lil updates ahead of cran submission

.Rbuildignore

@@ -34,3 +34,4 @@ pkgdown
 # others
 ^renv$
 ^renv\.lock$
+^cran-comments\.md$

DESCRIPTION

@@ -1,20 +1,22 @@
 Package: cardx
 Title: Extra Analysis Results Data Utilities
-Version: 0.0.0.9042
+Version: 0.1.0
 Authors@R: c(
-    person("Daniel", "Sjoberg", , "sjobergd@gene.com", role = c("aut", "cre")),
+    person("Daniel", "Sjoberg", , "danield.sjoberg@gmail.com", role = c("aut", "cre")),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
-Description: Extra Analysis Results Data (ARD) functions. The package
-    supplements the ARD functions from the 'cards' package, exporting
-    functions to put statistical results in the ARD format.
+Description: Create extra Analysis Results Data (ARD) summary objects.
+    The package supplements the simple ARD functions from the 'cards'
+    package, exporting functions to put statistical results in the ARD
+    format. These objects are used and re-used to construct summary
+    tables, visualizations, and written reports.
 License: Apache License 2.0
 URL: https://github.com/insightsengineering/cardx
 BugReports: https://github.com/insightsengineering/cardx/issues
 Depends:
     R (>= 4.1)
 Imports:
-    cards (>= 0.0.0.9049),
+    cards (>= 0.1.0),
     cli (>= 3.6.1),
     dplyr (>= 1.1.2),
     glue (>= 1.6.2),
@@ -26,8 +28,6 @@ Suggests:
     spelling,
     testthat (>= 3.2.0),
     withr
-Remotes: 
-    insightsengineering/cards
 Config/Needs/website: insightsengineering/nesttemplate
 Config/testthat/edition: 3
 Config/testthat/parallel: true

NEWS.md

@@ -1,4 +1,3 @@
-# cardx 0.0.0.9042
+# cardx 0.1.0
 
-### New Features
-* New package!
+* Initial release.

R/ard_mcnemartest.R

@@ -76,14 +76,15 @@ ard_mcnemartest <- function(data, by, variable, ...) {
 #' )
 #'
 #' @keywords internal
+#' @noRd
 .format_mcnemartest_results <- function(by, variable, lst_tidy, ...) {
   # build ARD ------------------------------------------------------------------
   ret <-
     cards::tidy_as_ard(
       lst_tidy = lst_tidy,
       tidy_result_names = c("statistic", "p.value", "method"),
       fun_args_to_record = c("correct"),
-      formals = formals(asNamespace("stats")[["mcnemar.test"]]),
+      # formals = formals(asNamespace("stats")[["mcnemar.test"]]),
       passed_args = dots_list(...),
       lst_ard_columns = list(group1 = by, variable = variable, context = "mcnemartest")
     )

R/ard_moodtest.R

@@ -70,13 +70,14 @@ ard_moodtest <- function(data, by, variable, ...) {
 #'         broom::tidy()
 #'     )
 #' )
+#' @noRd
 .format_moodtest_results <- function(by, variable, lst_tidy, ...) {
   # build ARD ------------------------------------------------------------------
   ret <-
     cards::tidy_as_ard(
       lst_tidy = lst_tidy,
       tidy_result_names = c("statistic", "p.value", "method", "alternative"),
-      formals = formals(asNamespace("stats")[["mood.test.default"]]),
+      # formals = formals(asNamespace("stats")[["mood.test.default"]]),
       passed_args = c(dots_list(...)),
       lst_ard_columns = list(group1 = by, variable = variable, context = "moodtest")
     )

R/ard_ttest.R

@@ -126,6 +126,7 @@ ard_paired_ttest <- function(data, by, variable, id, ...) {
 #'         broom::tidy()
 #'     )
 #' )
+#' @noRd
 .format_ttest_results <- function(by, variable, lst_tidy, paired, ...) {
   # build ARD ------------------------------------------------------------------
   ret <-
@@ -137,7 +138,7 @@ ard_paired_ttest <- function(data, by, variable, id, ...) {
         "method", "alternative"
       ),
       fun_args_to_record = c("mu", "paired", "var.equal", "conf.level"),
-      formals = formals(asNamespace("stats")[["t.test.default"]]),
+      # formals = formals(asNamespace("stats")[["t.test.default"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
       lst_ard_columns = list(group1 = by, variable = variable, context = "ttest")
     )
@@ -170,6 +171,7 @@ ard_paired_ttest <- function(data, by, variable, id, ...) {
 #'   dplyr::mutate(.by = ARM, USUBJID = dplyr::row_number()) |>
 #'   dplyr::arrange(USUBJID, ARM) |>
 #'   cardx:::.paired_data_pivot_wider(by = "ARM", variable = "AGE", id = "USUBJID")
+#' @noRd
 .paired_data_pivot_wider <- function(data, by, variable, id, env = rlang::caller_env()) {
   # check the number of levels before pivoting data to wider format
   if (dplyr::n_distinct(data[[by]], na.rm = TRUE) != 2L) {

R/ard_wilcoxtest.R

@@ -134,6 +134,7 @@ ard_paired_wilcoxtest <- function(data, by, variable, id, ...) {
 #' )
 #'
 #' @keywords internal
+#' @noRd
 .format_wilcoxtest_results <- function(by, variable, lst_tidy, paired, ...) {
   # build ARD ------------------------------------------------------------------
   ret <-
@@ -144,7 +145,7 @@ ard_paired_wilcoxtest <- function(data, by, variable, id, ...) {
         "mu", "paired", "exact", "correct", "conf.int",
         "conf.level", "tol.root", "digits.rank"
       ),
-      formals = formals(asNamespace("stats")[["wilcox.test.default"]]),
+      # formals = formals(asNamespace("stats")[["wilcox.test.default"]]),
       passed_args = c(list(paired = paired), dots_list(...)),
       lst_ard_columns = list(group1 = by, variable = variable, context = "ttest")
     )
@@ -159,41 +160,6 @@ ard_paired_wilcoxtest <- function(data, by, variable, id, ...) {
     cards::tidy_ard_column_order()
 }
 
-
-#' Convert long paired data to wide
-#'
-#'
-#' @param data (`data.frame`)\cr a data frame that is one line per subject per group
-#' @param by (`string`)\cr by column name
-#' @param variable (`string`)\cr variable column name
-#' @param id (`string`)\cr subject id column name
-#' @param env (`environment`) used for error messaging. Default is `rlang::caller_env()`
-#'
-#' @return a wide data frame
-#' @keywords internal
-#' @examples
-#' cards::ADSL[c("ARM", "AGE")] |>
-#'   dplyr::filter(ARM %in% c("Placebo", "Xanomeline High Dose")) |>
-#'   dplyr::mutate(.by = ARM, USUBJID = dplyr::row_number()) |>
-#'   dplyr::arrange(USUBJID, ARM) |>
-#'   cardx:::.paired_data_pivot_wider(by = "ARM", variable = "AGE", id = "USUBJID")
-.paired_data_pivot_wider <- function(data, by, variable, id, env = rlang::caller_env()) {
-  # check the number of levels before pivoting data to wider format
-  if (dplyr::n_distinct(data[[by]], na.rm = TRUE) != 2L) {
-    cli::cli_abort("The {.arg by} argument must have two and only two levels.", call = env)
-  }
-
-  data |>
-    # arrange data so the first group always appears first
-    dplyr::arrange(.data[[by]]) |>
-    tidyr::pivot_wider(
-      id_cols = all_of(id),
-      names_from = all_of(by),
-      values_from = all_of(variable)
-    ) |>
-    stats::setNames(c(id, "by1", "by2"))
-}
-
 .df_wilcoxtest_stat_labels <- function() {
   dplyr::tribble(
     ~stat_name, ~stat_label,

R/proportion_ci.R

@@ -344,6 +344,7 @@ proportion_ci_strat_wilson <- function(x,
 #' weights <- rep(1 / length(ns), length(ns))
 #'
 #' cardx:::.strata_normal_quantile(vars, weights, 0.95)
+#' @noRd
 .strata_normal_quantile <- function(vars, weights, conf.level) {
   summands <- weights^2 * vars
   # Stratified quantile
@@ -377,6 +378,7 @@ proportion_ci_strat_wilson <- function(x,
 #' ns <- c(22, 18, 17, 17, 14, 12)
 #'
 #' cardx:::.update_weights_strat_wilson(vs, sq, ws, ns, 100, 0.95, 0.001)
+#' @noRd
 .update_weights_strat_wilson <- function(vars,
                                          strata_qnorm,
                                          initial_weights,

README.md

@@ -1,4 +1,4 @@
-# cardx <a href="https://insightsengineering.github.io/cardx"><img src="man/figures/logo.png" align="right" height="138" alt="cardx website" /></a>
+# cardx <a href="https://insightsengineering.github.io/cardx/"><img src="man/figures/logo.png" align="right" height="138" alt="cardx website" /></a>
 
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/insightsengineering/cardx/actions/workflows/R-CMD-check.yaml)
@@ -11,9 +11,16 @@ This is the source repository of the `cardx` R package.
 
 ## Installation
 
-The latest development version of `{cardx}` can directly be installed from GitHub by running the following:
+Install cards from CRAN with:
 
-```r
-if (!require("pak")) install.packages("pak")
-pak::pak("insightsengineering/cardx")
+``` r
+install.packages("cardx")
+```
+
+You can install the development version of cards from
+[GitHub](https://github.com/) with:
+
+``` r
+# install.packages("devtools")
+devtools::install_github("insightsengineering/cardx")
 ```

cran-comments.md

@@ -0,0 +1,17 @@
+## Test environments
+* Ubuntu 18.04 LTS (on github actions), devel, release, oldrel-1, oldrel-2, oldrel-3, oldrel-4
+* Windows Server 2019 (on github actions), release
+* macOS (on github actions), release
+* win-builder devel
+
+## R CMD check results
+
+0 errors | 0 warnings | 1 note
+
+  Maintainer: ‘Daniel D. Sjoberg <[email protected]>’
+
+  New submission
+
+## Additional Comments
+
+* Thank you for your time!