address comments from PR review

Author: ayogasekaram

R/fda-table_02.R

@@ -8,13 +8,13 @@
 #' * 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"`.
 #'
-#' @inheritParams tbl_make_table_02
+#' @inheritParams make_table_02
 #' @inheritParams argument_convention
 #'
 #' @return A `gtsummary` table and, if `return_ard = TRUE`, an ARD.
 #'   If `return_ard = TRUE`, they will be returned as a list with named elements `table` and `ard`.
 #'
-#' @seealso [`tbl_make_table_02`]
+#' @seealso [`make_table_02`]
 #'
 #' @examples
 #' library(dplyr)
@@ -32,7 +32,6 @@
 #'
 #' @export
 make_table_02 <- function(df,
-                          denominator = NULL,
                           return_ard = TRUE,
                           arm_var = "ARM",
                           saffl_var = "SAFFL",
@@ -112,12 +111,11 @@ make_table_02 <- function(df,
 #'     AGE >= 65 & AGE < 75 ~ ">=65 to <75",
 #'     AGE >= 75 ~ ">=75"
 #'   )))
-#' tbl_rtables <- cardinal:::make_table_05_rtables(df = adsl)
+#' tbl_rtables <- make_table_02_rtables(df = adsl)
 #' tbl_rtables
 #' @rdname make_table_02
 #' @export
 make_table_02_rtables <- function(df,
-                                  alt_counts_df = NULL,
                                   show_colcounts = TRUE,
                                   arm_var = "ARM",
                                   saffl_var = "SAFFL",
@@ -134,8 +132,6 @@ make_table_02_rtables <- function(df,
     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) %>%
     analyze_vars(
@@ -148,7 +144,7 @@ make_table_02_rtables <- function(df,
     ) %>%
     append_topleft("Characteristic")
 
-  tbl <- build_table(lyt, df = df, alt_counts_df = alt_counts_df)
+  tbl <- build_table(lyt, df = df)
   if (prune_0) tbl <- prune_table(tbl)
 
   tbl

man/make_table_02.Rd

@@ -17,6 +17,9 @@ The `cardinal` package requires several packages available on CRAN.
 To use the `cardinal` package, ensure you have these necessary package dependencies installed by running the following code:
 
 ```{r, echo=TRUE, eval=FALSE}
+if (!require("gtsummary")) install.packages("gtsummary")
+if (!require("cards")) install.packages("cards")
+if (!require("cardx")) install.packages("cardx")
 if (!require("formatters")) install.packages("formatters")
 if (!require("rtables")) install.packages("rtables")
 if (!require("rlistings")) install.packages("rlistings")
@@ -63,7 +66,7 @@ Each template provided is associated with a function available within the `cardi
 
 ![](./assets/images/getting-started/gs-pan3.png){fig-align="center" width="90%"}
 
--   **Function Details**: This tab includes details on the table-generating function used for this template. Table functions use the naming convention `make_table_XX()` where `XX` is the table number taken from the FDA Standard Safety Table and Figures document (preceded by a 0 if the number is a single digit). Any required variables for the input datasets are listed along with a description of all function arguments. This information is mirrored by the function's help page accessible within R (i.e. `?make_table_XX`).
+-   **Function Details**: This tab includes details on the table-generating function used for this template. Table functions use the naming convention `make_table_XX()` where `XX` is the table number taken from the FDA Standard Safety Table and Figures document (preceded by a 0 if the number is a single digit). Any required variables for the input datasets are listed along with a description of all function arguments. This information is mirrored by the function's help page accessible within R (i.e. `?make_table_XX`). By default, all table generating functions use the {gtsummary} package - though we do support rtables functionality. To specify the use of which table engine is being used, engine specific functions can be called (`make_table_02_rtables`, for example).
 
 ![](./assets/images/getting-started/gs-pan4.png){fig-align="center" width="90%"}
 
@@ -90,8 +93,7 @@ adsl <- random.cdisc.data::cadsl %>%
     AGE >= 65 ~ ">=65",
     AGE >= 65 & AGE < 75 ~ ">=65 to <75",
     AGE >= 75 ~ ">=75"
-  )) %>% formatters::with_label("Age Group, years")) %>%
-  formatters::var_relabel(AGE = "Age, years")
+  ))) 
 
 # Create table
 tbl <- make_table_02(df = adsl)
@@ -115,18 +117,15 @@ anl <- left_join(adsl, advs, by = "USUBJID") %>% tern::df_explicit_na()
 
 tbl <- make_table_02(
   df = anl,
-  vars = c("SEX", "AGE", "RACE", "COUNTRY", "AVAL"),
-  lbl_vars = c("Sex", "Age, years", "Race", "Country of Participation", "Baseline Temperature (C)"),
-  lbl_overall = "Total\nPopulation",
-  na_rm = TRUE
+  vars = c("SEX", "AGE", "RACE", "COUNTRY", "AVAL")
 )
-tbl
+tbl$tbl
 ```
 
 Note that the `prune_0` argument can be set to specify whether all-zero rows should be included in a table. For example, see that the demographics table below includes rows for `OTHER` and `UNKNOWN` for which all values are zero, whereas these two rows were excluded from the previous tables (`prune_0` defaults to `TRUE` in `make_table_02()`).
 
 ```{r, echo=TRUE}
-make_table_02(df = anl, vars = "RACE", prune_0 = FALSE)
+make_table_02_rtables(df = anl, vars = "RACE", prune_0 = FALSE)
 ```
 
 ### Feature Requests

quarto/getting_started.qmd

@@ -35,7 +35,7 @@ adsl <- adsl %>%
 # Output Table
 make_table_02(
   df = adsl,
-  vars = c("SEX", "AGE", "AGEGR1", "RACE", "ETHNIC", "COUNTRY", "AVAL"),
+  vars = c("SEX", "AGE", "AGEGR1", "RACE", "ETHNIC", "COUNTRY"),
   return_ard = FALSE
 )
 ```
@@ -59,7 +59,7 @@ Required variables:
 -   **`denominator`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var`.
 
 |  |  |  |
-|----|----|----|
+|------------------------|------------------------|------------------------|
 | **Argument** | **Description** | **Default** |
 | `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
 | `return_ard` | (`flag`) Whether an ARD should be returned. | `TRUE` |
@@ -98,7 +98,7 @@ adsl <- adsl %>%
 # Create Table & ARD
 result <- make_table_02(
   df = adsl,
-  vars = c("SEX", "AGE", "AGEGR1", "RACE", "ETHNIC", "COUNTRY", "AVAL")
+  vars = c("SEX", "AGE", "AGEGR1", "RACE", "ETHNIC", "COUNTRY")
 )
 
 # Output ARD
@@ -109,7 +109,7 @@ result$ard
 
 ```{r tbl1-print, echo=FALSE}
 options(width = 9999)
-print(result$ard, columns = "all", n = Inf)
+print(result$ard, columns = "all")
 ```
 
 ## rtables Table
@@ -143,7 +143,7 @@ advs <- advs %>%
 anl <- left_join(adsl, advs, by = "USUBJID")
 
 # Output Table
-make_table_02(
+make_table_02_rtables(
   df = anl,
   vars = c("SEX", "AGE", "AGEGR1", "RACE", "ETHNIC", "COUNTRY", "AVAL"),
   lbl_vars = c(
@@ -172,7 +172,7 @@ Required variables:
 -   **`alt_counts_df`** (if specified): `USUBJID` and the variables specified by `arm_var` and `saffl_var`.
 
 | **Argument** | **Description** | **Default** |
-|:---|:---|:---|
+|:-----------------------|:-----------------------|:-----------------------|
 | `df` | (`data.frame`) Dataset (typically ADSL) required to build table. | *No default* |
 | `alt_counts_df` | (`character`) Alternative dataset used only to calculate column counts. | `NULL` |
 | `show_colcounts` | (`flag`) Whether column counts should be printed. | `TRUE` |