ready for review

Author: aassuied-ps

NEWS.md

@@ -15,6 +15,8 @@
   `make_table_09_gtsum`, `make_table_32_gtsum`.
 * Added option to include risk difference columns in tables using the `split_cols_by_arm` function via the `risk_diff` argument.
 * Added risk difference functionality into relevant table-generating functions via the `risk_diff` argument.
+* Added new function for creating standard FDA tables using additional packages:  
+`make_table_33_gtsum`.
 
 ### Miscellaneous
 * Initialized the package.

quarto/index-templates.qmd

@@ -53,9 +53,9 @@ title: Template Library Index
 
 -   [FDA Table 35 -- Patients With Adverse Events by System Organ Class, Safety Population, Pooled Analysis (or Trial X)](table-templates/template-table_35.qmd)
 
--   [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 Events by System Organ Class and Preferred Term, Safety Population, Pooled Analysis (or Trial X)](table-templates/template-table_36.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)
+-   [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)
 
 
 ------------------------------------------------------------------------

quarto/table-templates/template-table_33.qmd

@@ -70,5 +70,49 @@ Required variables:
 | `annotations`    | (named `list` of `character`) List of annotations to add to the table. Valid annotation types are `title`, `subtitles`, `main_footer`, and `prov_footer.` Each name-value pair should use the annotation type as name and the desired string as value.       | `NULL`       |
 +------------------+--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------+--------------+
 
+Source code for this function is available [here](https://github.com/pharmaverse/falcon/blob/main/R/fda-table_33.R).
+
+## gtsummary Table
+
+```{r tbl_gtsum, message=FALSE, warning=FALSE}
+# Load Libraries & Data
+library(falcon)
+
+adsl <- random.cdisc.data::cadsl
+advs <- random.cdisc.data::cadvs
+advs$AVAL <- advs$AVAL - 100
+
+# Output table
+tbl <- make_table_33_gtsum(advs = advs)
+tbl
+```
+
+## gtsummary Table Setup
+
+```{r tbl_gtsum, eval=FALSE, echo=TRUE}
+```
+
+## Function Details: `make_table_33_gtsum`
+
+### `make_table_33_gtsum()`
+
+------------------------------------------------------------------------
+
+Required variables:
+
+-   **`advs`**: `USUBJID`, `AVISITN`, `PARAMCD`, `AVAL`, `AVALU`, and the variables specified by `arm_var` and `saffl_var`.
+
++---------------+--------------------------------------------------------------------------------------------------------------------+----------------------+
+| Argument      | Description                                                                                                        | Default              |
++:==============+:===================================================================================================================+:=====================+
+| `advs`        | (`data.frame`) Dataset (typically ADVS) required to build table.                                                   | *No default*         |
++---------------+--------------------------------------------------------------------------------------------------------------------+----------------------+
+| `arm_var`     | (`character`) Arm variable used to split table into columns.                                                       | `"ARM"`              |
++---------------+--------------------------------------------------------------------------------------------------------------------+----------------------+
+| `saffl_var`   | (`character`) Flag variable used to indicate inclusion in safety population.                                       | `"SAFFL"`            |
++---------------+--------------------------------------------------------------------------------------------------------------------+----------------------+
+| `lbl_overall` | (`character`) If specified, an overall column will be added to the table with the given value as the column label. | `"Total Population"` |
++---------------+--------------------------------------------------------------------------------------------------------------------+----------------------+
+
 Source code for this function is available [here](https://github.com/pharmaverse/falcon/blob/main/R/fda-table_33.R).
 :::

tests/testthat/_snaps/fda-table_33.md

@@ -54,3 +54,25 @@
       SBP <90          85 (63.4%)    84 (62.7%)     90 (68.2%)         -0.7 (-12.3 - 10.8)     
       DBP <60          133 (99.3%)   134 (100%)     132 (100%)           0.7 (-0.7 - 2.2)      
 
+# Table 33 (gtsum) generation works with default values
+
+    Code
+      res
+    Output
+      # A tibble: 2 x 8
+        variable var_type    var_label  row_type label      stat_1      stat_2  stat_3
+        <chr>    <chr>       <chr>      <chr>    <chr>      <chr>       <chr>   <chr> 
+      1 SBP90    dichotomous SBP &lt;90 label    SBP &lt;90 85 (63.4%)  84 (62~ 90 (6~
+      2 DBP60    dichotomous DBP &lt;60 label    DBP &lt;60 133 (99.3%) 134 (1~ 132 (~
+
+# Table 33 (gtsum) generation works with custom values
+
+    Code
+      res
+    Output
+      # A tibble: 2 x 9
+        variable var_type    var_label  row_type label     stat_1 stat_2 stat_3 stat_0
+        <chr>    <chr>       <chr>      <chr>    <chr>     <chr>  <chr>  <chr>  <chr> 
+      1 SBP90    dichotomous SBP &lt;90 label    SBP &lt;~ 85 (6~ 84 (6~ 90 (6~ 259 (~
+      2 DBP60    dichotomous DBP &lt;60 label    DBP &lt;~ 133 (~ 134 (~ 132 (~ 399 (~
+

tests/testthat/test-fda-table_33.R

@@ -50,3 +50,18 @@ test_that("Table 33 generation works with risk difference column", {
   res <- expect_silent(result)
   expect_snapshot(res)
 })
+
+test_that("Table 33 (gtsum) generation works with default values", {
+  result <- suppressWarnings(make_table_33_gtsum(advs = advs) %>% gt::extract_body())
+  res <- expect_silent(result)
+  expect_snapshot(res)
+})
+
+test_that("Table 33 (gtsum) generation works with custom values", {
+  result <- suppressWarnings(
+    make_table_33_gtsum(advs = advs, lbl_overall = "Total Population") %>% gt::extract_body()
+  )
+
+  res <- expect_silent(result)
+  expect_snapshot(res)
+})