From 47decd452523ce5dab2865fde974c6610a0f5b67 Mon Sep 17 00:00:00 2001 From: *** Li Ma *** Date: Fri, 20 Mar 2026 14:37:13 -0400 Subject: [PATCH 1/4] Check-in - Add 'bisection' argument to 'prepare_ae_forestly' per Issue_120 --- R/prepare_ae_forestly.R | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R index 6aac709..35acddd 100644 --- a/R/prepare_ae_forestly.R +++ b/R/prepare_ae_forestly.R @@ -47,7 +47,10 @@ 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 @@ -103,7 +106,10 @@ 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) }) From c5010522ef07dcaaf528cf1970db13366d873eaf Mon Sep 17 00:00:00 2001 From: *** Li Ma *** Date: Wed, 25 Mar 2026 10:17:11 -0400 Subject: [PATCH 2/4] Check-in - document update after adding 'bisection' argument to 'prepare_ae_forestly' per Issue_120 --- man/prepare_ae_forestly.Rd | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/man/prepare_ae_forestly.Rd b/man/prepare_ae_forestly.Rd index b6bafc5..52a1132 100644 --- a/man/prepare_ae_forestly.Rd +++ b/man/prepare_ae_forestly.Rd @@ -13,7 +13,9 @@ prepare_ae_forestly( reference_group = NULL, ae_listing_display = c("USUBJID", "SITEID", "SEX", "RACE", "AGE", "ASTDY", "AESER", "AEREL", "AEACN", "AEOUT", "ADURN", "ADURU"), - ae_listing_unique = FALSE + ae_listing_unique = FALSE, + bisection = 100, + ... ) } \arguments{ From 9b63e8ae50fbe5c670731acd76f4861ce6b7f01c Mon Sep 17 00:00:00 2001 From: *** Li Ma *** Date: Thu, 26 Mar 2026 15:10:18 -0400 Subject: [PATCH 3/4] Check-in - document update after adding 'bisection' argument --- R/prepare_ae_forestly.R | 14 +++++++++++++- man/prepare_ae_forestly.Rd | 6 +++++- 2 files changed, 18 insertions(+), 2 deletions(-) diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R index 35acddd..d75a516 100644 --- a/R/prepare_ae_forestly.R +++ b/R/prepare_ae_forestly.R @@ -19,11 +19,23 @@ #' 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`. #' @return An `outdata` object. #' #' @export diff --git a/man/prepare_ae_forestly.Rd b/man/prepare_ae_forestly.Rd index 52a1132..29c2af5 100644 --- a/man/prepare_ae_forestly.Rd +++ b/man/prepare_ae_forestly.Rd @@ -30,7 +30,7 @@ The term name is used as key to link information.} \item{parameter}{A character value of parameter term name. The term name is used as key to link information.} -\item{components}{A character vector of components name.} +\item{components}{A character vector of components name, default value is \code{"par"}.} \item{reference_group}{An integer to indicate reference group. Default is 2 if there are 2 groups, otherwise, the default is 1.} @@ -40,6 +40,10 @@ on AE listing table.} \item{ae_listing_unique}{A logical value to display only unique records on AE listing table.} + +\item{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 \code{1e2}.} } \value{ An \code{outdata} object. From 8fff915eca450b31e46cce45b458924e6f4a82fa Mon Sep 17 00:00:00 2001 From: "Wang, Benjamin" Date: Mon, 13 Apr 2026 15:53:21 -0400 Subject: [PATCH 4/4] update document --- R/prepare_ae_forestly.R | 1 + man/prepare_ae_forestly.Rd | 2 ++ 2 files changed, 3 insertions(+) diff --git a/R/prepare_ae_forestly.R b/R/prepare_ae_forestly.R index d75a516..c2d6419 100644 --- a/R/prepare_ae_forestly.R +++ b/R/prepare_ae_forestly.R @@ -36,6 +36,7 @@ #' @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 diff --git a/man/prepare_ae_forestly.Rd b/man/prepare_ae_forestly.Rd index 29c2af5..190c888 100644 --- a/man/prepare_ae_forestly.Rd +++ b/man/prepare_ae_forestly.Rd @@ -44,6 +44,8 @@ on AE listing table.} \item{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 \code{1e2}.} + +\item{...}{Additional arguments passed to \code{\link[metalite.ae:rate_compare_sum]{metalite.ae::rate_compare_sum()}}.} } \value{ An \code{outdata} object.