 +33,7 @@ export(make_table_32_gtsum)
 export(make_table_33)
 export(make_table_34)
 export(make_table_35)
+export(make_table_36)
 export(make_table_38)
 export(split_cols_by_arm)
 import(Tplyr)

NEWS.md

@@ -4,7 +4,7 @@
 * Added new functions for creating standard FDA tables: `make_table_02`, `make_table_03`, `make_table_04`, `make_table_05`, 
   `make_table_06`, `make_table_07`, `make_table_08`, `make_table_09`, `make_table_10`, `make_table_11`, `make_table_12`, 
   `make_table_13`, `make_table_14`, `make_table_15`, `make_table_16`, `make_table_17`, `make_table_18`, `make_table_20`, 
-  `make_table_21`, `make_table_22`, `make_table_32`, `make_table_33`, `make_table_34`, `make_table_35`.
+  `make_table_21`, `make_table_22`, `make_table_32`, `make_table_33`, `make_table_34`, `make_table_35`, `make_table_36`.
 * Added new functions for creating standard FDA figures: `make_fig_01`, `make_fig_02`, `make_fig_14`.
 * Added helper functions used within table functions:
   * `basic_table_annot` for adding basic table annotations (titles, footnotes, column counts).

R/fda-table_36.R

@@ -0,0 +1,73 @@
+#' Table 36. Patients With Adverse Events by System Organ Class and Preferred Term, Safety
+#' Population, Pooled Analysis (or Trial X)
+#'
+#' @details
+#' * `adae` must contain the variables specified by `id_var`, `arm_var`, `saffl_var`, `soc_var`,
+#'   and `pref_var`.
+#' * If specified, `alt_counts_df` must contain the variables specified by `arm_var`, `id_var`, and `saffl_var`.
+#' * 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
+#'
+#' @return
+#' * `make_table_36` returns an `rtables` table object.
+#'
+#' @examples
+#' adsl <- random.cdisc.data::cadsl
+#' adae <- random.cdisc.data::cadae
+#'
+#' tbl <- make_table_35(adae = adae, alt_counts_df = adsl)
+#' tbl
+#'
+#' @export
+make_table_36 <- function(
+    adae,
+    alt_counts_df = NULL,
+    show_colcounts = TRUE,
+    id_var = "USUBJID",
+    arm_var = "ARM",
+    saffl_var = "SAFFL",
+    soc_var = "AESOC",
+    pref_var = "AEDECOD",
+    lbl_soc_var = formatters::var_labels(adae, fill = TRUE)[soc_var],
+    lbl_overall = NULL,
+    risk_diff = NULL,
+    prune_0 = FALSE,
+    annotations = NULL) {
+  adae <- adae %>%
+    filter(.data[[saffl_var]] == "Y") %>%
+    df_explicit_na()
+
+  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(
+      soc_var,
+      label_pos = "topleft",
+      split_label = lbl_soc_var
+    ) %>%
+    summarize_num_patients(
+      var = id_var,
+      riskdiff = !is.null(risk_diff),
+      .stats = "unique",
+      .labels = c(unique = NULL)
+    ) %>%
+    count_occurrences(
+      vars = pref_var,
+      drop = FALSE,
+      riskdiff = !is.null(risk_diff)
+    )
+
+  tbl <- build_table(lyt, df = adae, alt_counts_df = alt_counts_df)
+  if (prune_0) tbl <- prune_table(tbl)
+
+  tbl
+}

_quarto.yml

@@ -103,6 +103,7 @@ website:
           - quarto/table-templates/template-table_33.qmd
           - quarto/table-templates/template-table_34.qmd
           - quarto/table-templates/template-table_35.qmd
+          - quarto/table-templates/template-table_36.qmd
           - quarto/figure-templates/template-fig_01.qmd
           - quarto/figure-templates/template-fig_02.qmd
           - quarto/figure-templates/template-fig_14.qmd

inst/WORDLIST

@@ -3,12 +3,29 @@ ADEX
 ADSL
 ADSUB
 ADVS
+AE
+ARD
+Abinaya
+Assuied
 CDISC
+CDISC's
 FMQ
+Huan
 Hypotension
+Knizia
+Korbinian
+Koujin
 Pharmaverse
 Postbaseline
 Pre
+Rua
 TLGs
+Yichen
+Yogasekaram
+Yoshito
+Yuye
 datetime
+de
+ncol
+pharmaverse
 pre

man/make_table_36.Rd

@@ -55,6 +55,8 @@ title: Template Library Index
 
 -   [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)](table-templates/template-table_38.qmd)
 
+-   [FDA Table 36 -- Patients With Adverse Events1 by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)](table-templates/template-table_35.qmd)
+
 
 ------------------------------------------------------------------------