From 108edfd5461c313ee04da91699afe16d79ef9456 Mon Sep 17 00:00:00 2001
From: Zelos Zhu <zelos.zhu@atorusresearch.com>
Date: Thu, 2 May 2024 17:40:32 +0000
Subject: [PATCH 1/3] add appropriate argument to functions

---
 R/ard_effectsize_cohens_d.R        | 10 ++++++----
 R/ard_effectsize_hedges_g.R        | 10 ++++++----
 R/ard_stats_fisher_test.R          |  6 ++++--
 R/ard_stats_prop_test.R            |  5 ++++-
 R/ard_stats_t_test.R               | 10 ++++++----
 R/ard_stats_wilcox_test.R          | 10 ++++++----
 man/ard_effectsize_cohens_d.Rd     |  7 +++++--
 man/ard_effectsize_hedges_g.Rd     |  7 +++++--
 man/ard_stats_fisher_test.Rd       |  5 ++++-
 man/ard_stats_prop_test.Rd         |  5 ++++-
 man/ard_stats_t_test.Rd            |  7 +++++--
 man/ard_stats_wilcox_test.Rd       |  7 +++++--
 man/dot-format_cohens_d_results.Rd |  2 +-
 man/dot-format_hedges_g_results.Rd |  2 +-
 14 files changed, 62 insertions(+), 31 deletions(-)

diff --git a/R/ard_effectsize_cohens_d.R b/R/ard_effectsize_cohens_d.R
index b0c51df9b..156a5a9ee 100644
--- a/R/ard_effectsize_cohens_d.R
+++ b/R/ard_effectsize_cohens_d.R
@@ -13,6 +13,8 @@
 #'   Independent tests will be run for each variable.
 #' @param id ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column name of the subject or participant ID
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... arguments passed to `effectsize::cohens_d(...)`
 #'
 #' @return ARD data frame
@@ -46,7 +48,7 @@ NULL
 
 #' @rdname ard_effectsize_cohens_d
 #' @export
-ard_effectsize_cohens_d <- function(data, by, variables, ...) {
+ard_effectsize_cohens_d <- function(data, by, variables, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -75,7 +77,7 @@ ard_effectsize_cohens_d <- function(data, by, variables, ...) {
         variable = variable,
         lst_tidy =
           cards::eval_capture_conditions(
-            effectsize::cohens_d(data[[variable]] ~ data[[by]], data = data, paired = FALSE, ...) |>
+            effectsize::cohens_d(data[[variable]] ~ data[[by]], data = data, paired = FALSE, ci = conf.level, ...) |>
               parameters::standardize_names(style = "broom")
           ),
         paired = FALSE,
@@ -89,7 +91,7 @@ ard_effectsize_cohens_d <- function(data, by, variables, ...) {
 
 #' @rdname ard_effectsize_cohens_d
 #' @export
-ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
+ard_effectsize_paired_cohens_d <- function(data, by, variables, id, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -123,7 +125,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, ...) {
             # adding this reshape inside the eval, so if there is an error it's captured in the ARD object
             data_wide <- .paired_data_pivot_wider(data, by = by, variable = variable, id = id)
             # perform paired cohen's d test
-            effectsize::cohens_d(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ...) |>
+            effectsize::cohens_d(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ci = conf.level, ...) |>
               parameters::standardize_names(style = "broom")
           }),
         paired = TRUE,
diff --git a/R/ard_effectsize_hedges_g.R b/R/ard_effectsize_hedges_g.R
index 3cdcf3a8d..d6575921d 100644
--- a/R/ard_effectsize_hedges_g.R
+++ b/R/ard_effectsize_hedges_g.R
@@ -13,6 +13,8 @@
 #'   tests will be run for each variable
 #' @param id ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column name of the subject or participant ID
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... arguments passed to `effectsize::hedges_g(...)`
 #'
 #' @return ARD data frame
@@ -46,7 +48,7 @@ NULL
 
 #' @rdname ard_effectsize_hedges_g
 #' @export
-ard_effectsize_hedges_g <- function(data, by, variables, ...) {
+ard_effectsize_hedges_g <- function(data, by, variables, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -79,7 +81,7 @@ ard_effectsize_hedges_g <- function(data, by, variables, ...) {
             # Will also need to remove `hedges_g` from globalVariables()
             withr::with_namespace(
               package = "effectsize",
-              code = hedges_g(data[[variable]] ~ data[[by]], paired = FALSE, ...)
+              code = hedges_g(data[[variable]] ~ data[[by]], paired = FALSE, ci = conf.level, ...)
             ) |>
               parameters::standardize_names(style = "broom")
           ),
@@ -93,7 +95,7 @@ ard_effectsize_hedges_g <- function(data, by, variables, ...) {
 
 #' @rdname ard_effectsize_hedges_g
 #' @export
-ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
+ard_effectsize_paired_hedges_g <- function(data, by, variables, id, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -129,7 +131,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, ...) {
             # perform paired cohen's d test
             withr::with_namespace(
               package = "effectsize",
-              code = hedges_g(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ...)
+              code = hedges_g(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ci = conf.level, ...)
             ) |>
               parameters::standardize_names(style = "broom")
           }),
diff --git a/R/ard_stats_fisher_test.R b/R/ard_stats_fisher_test.R
index 8fa50ce46..b4483c911 100644
--- a/R/ard_stats_fisher_test.R
+++ b/R/ard_stats_fisher_test.R
@@ -12,6 +12,8 @@
 #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column names to be compared. Independent tests will be computed for
 #'   each variable.
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... additional arguments passed to `fisher.test(...)`
 #'
 #' @return ARD data frame
@@ -20,7 +22,7 @@
 #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' cards::ADSL[1:30, ] |>
 #'   ard_stats_fisher_test(by = "ARM", variables = "AGEGR1")
-ard_stats_fisher_test <- function(data, by, variables, ...) {
+ard_stats_fisher_test <- function(data, by, variables, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -45,7 +47,7 @@ ard_stats_fisher_test <- function(data, by, variables, ...) {
       cards::tidy_as_ard(
         lst_tidy =
           cards::eval_capture_conditions(
-            stats::fisher.test(x = data[[variable]], y = data[[by]], ...) |>
+            stats::fisher.test(x = data[[variable]], y = data[[by]], conf.level = conf.level, ...) |>
               broom::tidy()
           ),
         tidy_result_names =
diff --git a/R/ard_stats_prop_test.R b/R/ard_stats_prop_test.R
index f96784737..071ae9264 100644
--- a/R/ard_stats_prop_test.R
+++ b/R/ard_stats_prop_test.R
@@ -10,6 +10,8 @@
 #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column names to be compared. Must be a binary column coded as `TRUE`/`FALSE`
 #'   or `1`/`0`. Independent tests will be computed for each variable.
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... arguments passed to `prop.test(...)`
 #'
 #' @return ARD data frame
@@ -18,7 +20,7 @@
 #' @examplesIf do.call(asNamespace("cardx")$is_pkg_installed, list(pkg = "broom", reference_pkg = "cardx"))
 #' mtcars |>
 #'   ard_stats_prop_test(by = vs, variables = am)
-ard_stats_prop_test <- function(data, by, variables, ...) {
+ard_stats_prop_test <- function(data, by, variables, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -72,6 +74,7 @@ ard_stats_prop_test <- function(data, by, variables, ...) {
             stats::prop.test(
               x = data_counts[["x"]],
               n = data_counts[["n"]],
+              conf.level = conf.level,
               ...
             ) |>
               broom::tidy() |>
diff --git a/R/ard_stats_t_test.R b/R/ard_stats_t_test.R
index b506d981c..010c1d571 100644
--- a/R/ard_stats_t_test.R
+++ b/R/ard_stats_t_test.R
@@ -12,6 +12,8 @@
 #'   each variable.
 #' @param id ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column name of the subject or participant ID
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... arguments passed to `t.test(...)`
 #'
 #' @return ARD data frame
@@ -43,7 +45,7 @@ NULL
 
 #' @rdname ard_stats_t_test
 #' @export
-ard_stats_t_test <- function(data, variables, by = NULL, ...) {
+ard_stats_t_test <- function(data, variables, by = NULL, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -72,7 +74,7 @@ ard_stats_t_test <- function(data, variables, by = NULL, ...) {
         lst_tidy =
           # styler: off
           cards::eval_capture_conditions(
-            if (!is_empty(by)) stats::t.test(data[[variable]] ~ data[[by]], ...) |> broom::tidy()
+            if (!is_empty(by)) stats::t.test(data[[variable]] ~ data[[by]], conf.level = conf.level, ...) |> broom::tidy()
             else stats::t.test(data[[variable]], ...) |> broom::tidy()
           ),
         # styler: on
@@ -86,7 +88,7 @@ ard_stats_t_test <- function(data, variables, by = NULL, ...) {
 
 #' @rdname ard_stats_t_test
 #' @export
-ard_stats_paired_t_test <- function(data, by, variables, id, ...) {
+ard_stats_paired_t_test <- function(data, by, variables, id, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -120,7 +122,7 @@ ard_stats_paired_t_test <- function(data, by, variables, id, ...) {
             # adding this reshape inside the eval, so if there is an error it's captured in the ARD object
             data_wide <- .paired_data_pivot_wider(data, by = by, variable = variable, id = id)
             # perform paired t-test
-            stats::t.test(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ...) |>
+            stats::t.test(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, conf.level = conf.level, ...) |>
               broom::tidy()
           }),
         paired = TRUE,
diff --git a/R/ard_stats_wilcox_test.R b/R/ard_stats_wilcox_test.R
index c2a14bd49..7c01fcb00 100644
--- a/R/ard_stats_wilcox_test.R
+++ b/R/ard_stats_wilcox_test.R
@@ -12,6 +12,8 @@
 #'   each variable.
 #' @param id ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column name of the subject or participant ID.
+#' @param conf.level (scalar `numeric`)\cr
+#'   confidence level for confidence interval. Default is `0.95`.
 #' @param ... arguments passed to `wilcox.test(...)`
 #'
 #' @return ARD data frame
@@ -43,7 +45,7 @@ NULL
 
 #' @rdname ard_stats_wilcox_test
 #' @export
-ard_stats_wilcox_test <- function(data, variables, by = NULL, ...) {
+ard_stats_wilcox_test <- function(data, variables, by = NULL, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -73,7 +75,7 @@ ard_stats_wilcox_test <- function(data, variables, by = NULL, ...) {
           # styler: off
           cards::eval_capture_conditions(
             if (!is_empty(by)) {
-              stats::wilcox.test(data[[variable]] ~ data[[by]], ...) |>
+              stats::wilcox.test(data[[variable]] ~ data[[by]], conf.level = conf.level, ...) |>
                 broom::tidy()
             }
             else {
@@ -92,7 +94,7 @@ ard_stats_wilcox_test <- function(data, variables, by = NULL, ...) {
 
 #' @rdname ard_stats_wilcox_test
 #' @export
-ard_stats_paired_wilcox_test <- function(data, by, variables, id, ...) {
+ard_stats_paired_wilcox_test <- function(data, by, variables, id, conf.level = 0.95, ...) {
   set_cli_abort_call()
 
   # check installed packages ---------------------------------------------------
@@ -126,7 +128,7 @@ ard_stats_paired_wilcox_test <- function(data, by, variables, id, ...) {
             # adding this reshape inside the eval, so if there is an error it's captured in the ARD object
             data_wide <- .paired_data_pivot_wider(data, by = by, variable = variable, id = id)
             # perform paired wilcox test
-            stats::wilcox.test(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, ...) |>
+            stats::wilcox.test(x = data_wide[["by1"]], y = data_wide[["by2"]], paired = TRUE, conf.level = conf.level, ...) |>
               broom::tidy()
           }),
         paired = TRUE,
diff --git a/man/ard_effectsize_cohens_d.Rd b/man/ard_effectsize_cohens_d.Rd
index 3eb2ac94e..93c907aa6 100644
--- a/man/ard_effectsize_cohens_d.Rd
+++ b/man/ard_effectsize_cohens_d.Rd
@@ -5,9 +5,9 @@
 \alias{ard_effectsize_paired_cohens_d}
 \title{ARD Cohen's D Test}
 \usage{
-ard_effectsize_cohens_d(data, by, variables, ...)
+ard_effectsize_cohens_d(data, by, variables, conf.level = 0.95, ...)
 
-ard_effectsize_paired_cohens_d(data, by, variables, id, ...)
+ard_effectsize_paired_cohens_d(data, by, variables, id, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -20,6 +20,9 @@ column name to compare by. Must be a categorical variable with exactly two level
 column names to be compared. Must be a continuous variables.
 Independent tests will be run for each variable.}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{arguments passed to \code{effectsize::cohens_d(...)}}
 
 \item{id}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
diff --git a/man/ard_effectsize_hedges_g.Rd b/man/ard_effectsize_hedges_g.Rd
index 5ec59117a..23c43e8d2 100644
--- a/man/ard_effectsize_hedges_g.Rd
+++ b/man/ard_effectsize_hedges_g.Rd
@@ -5,9 +5,9 @@
 \alias{ard_effectsize_paired_hedges_g}
 \title{ARD Hedge's G Test}
 \usage{
-ard_effectsize_hedges_g(data, by, variables, ...)
+ard_effectsize_hedges_g(data, by, variables, conf.level = 0.95, ...)
 
-ard_effectsize_paired_hedges_g(data, by, variables, id, ...)
+ard_effectsize_paired_hedges_g(data, by, variables, id, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -20,6 +20,9 @@ column name to compare by. Must be a categorical variable with exactly two level
 column names to be compared. Must be a continuous variable. Independent
 tests will be run for each variable}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{arguments passed to \code{effectsize::hedges_g(...)}}
 
 \item{id}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
diff --git a/man/ard_stats_fisher_test.Rd b/man/ard_stats_fisher_test.Rd
index 1e07809b0..7831e81e9 100644
--- a/man/ard_stats_fisher_test.Rd
+++ b/man/ard_stats_fisher_test.Rd
@@ -4,7 +4,7 @@
 \alias{ard_stats_fisher_test}
 \title{ARD Fisher's Exact Test}
 \usage{
-ard_stats_fisher_test(data, by, variables, ...)
+ard_stats_fisher_test(data, by, variables, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -17,6 +17,9 @@ column name to compare by}
 column names to be compared. Independent tests will be computed for
 each variable.}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{additional arguments passed to \code{fisher.test(...)}}
 }
 \value{
diff --git a/man/ard_stats_prop_test.Rd b/man/ard_stats_prop_test.Rd
index cb966e1c4..61bf61791 100644
--- a/man/ard_stats_prop_test.Rd
+++ b/man/ard_stats_prop_test.Rd
@@ -4,7 +4,7 @@
 \alias{ard_stats_prop_test}
 \title{ARD 2-sample proportion test}
 \usage{
-ard_stats_prop_test(data, by, variables, ...)
+ard_stats_prop_test(data, by, variables, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -17,6 +17,9 @@ column name to compare by}
 column names to be compared. Must be a binary column coded as \code{TRUE}/\code{FALSE}
 or \code{1}/\code{0}. Independent tests will be computed for each variable.}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{arguments passed to \code{prop.test(...)}}
 }
 \value{
diff --git a/man/ard_stats_t_test.Rd b/man/ard_stats_t_test.Rd
index 1bfb7fbe9..edd55ee94 100644
--- a/man/ard_stats_t_test.Rd
+++ b/man/ard_stats_t_test.Rd
@@ -5,9 +5,9 @@
 \alias{ard_stats_paired_t_test}
 \title{ARD t-test}
 \usage{
-ard_stats_t_test(data, variables, by = NULL, ...)
+ard_stats_t_test(data, variables, by = NULL, conf.level = 0.95, ...)
 
-ard_stats_paired_t_test(data, by, variables, id, ...)
+ard_stats_paired_t_test(data, by, variables, id, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -20,6 +20,9 @@ each variable.}
 \item{by}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
 optional column name to compare by.}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{arguments passed to \code{t.test(...)}}
 
 \item{id}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
diff --git a/man/ard_stats_wilcox_test.Rd b/man/ard_stats_wilcox_test.Rd
index 14f48b213..86486171b 100644
--- a/man/ard_stats_wilcox_test.Rd
+++ b/man/ard_stats_wilcox_test.Rd
@@ -5,9 +5,9 @@
 \alias{ard_stats_paired_wilcox_test}
 \title{ARD Wilcoxon Rank-Sum Test}
 \usage{
-ard_stats_wilcox_test(data, variables, by = NULL, ...)
+ard_stats_wilcox_test(data, variables, by = NULL, conf.level = 0.95, ...)
 
-ard_stats_paired_wilcox_test(data, by, variables, id, ...)
+ard_stats_paired_wilcox_test(data, by, variables, id, conf.level = 0.95, ...)
 }
 \arguments{
 \item{data}{(\code{data.frame})\cr
@@ -20,6 +20,9 @@ each variable.}
 \item{by}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
 optional column name to compare by.}
 
+\item{conf.level}{(scalar \code{numeric})\cr
+confidence level for confidence interval. Default is \code{0.95}.}
+
 \item{...}{arguments passed to \code{wilcox.test(...)}}
 
 \item{id}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
diff --git a/man/dot-format_cohens_d_results.Rd b/man/dot-format_cohens_d_results.Rd
index 20edfa95e..ca65e400c 100644
--- a/man/dot-format_cohens_d_results.Rd
+++ b/man/dot-format_cohens_d_results.Rd
@@ -17,7 +17,7 @@ e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy
 
 \item{paired}{If \code{TRUE}, the values of \code{x} and \code{y} are considered as paired.
 This produces an effect size that is equivalent to the one-sample effect
-size on \code{x - y}. See also \code{\link[effectsize:repeated_measures_d]{repeated_measures_d()}} for more options.}
+size on \code{x - y}.}
 
 \item{...}{passed to \code{cohens_d(...)}}
 }
diff --git a/man/dot-format_hedges_g_results.Rd b/man/dot-format_hedges_g_results.Rd
index d22e5b762..e0f0328b3 100644
--- a/man/dot-format_hedges_g_results.Rd
+++ b/man/dot-format_hedges_g_results.Rd
@@ -17,7 +17,7 @@ e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy
 
 \item{paired}{If \code{TRUE}, the values of \code{x} and \code{y} are considered as paired.
 This produces an effect size that is equivalent to the one-sample effect
-size on \code{x - y}. See also \code{\link[effectsize:repeated_measures_d]{repeated_measures_d()}} for more options.}
+size on \code{x - y}.}
 
 \item{...}{passed to \code{hedges_g(...)}}
 }

From 3fe8e28ecaeca7a561702eb89c73bcdcc339a4b4 Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 3 May 2024 16:09:26 -0700
Subject: [PATCH 2/3] redoc

---
 man/dot-format_cohens_d_results.Rd | 2 +-
 man/dot-format_hedges_g_results.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/man/dot-format_cohens_d_results.Rd b/man/dot-format_cohens_d_results.Rd
index ca65e400c..20edfa95e 100644
--- a/man/dot-format_cohens_d_results.Rd
+++ b/man/dot-format_cohens_d_results.Rd
@@ -17,7 +17,7 @@ e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy
 
 \item{paired}{If \code{TRUE}, the values of \code{x} and \code{y} are considered as paired.
 This produces an effect size that is equivalent to the one-sample effect
-size on \code{x - y}.}
+size on \code{x - y}. See also \code{\link[effectsize:repeated_measures_d]{repeated_measures_d()}} for more options.}
 
 \item{...}{passed to \code{cohens_d(...)}}
 }
diff --git a/man/dot-format_hedges_g_results.Rd b/man/dot-format_hedges_g_results.Rd
index e0f0328b3..d22e5b762 100644
--- a/man/dot-format_hedges_g_results.Rd
+++ b/man/dot-format_hedges_g_results.Rd
@@ -17,7 +17,7 @@ e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy
 
 \item{paired}{If \code{TRUE}, the values of \code{x} and \code{y} are considered as paired.
 This produces an effect size that is equivalent to the one-sample effect
-size on \code{x - y}.}
+size on \code{x - y}. See also \code{\link[effectsize:repeated_measures_d]{repeated_measures_d()}} for more options.}
 
 \item{...}{passed to \code{hedges_g(...)}}
 }

From 0d415ff412760085d5c77bed52f7ddfbfb90c25f Mon Sep 17 00:00:00 2001
From: Daniel Sjoberg <danield.sjoberg@gmail.com>
Date: Fri, 3 May 2024 16:19:07 -0700
Subject: [PATCH 3/3] adding check

---
 R/ard_effectsize_cohens_d.R | 3 ++-
 R/ard_effectsize_hedges_g.R | 2 ++
 R/ard_stats_fisher_test.R   | 1 +
 R/ard_stats_prop_test.R     | 1 +
 R/ard_stats_t_test.R        | 1 +
 R/ard_stats_wilcox_test.R   | 1 +
 R/ard_survey_svychisq.R     | 2 +-
 man/ard_survey_svychisq.Rd  | 2 +-
 8 files changed, 10 insertions(+), 3 deletions(-)

diff --git a/R/ard_effectsize_cohens_d.R b/R/ard_effectsize_cohens_d.R
index 156a5a9ee..91f5441a1 100644
--- a/R/ard_effectsize_cohens_d.R
+++ b/R/ard_effectsize_cohens_d.R
@@ -62,7 +62,7 @@ ard_effectsize_cohens_d <- function(data, by, variables, conf.level = 0.95, ...)
   data <- dplyr::ungroup(data)
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
   check_scalar(by)
-
+  check_range(conf.level, range = c(0, 1))
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
     return(dplyr::tibble())
@@ -107,6 +107,7 @@ ard_effectsize_paired_cohens_d <- function(data, by, variables, id, conf.level =
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }}, id = {{ id }})
   check_scalar(by)
   check_scalar(id)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
diff --git a/R/ard_effectsize_hedges_g.R b/R/ard_effectsize_hedges_g.R
index d6575921d..58b228b5d 100644
--- a/R/ard_effectsize_hedges_g.R
+++ b/R/ard_effectsize_hedges_g.R
@@ -61,6 +61,7 @@ ard_effectsize_hedges_g <- function(data, by, variables, conf.level = 0.95, ...)
   data <- dplyr::ungroup(data)
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
   check_scalar(by)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
@@ -111,6 +112,7 @@ ard_effectsize_paired_hedges_g <- function(data, by, variables, id, conf.level =
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }}, id = {{ id }})
   check_scalar(by)
   check_scalar(id)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
diff --git a/R/ard_stats_fisher_test.R b/R/ard_stats_fisher_test.R
index b4483c911..0831f45bc 100644
--- a/R/ard_stats_fisher_test.R
+++ b/R/ard_stats_fisher_test.R
@@ -35,6 +35,7 @@ ard_stats_fisher_test <- function(data, by, variables, conf.level = 0.95, ...) {
   check_data_frame(data)
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
   check_scalar(by)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
diff --git a/R/ard_stats_prop_test.R b/R/ard_stats_prop_test.R
index 071ae9264..1b4389814 100644
--- a/R/ard_stats_prop_test.R
+++ b/R/ard_stats_prop_test.R
@@ -31,6 +31,7 @@ ard_stats_prop_test <- function(data, by, variables, conf.level = 0.95, ...) {
   check_not_missing(variables)
   check_not_missing(by)
   check_data_frame(data)
+  check_range(conf.level, range = c(0, 1))
 
   # process inputs -------------------------------------------------------------
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
diff --git a/R/ard_stats_t_test.R b/R/ard_stats_t_test.R
index 010c1d571..91e603c58 100644
--- a/R/ard_stats_t_test.R
+++ b/R/ard_stats_t_test.R
@@ -58,6 +58,7 @@ ard_stats_t_test <- function(data, variables, by = NULL, conf.level = 0.95, ...)
   data <- dplyr::ungroup(data)
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
   check_scalar(by, allow_empty = TRUE)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
diff --git a/R/ard_stats_wilcox_test.R b/R/ard_stats_wilcox_test.R
index 7c01fcb00..5972230bb 100644
--- a/R/ard_stats_wilcox_test.R
+++ b/R/ard_stats_wilcox_test.R
@@ -58,6 +58,7 @@ ard_stats_wilcox_test <- function(data, variables, by = NULL, conf.level = 0.95,
   data <- dplyr::ungroup(data)
   cards::process_selectors(data, by = {{ by }}, variables = {{ variables }})
   check_scalar(by, allow_empty = TRUE)
+  check_range(conf.level, range = c(0, 1))
 
   # if no variables selected, return empty tibble ------------------------------
   if (is_empty(variables)) {
diff --git a/R/ard_survey_svychisq.R b/R/ard_survey_svychisq.R
index 8fb57325f..5ad520a42 100644
--- a/R/ard_survey_svychisq.R
+++ b/R/ard_survey_svychisq.R
@@ -5,7 +5,7 @@
 #' Only two-way comparisons are supported.
 #'
 #' @param data (`survey.design`)\cr
-#'   a survey design object often created with the {survey} package
+#'   a survey design object often created with the \{survey\} package
 #' @param by ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
 #'   column name to compare by.
 #' @param variables ([`tidy-select`][dplyr::dplyr_tidy_select])\cr
diff --git a/man/ard_survey_svychisq.Rd b/man/ard_survey_svychisq.Rd
index e645f5c00..05d660264 100644
--- a/man/ard_survey_svychisq.Rd
+++ b/man/ard_survey_svychisq.Rd
@@ -8,7 +8,7 @@ ard_survey_svychisq(data, by, variables, statistic = "F", ...)
 }
 \arguments{
 \item{data}{(\code{survey.design})\cr
-a survey design object often created with the {survey} package}
+a survey design object often created with the \{survey\} package}
 
 \item{by}{(\code{\link[dplyr:dplyr_tidy_select]{tidy-select}})\cr
 column name to compare by.}