From 20c7bdc7d03409c07d4e69e0b996e02e9bc6de9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Fri, 22 May 2026 15:13:00 +0200 Subject: [PATCH 1/4] Fixes issues with cross-links (Update documentation to latest roxygen2) --- DESCRIPTION | 2 +- man/ard_effectsize_hedges_g.Rd | 2 +- man/ard_emmeans.Rd | 3 ++- man/cardx-package.Rd | 1 + man/reexports.Rd | 4 ++-- 5 files changed, 7 insertions(+), 5 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0bd36fe2c..f17f25707 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -49,10 +49,10 @@ Suggests: Remotes: insightsengineering/cards@main Config/Needs/website: insightsengineering/nesttemplate +Config/roxygen2/version: 8.0.0 Config/testthat/edition: 3 Config/testthat/parallel: true Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 diff --git a/man/ard_effectsize_hedges_g.Rd b/man/ard_effectsize_hedges_g.Rd index 32d8148db..cf47c9acf 100644 --- a/man/ard_effectsize_hedges_g.Rd +++ b/man/ard_effectsize_hedges_g.Rd @@ -33,7 +33,7 @@ ARD data frame } \description{ Analysis results data for paired and non-paired Hedge's G Effect Size Test -using \code{\link[effectsize:cohens_d]{effectsize::hedges_g()}}. +using \code{\link[effectsize:hedges_g]{effectsize::hedges_g()}}. } \details{ For the \code{ard_effectsize_hedges_g()} function, the data is expected to be one row per subject. diff --git a/man/ard_emmeans.Rd b/man/ard_emmeans.Rd index b7e5f180b..635688973 100644 --- a/man/ard_emmeans.Rd +++ b/man/ard_emmeans.Rd @@ -1,5 +1,6 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ard_emmeans_contrast.R, R/ard_emmeans_emmeans.R +% Please edit documentation in R/ard_emmeans_contrast.R, +% R/ard_emmeans_emmeans.R \name{ard_emmeans_contrast} \alias{ard_emmeans_contrast} \alias{ard_emmeans_emmeans} diff --git a/man/cardx-package.Rd b/man/cardx-package.Rd index b0cfa13d9..acd66dc07 100644 --- a/man/cardx-package.Rd +++ b/man/cardx-package.Rd @@ -24,6 +24,7 @@ Useful links: Authors: \itemize{ + \item Daniel D. Sjoberg \email{danield.sjoberg@gmail.com} (\href{https://orcid.org/0000-0003-0862-2018}{ORCID}) \item Abinaya Yogasekaram \email{abinaya.yogasekaram@contractors.roche.com} \item Emily de la Rua \email{emily.de_la_rua@contractors.roche.com} } diff --git a/man/reexports.Rd b/man/reexports.Rd index 1105c1cf2..00c5c2bfc 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -31,8 +31,8 @@ These objects are imported from other packages. Follow the links below to see their documentation. \describe{ - \item{cards}{\code{\link[cards]{ard_attributes}}, \code{\link[cards:deprecated]{ard_categorical}}, \code{\link[cards:deprecated]{ard_continuous}}, \code{\link[cards:deprecated]{ard_dichotomous}}, \code{\link[cards]{ard_missing}}, \code{\link[cards]{ard_summary}}, \code{\link[cards]{ard_tabulate}}, \code{\link[cards]{ard_tabulate_value}}, \code{\link[cards]{ard_total_n}}} + \item{cards}{\code{\link[cards:ard_attributes]{ard_attributes()}}, \code{\link[cards:ard_categorical]{ard_categorical()}}, \code{\link[cards:ard_continuous]{ard_continuous()}}, \code{\link[cards:ard_dichotomous]{ard_dichotomous()}}, \code{\link[cards:ard_missing]{ard_missing()}}, \code{\link[cards:ard_summary]{ard_summary()}}, \code{\link[cards:ard_tabulate]{ard_tabulate()}}, \code{\link[cards:ard_tabulate_value]{ard_tabulate_value()}}, \code{\link[cards:ard_total_n]{ard_total_n()}}} - \item{dplyr}{\code{\link[dplyr:reexports]{\%>\%}}, \code{\link[dplyr:reexports]{all_of}}, \code{\link[dplyr:reexports]{any_of}}, \code{\link[dplyr:reexports]{contains}}, \code{\link[dplyr:reexports]{ends_with}}, \code{\link[dplyr:reexports]{everything}}, \code{\link[dplyr:reexports]{last_col}}, \code{\link[dplyr:reexports]{matches}}, \code{\link[dplyr:reexports]{num_range}}, \code{\link[dplyr:reexports]{one_of}}, \code{\link[dplyr:reexports]{starts_with}}, \code{\link[dplyr:reexports]{where}}} + \item{dplyr}{\code{\link[dplyr:\%>\%]{\%>\%}}, \code{\link[dplyr:all_of]{all_of}}, \code{\link[dplyr:any_of]{any_of}}, \code{\link[dplyr:contains]{contains}}, \code{\link[dplyr:ends_with]{ends_with}}, \code{\link[dplyr:everything]{everything}}, \code{\link[dplyr:last_col]{last_col}}, \code{\link[dplyr:matches]{matches}}, \code{\link[dplyr:num_range]{num_range}}, \code{\link[dplyr:one_of]{one_of}}, \code{\link[dplyr:starts_with]{starts_with}}, \code{\link[dplyr:where]{where}}} }} From f0bdda835dfed935773480cabd72338258e03912 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Fri, 22 May 2026 18:02:46 +0200 Subject: [PATCH 2/4] Remove the help page for internal functions --- R/ard_aod_wald_test.R | 2 +- R/ard_stats_prop_test.R | 2 +- man/dot-extract_wald_results.Rd | 18 ------------------ man/dot-format_proptest_results.Rd | 26 -------------------------- 4 files changed, 2 insertions(+), 46 deletions(-) delete mode 100644 man/dot-extract_wald_results.Rd delete mode 100644 man/dot-format_proptest_results.Rd diff --git a/R/ard_aod_wald_test.R b/R/ard_aod_wald_test.R index d3ed94f4d..5406b8efa 100644 --- a/R/ard_aod_wald_test.R +++ b/R/ard_aod_wald_test.R @@ -109,7 +109,7 @@ ard_aod_wald_test <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or_pa #' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()` #' #' @return a data frame containing the wald test results. -#' @keywords internal +#' @noRd .extract_wald_results <- function(wald_test) { df <- wald_test$result$chi2[("df")] statistic <- wald_test$result$chi2[("chi2")] diff --git a/R/ard_stats_prop_test.R b/R/ard_stats_prop_test.R index 7e00c744e..89ce455fe 100644 --- a/R/ard_stats_prop_test.R +++ b/R/ard_stats_prop_test.R @@ -98,7 +98,7 @@ ard_stats_prop_test <- function(data, by, variables, conf.level = 0.95, ...) { #' @param ... passed to `prop.test(...)` #' #' @return ARD data frame -#' @keywords internal +#' @noRd .format_proptest_results <- function(by, variable, lst_tidy, ...) { # build ARD ------------------------------------------------------------------ ret <- diff --git a/man/dot-extract_wald_results.Rd b/man/dot-extract_wald_results.Rd deleted file mode 100644 index 24b23eb78..000000000 --- a/man/dot-extract_wald_results.Rd +++ /dev/null @@ -1,18 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ard_aod_wald_test.R -\name{.extract_wald_results} -\alias{.extract_wald_results} -\title{Extract data from wald.test object} -\usage{ -.extract_wald_results(wald_test) -} -\arguments{ -\item{wald_test}{(\code{data.frame})\cr wald test object object from \code{aod::wald.test()}} -} -\value{ -a data frame containing the wald test results. -} -\description{ -Extract data from wald.test object -} -\keyword{internal} diff --git a/man/dot-format_proptest_results.Rd b/man/dot-format_proptest_results.Rd deleted file mode 100644 index 05c97ef24..000000000 --- a/man/dot-format_proptest_results.Rd +++ /dev/null @@ -1,26 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/ard_stats_prop_test.R -\name{.format_proptest_results} -\alias{.format_proptest_results} -\title{Convert prop.test to ARD} -\usage{ -.format_proptest_results(by, variable, lst_tidy, ...) -} -\arguments{ -\item{by}{(\code{string})\cr by column name} - -\item{variable}{(\code{string})\cr variable column name} - -\item{lst_tidy}{(named \code{list})\cr -list of tidied results constructed with \code{\link[cards:eval_capture_conditions]{eval_capture_conditions()}}, -e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy())}.} - -\item{...}{passed to \code{prop.test(...)}} -} -\value{ -ARD data frame -} -\description{ -Convert prop.test to ARD -} -\keyword{internal} From 5d050730f82add8623ed1a0cfd1dc4b17a034d78 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Fri, 22 May 2026 18:03:20 +0200 Subject: [PATCH 3/4] Prevent CRAN reviewer comments on missing sections --- R/deprecated.R | 4 ++++ man/deprecated.Rd | 6 ++++++ 2 files changed, 10 insertions(+) diff --git a/R/deprecated.R b/R/deprecated.R index aa0e62927..8b0e5bc78 100644 --- a/R/deprecated.R +++ b/R/deprecated.R @@ -7,6 +7,10 @@ #' #' @name deprecated #' @keywords internal +#' @examples +#' NULL +#' @returns See each individual function help page. +#' NULL # v0.3.0 ----------------------------------------------------------------------- diff --git a/man/deprecated.Rd b/man/deprecated.Rd index f6641ca52..64a3ecb72 100644 --- a/man/deprecated.Rd +++ b/man/deprecated.Rd @@ -19,9 +19,15 @@ ard_categorical_max(...) ard_emmeans_mean_difference(...) } +\value{ +See each individual function help page. +} \description{ \ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}}\cr Some functions have been deprecated and are no longer being actively supported. } +\examples{ +NULL +} \keyword{internal} From a4aef8d61b7103328b9b36a58ad63e5551a38a1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Tue, 26 May 2026 08:55:22 +0200 Subject: [PATCH 4/4] Add back the help pages --- R/ard_aod_wald_test.R | 5 ++++- R/ard_stats_prop_test.R | 5 ++++- man/dot-extract_wald_results.Rd | 22 ++++++++++++++++++++++ man/dot-format_proptest_results.Rd | 30 ++++++++++++++++++++++++++++++ 4 files changed, 60 insertions(+), 2 deletions(-) create mode 100644 man/dot-extract_wald_results.Rd create mode 100644 man/dot-format_proptest_results.Rd diff --git a/R/ard_aod_wald_test.R b/R/ard_aod_wald_test.R index 5406b8efa..517a40b38 100644 --- a/R/ard_aod_wald_test.R +++ b/R/ard_aod_wald_test.R @@ -109,7 +109,10 @@ ard_aod_wald_test <- function(x, tidy_fun = broom.helpers::tidy_with_broom_or_pa #' @param wald_test (`data.frame`)\cr wald test object object from `aod::wald.test()` #' #' @return a data frame containing the wald test results. -#' @noRd +#' @examples +#' NULL +#' +#' @keywords internal .extract_wald_results <- function(wald_test) { df <- wald_test$result$chi2[("df")] statistic <- wald_test$result$chi2[("chi2")] diff --git a/R/ard_stats_prop_test.R b/R/ard_stats_prop_test.R index 89ce455fe..7312a511b 100644 --- a/R/ard_stats_prop_test.R +++ b/R/ard_stats_prop_test.R @@ -98,7 +98,10 @@ ard_stats_prop_test <- function(data, by, variables, conf.level = 0.95, ...) { #' @param ... passed to `prop.test(...)` #' #' @return ARD data frame -#' @noRd +#' @examples +#' NULL +#' +#' @keywords internal .format_proptest_results <- function(by, variable, lst_tidy, ...) { # build ARD ------------------------------------------------------------------ ret <- diff --git a/man/dot-extract_wald_results.Rd b/man/dot-extract_wald_results.Rd new file mode 100644 index 000000000..0b718e806 --- /dev/null +++ b/man/dot-extract_wald_results.Rd @@ -0,0 +1,22 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ard_aod_wald_test.R +\name{.extract_wald_results} +\alias{.extract_wald_results} +\title{Extract data from wald.test object} +\usage{ +.extract_wald_results(wald_test) +} +\arguments{ +\item{wald_test}{(\code{data.frame})\cr wald test object object from \code{aod::wald.test()}} +} +\value{ +a data frame containing the wald test results. +} +\description{ +Extract data from wald.test object +} +\examples{ +NULL + +} +\keyword{internal} diff --git a/man/dot-format_proptest_results.Rd b/man/dot-format_proptest_results.Rd new file mode 100644 index 000000000..b3c601010 --- /dev/null +++ b/man/dot-format_proptest_results.Rd @@ -0,0 +1,30 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/ard_stats_prop_test.R +\name{.format_proptest_results} +\alias{.format_proptest_results} +\title{Convert prop.test to ARD} +\usage{ +.format_proptest_results(by, variable, lst_tidy, ...) +} +\arguments{ +\item{by}{(\code{string})\cr by column name} + +\item{variable}{(\code{string})\cr variable column name} + +\item{lst_tidy}{(named \code{list})\cr +list of tidied results constructed with \code{\link[cards:eval_capture_conditions]{eval_capture_conditions()}}, +e.g. \code{eval_capture_conditions(t.test(mtcars$mpg ~ mtcars$am) |> broom::tidy())}.} + +\item{...}{passed to \code{prop.test(...)}} +} +\value{ +ARD data frame +} +\description{ +Convert prop.test to ARD +} +\examples{ +NULL + +} +\keyword{internal}