From 38326aa4b353bbdc0e9101bc45e7903724797874 Mon Sep 17 00:00:00 2001
From: unknown <guk@hspharm.com>
Date: Thu, 5 Dec 2024 00:10:07 +0800
Subject: [PATCH] fix error of unconfirmed BOR calculation

---
 R/onco_resp.R                   |  2 +-
 man/sfreq.Rd                    | 34 ++++++++++++++++++++++-----------
 tests/testthat/test-onco_resp.R |  8 ++++----
 3 files changed, 28 insertions(+), 16 deletions(-)

diff --git a/R/onco_resp.R b/R/onco_resp.R
index a2f15b4..c57bc2b 100644
--- a/R/onco_resp.R
+++ b/R/onco_resp.R
@@ -177,7 +177,7 @@ derive_bor <- function(data,
           TRUE ~ AVALC
         )
       ) %>%
-      left_join(aval_map, by = c("AVALC" = "avalc_temp")) %>%
+      left_join(aval_map, by = "avalc_temp") %>%
       mutate(AVAL = .data$aval_temp) %>%
       arrange(!!sym(unique_id), AVAL, ADT) %>%
       # select the best and first one as the best overall response.
diff --git a/man/sfreq.Rd b/man/sfreq.Rd
index 38c7be7..760b00c 100644
--- a/man/sfreq.Rd
+++ b/man/sfreq.Rd
@@ -43,24 +43,36 @@ h_count_sort(data, df, sort_var, row_tot, nested_row = FALSE, .order = NULL)
 \item{data}{(\code{data.frame})\cr a data frame that contains the variables to be
 summarized and grouped.}
 
-\item{var}{(\code{vector})\cr a character vector of variables to be summarized within \code{data}.}
+\item{var}{(\code{string})\cr a character variable to be summarized within \code{data}.}
+
+\item{nested_vars}{(\code{string})\cr a character variable as the nested level to
+be summarized along with \code{var}.}
 
 \item{by}{(\code{string})\cr a character variable for grouping within \code{data}.}
 
-\item{denom}{(\code{data.frame})\cr the denominator to use for the percentage, but
-not use temporarily. By default, it's NULL, meaning the function will use
-the number of values of the \code{data}, including missing value.}
+\item{fmt}{(\code{string})\cr formatting string from \code{formatters::list_valid_format_labels()}
+for frequency counts and percentages.}
+
+\item{denom}{(\code{numeric} or \code{data.frame})\cr denominator for proportion can be a
+numeric vector of denominators or a data frame where we can count the \code{var} inside.}
+
+\item{distinct}{(\code{string})\cr a character variable to determine which level should
+be kept only unique rows from \code{data}. Default is 'USUBJID' for normal counting, but
+it can be set as 'STUDYID' for AE events if necessary.}
 
 \item{fctdrop}{(\code{logical})\cr whether to include the levels of the variables
 but with no records.}
 
-\item{na_str}{(\code{string})\cr a string to replace \code{NA} in the output if no records
-will be counted for any category.}
+\item{col_tot}{(\code{logical})\cr whether to add total column in the output or not.}
 
-\item{format}{(\code{string})\cr formatting string from \code{formatters::list_valid_format_labels()}
-for frequency counts and percentages.}
+\item{row_tot}{(\code{string})\cr Default set as NULL for no total row, but if set as
+'n' or other words that will be defined as a label for total row.}
 
-\item{addtot}{(\code{logical})\cr whether to add total column in the output or not.}
+\item{nested_row}{(\code{logical})\cr whether to add nested variable in the label row.
+Set to TRUE for AE counting.}
+
+\item{na_str}{(\code{string})\cr a string to replace \code{NA} in the output if no records
+will be counted for any category, but not used.}
 }
 \value{
 A object \code{Desc} contains an intermediate data with long form for
@@ -69,8 +81,8 @@ post-processing and final data with wide form for presentation.
 \description{
 \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#experimental}{\figure{lifecycle-experimental.svg}{options: alt='[Experimental]'}}}{\strong{[Experimental]}}
 
-Create a summary table for one or more variables by one group, as well as a
-total column if necessary.
+Create a summary table for one variable or nested variable by one group, as
+well as a total column if necessary.
 }
 \section{Functions}{
 \itemize{
diff --git a/tests/testthat/test-onco_resp.R b/tests/testthat/test-onco_resp.R
index 7b932dd..fbb3fe5 100644
--- a/tests/testthat/test-onco_resp.R
+++ b/tests/testthat/test-onco_resp.R
@@ -33,7 +33,7 @@ test_that("derive_bor works as expected with default arguments", {
     ) %>%
     select(-TRTSDTC)
 
-  res <- derive_bor(data = adrs)
+  res <- suppressWarnings(derive_bor(data = adrs))
   expect_tibble(res)
   expect_identical(
     res,
@@ -91,7 +91,7 @@ test_that("derive_bor works as expected for confirmed BOR", {
     ) %>%
     select(-TRTSDTC)
 
-  res <- derive_bor(data = adrs, confirm = TRUE)
+  res <- suppressWarnings(derive_bor(data = adrs, confirm = TRUE))
   expect_identical(
     res,
     tibble::tibble(
@@ -148,7 +148,7 @@ test_that("derive_bor works as expected with zero NE", {
     ) %>%
     select(-TRTSDTC)
 
-  res <- derive_bor(data = adrs, max_ne = 0, confirm = TRUE)
+  res <- suppressWarnings(derive_bor(data = adrs, max_ne = 0, confirm = TRUE))
   expect_identical(
     res,
     tibble::tibble(
@@ -206,7 +206,7 @@ test_that("derive_bor works as expected with at least 56 days of reference inter
     ) %>%
     select(-TRTSDTC)
 
-  res <- derive_bor(data = adrs, ref_start_window = 56, ref_interval = 56, confirm = TRUE)
+  res <- suppressWarnings(derive_bor(data = adrs, ref_start_window = 56, ref_interval = 56, confirm = TRUE))
   expect_identical(
     res,
     tibble::tibble(