From 2f3c6bb1b22c5921011c5a7ee4c785fe0764a8ee Mon Sep 17 00:00:00 2001
From: "Wang, Benjamin" <benjamin.wang@merck.com>
Date: Mon, 17 Jul 2023 21:41:41 -0400
Subject: [PATCH 1/5] add argument na_name

---
 R/collect_n_subject.R |  9 ++++++---
 man/n_subject.Rd      | 11 ++++++++++-
 2 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/R/collect_n_subject.R b/R/collect_n_subject.R
index 848ebb9..21aecbd 100644
--- a/R/collect_n_subject.R
+++ b/R/collect_n_subject.R
@@ -23,6 +23,7 @@
 #' @param par A character vector of parameter name.
 #' @param use_na A character value for whether to include `NA` values
 #'   in the table. See the `useNA` argument in [base::table()] for more details.
+#' @param na_name A character value for missing value label, default is "Missing".
 #'
 #' @return A data frame summarizing the number of unique subjects
 #'   in different arms.
@@ -38,14 +39,16 @@
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX)
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = "always")
+#' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na_name = "Null")
 n_subject <- function(id,
                       group,
                       par = NULL,
-                      use_na = c("ifany", "no", "always")) {
+                      use_na = c("ifany", "no", "always"),
+                      na_name = "Missing") {
   use_na <- match.arg(use_na)
 
   if ("factor" %in% class(group)) {
-    u_group <- c(as.character(levels(group)), "Missing")
+    u_group <- c(as.character(levels(group)), na_name)
   } else {
     stop("n_subject: group variable must be a factor")
   }
@@ -61,7 +64,7 @@ n_subject <- function(id,
     db <- data.frame(id = id, group = group, par = par)
     res <- table(unique(db)[, c("group", "par")], useNA = use_na)
     name <- colnames(res)
-    name[is.na(name)] <- "Missing"
+    name[is.na(name)] <- na_name
 
     n_row <- nrow(res)
     n_col <- ncol(res)
diff --git a/man/n_subject.Rd b/man/n_subject.Rd
index bb632f8..57cc6b3 100644
--- a/man/n_subject.Rd
+++ b/man/n_subject.Rd
@@ -4,7 +4,13 @@
 \alias{n_subject}
 \title{Count number of unique subjects}
 \usage{
-n_subject(id, group, par = NULL, use_na = c("ifany", "no", "always"))
+n_subject(
+  id,
+  group,
+  par = NULL,
+  use_na = c("ifany", "no", "always"),
+  na_name = "Missing"
+)
 }
 \arguments{
 \item{id}{A character vector of subject identifier.}
@@ -15,6 +21,8 @@ n_subject(id, group, par = NULL, use_na = c("ifany", "no", "always"))
 
 \item{use_na}{A character value for whether to include \code{NA} values
 in the table. See the \code{useNA} argument in \code{\link[base:table]{base::table()}} for more details.}
+
+\item{na_name}{A character value for missing value label, default is "Missing".}
 }
 \value{
 A data frame summarizing the number of unique subjects
@@ -32,4 +40,5 @@ r2rtf_adae$SEX[1:5] <- NA
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX)
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = "always")
+n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na_name = "Null")
 }

From ddf5408b9b292b5d00c1fd6538a28a4ed4de7eed Mon Sep 17 00:00:00 2001
From: "Wang, Benjamin" <benjamin.wang@merck.com>
Date: Tue, 18 Jul 2023 13:07:48 -0400
Subject: [PATCH 2/5] change documentation

---
 R/collect_n_subject.R | 9 +++++----
 man/n_subject.Rd      | 8 ++++----
 2 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/R/collect_n_subject.R b/R/collect_n_subject.R
index 21aecbd..e1251a3 100644
--- a/R/collect_n_subject.R
+++ b/R/collect_n_subject.R
@@ -21,9 +21,9 @@
 #' @param id A character vector of subject identifier.
 #' @param group A factor vector of group name.
 #' @param par A character vector of parameter name.
+#' @param na A character string used to label missing values. Defaults to `"Missing"`.
 #' @param use_na A character value for whether to include `NA` values
 #'   in the table. See the `useNA` argument in [base::table()] for more details.
-#' @param na_name A character value for missing value label, default is "Missing".
 #'
 #' @return A data frame summarizing the number of unique subjects
 #'   in different arms.
@@ -39,12 +39,13 @@
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX)
 #' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = "always")
-#' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na_name = "Null")
+#' n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na = "Null")
 n_subject <- function(id,
                       group,
                       par = NULL,
-                      use_na = c("ifany", "no", "always"),
-                      na_name = "Missing") {
+                      na_name = "Missing",
+                      use_na = c("ifany", "no", "always")
+                      ) {
   use_na <- match.arg(use_na)
 
   if ("factor" %in% class(group)) {
diff --git a/man/n_subject.Rd b/man/n_subject.Rd
index 57cc6b3..2cf1a6d 100644
--- a/man/n_subject.Rd
+++ b/man/n_subject.Rd
@@ -8,8 +8,8 @@ n_subject(
   id,
   group,
   par = NULL,
-  use_na = c("ifany", "no", "always"),
-  na_name = "Missing"
+  na_name = "Missing",
+  use_na = c("ifany", "no", "always")
 )
 }
 \arguments{
@@ -22,7 +22,7 @@ n_subject(
 \item{use_na}{A character value for whether to include \code{NA} values
 in the table. See the \code{useNA} argument in \code{\link[base:table]{base::table()}} for more details.}
 
-\item{na_name}{A character value for missing value label, default is "Missing".}
+\item{na}{A character string used to label missing values. Defaults to \code{"Missing"}.}
 }
 \value{
 A data frame summarizing the number of unique subjects
@@ -40,5 +40,5 @@ r2rtf_adae$SEX[1:5] <- NA
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA)
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX)
 n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, use_na = "always")
-n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na_name = "Null")
+n_subject(r2rtf_adae$USUBJID, r2rtf_adae$TRTA, r2rtf_adae$SEX, na = "Null")
 }

From 8bcbdac40706b54b976410ee7757f4fe3e282805 Mon Sep 17 00:00:00 2001
From: wangben718 <wangben718@users.noreply.github.com>
Date: Tue, 18 Jul 2023 17:09:50 +0000
Subject: [PATCH 3/5] Style code (GHA)

---
 R/collect_n_subject.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/collect_n_subject.R b/R/collect_n_subject.R
index e1251a3..0209ca0 100644
--- a/R/collect_n_subject.R
+++ b/R/collect_n_subject.R
@@ -44,8 +44,7 @@ n_subject <- function(id,
                       group,
                       par = NULL,
                       na_name = "Missing",
-                      use_na = c("ifany", "no", "always")
-                      ) {
+                      use_na = c("ifany", "no", "always")) {
   use_na <- match.arg(use_na)
 
   if ("factor" %in% class(group)) {

From e30dce88cb2f88d08b75d343f94709d1a5b6e2fd Mon Sep 17 00:00:00 2001
From: "Wang, Benjamin" <benjamin.wang@merck.com>
Date: Tue, 18 Jul 2023 13:11:31 -0400
Subject: [PATCH 4/5] change argument name

---
 R/collect_n_subject.R | 2 +-
 man/n_subject.Rd      | 6 +++---
 2 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/collect_n_subject.R b/R/collect_n_subject.R
index e1251a3..18331ca 100644
--- a/R/collect_n_subject.R
+++ b/R/collect_n_subject.R
@@ -43,7 +43,7 @@
 n_subject <- function(id,
                       group,
                       par = NULL,
-                      na_name = "Missing",
+                      na = "Missing",
                       use_na = c("ifany", "no", "always")
                       ) {
   use_na <- match.arg(use_na)
diff --git a/man/n_subject.Rd b/man/n_subject.Rd
index 2cf1a6d..9c4f8d3 100644
--- a/man/n_subject.Rd
+++ b/man/n_subject.Rd
@@ -8,7 +8,7 @@ n_subject(
   id,
   group,
   par = NULL,
-  na_name = "Missing",
+  na = "Missing",
   use_na = c("ifany", "no", "always")
 )
 }
@@ -19,10 +19,10 @@ n_subject(
 
 \item{par}{A character vector of parameter name.}
 
+\item{na}{A character string used to label missing values. Defaults to \code{"Missing"}.}
+
 \item{use_na}{A character value for whether to include \code{NA} values
 in the table. See the \code{useNA} argument in \code{\link[base:table]{base::table()}} for more details.}
-
-\item{na}{A character string used to label missing values. Defaults to \code{"Missing"}.}
 }
 \value{
 A data frame summarizing the number of unique subjects

From fde864d07ab6e68348d974960fbb50e59d30f143 Mon Sep 17 00:00:00 2001
From: wangben718 <wangben718@users.noreply.github.com>
Date: Tue, 18 Jul 2023 17:15:09 +0000
Subject: [PATCH 5/5] Style code (GHA)

---
 R/collect_n_subject.R | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/R/collect_n_subject.R b/R/collect_n_subject.R
index e991f11..ea53522 100644
--- a/R/collect_n_subject.R
+++ b/R/collect_n_subject.R
@@ -44,8 +44,7 @@ n_subject <- function(id,
                       group,
                       par = NULL,
                       na = "Missing",
-                      use_na = c("ifany", "no", "always")
-                      ) {
+                      use_na = c("ifany", "no", "always")) {
   use_na <- match.arg(use_na)
 
   if ("factor" %in% class(group)) {