Merge pull request #122 from Merck/Issue120_add_bisection_argument_for_prepare_ae_forestly

Check-in - Add 'bisection' argument to 'prepare_ae_forestly' per Issu…

Author: wangben718

R/prepare_ae_forestly.R

@@ -19,11 +19,24 @@
 #' Prepare datasets for interactive forest plot
 #'
 #' @inheritParams metalite.ae::prepare_ae_specific
+#' @param meta A metadata object created by metalite.
+#' @param population A character value of population term name.
+#'   The term name is used as key to link information.
+#' @param observation A character value of observation term name.
+#'   The term name is used as key to link information.
+#' @param parameter A character value of parameter term name.
+#'   The term name is used as key to link information.
+#' @param components A character vector of components name, default value is `"par"`.
+#' @param reference_group An integer to indicate reference group.
+#'   Default is 2 if there are 2 groups, otherwise, the default is 1.
 #' @param ae_listing_display A vector of name of variables used to display
 #'   on AE listing table.
 #' @param ae_listing_unique A logical value to display only unique records
 #'   on AE listing table.
-#'
+#' @param bisection A numeric value. A control parameter for the bisection
+#'   method used to calculate confidence the lower and upper confidence
+#'   interval bounds for the risk. The default value is `1e2`.
+#' @param ... Additional arguments passed to [metalite.ae::rate_compare_sum()].
 #' @return An `outdata` object.
 #'
 #' @export
@@ -47,7 +60,10 @@ prepare_ae_forestly <- function(
       "USUBJID", "SITEID", "SEX", "RACE", "AGE", "ASTDY", "AESER",
       "AEREL", "AEACN", "AEOUT", "ADURN", "ADURU"
     ),
-    ae_listing_unique = FALSE) {
+    ae_listing_unique = FALSE,
+    bisection = 1e2,
+    ...
+    ) {
   if (is.null(population)) {
     if (length(meta$population) == 1) {
       population <- meta$population[[1]]$name
@@ -121,7 +137,10 @@ prepare_ae_forestly <- function(
       components = components,
       reference_group = reference_group
     ) |>
-      metalite.ae::extend_ae_specific_inference() |>
+      metalite.ae::extend_ae_specific_inference(
+        bisection = bisection,
+        ...
+      ) |>
       collect_ae_listing(display = ae_listing_display) |>
       format_ae_listing(display_unique_records = ae_listing_unique)
   })