prepping for release

ddsjoberg · Sep 5, 2024 · 8dba09e · 8dba09e
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -0,0 +1,3 @@
+Version: 2.0.2
+Date: 2024-09-05 14:14:07 UTC
+SHA: f6e052973a1ae3b8b5c7957ccf8c3290636656d2
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result Tables
-Version: 2.0.1.9013
+Version: 2.0.2
 Authors@R: c(
     person("Daniel D.", "Sjoberg", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0003-0862-2018")),

diff --git a/NEWS.md b/NEWS.md
@@ -1,4 +1,4 @@
-# gtsummary (development version)
+# gtsummary 2.0.2
 
 Updates to address regressions in the v2.0.0 release:
 
@@ -10,6 +10,8 @@ Updates to address regressions in the v2.0.0 release:
 
 ### Other updates
 
+* The Themes and Inline Text vignettes have been converted to articles (that is, they are no longer bundled with the package, but are still available on the website).
+
 * The total N is now returned with `.$cards` using the `cards::ard_total_n()` function for the calculation.
 
 * The default headers for `tbl_ard_*()` functions no longer include counts, as these are not required data to be passed along in the ARD input.

diff --git a/tests/testthat/test-add_difference.tbl_summary.R b/tests/testthat/test-add_difference.tbl_summary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c(
   "broom", "broom.helpers", "lme4", "smd",
   "effectsize", "emmeans"

diff --git a/tests/testthat/test-add_difference.tbl_svysummary.R b/tests/testthat/test-add_difference.tbl_svysummary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("survey", "cardx"), reference_pkg = "gtsummary"))
 
 svy_titanic <- survey::svydesign(~1, data = as.data.frame(Titanic), weights = ~Freq)

diff --git a/tests/testthat/test-add_glance.R b/tests/testthat/test-add_glance.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom.helpers", "cardx"), reference_pkg = "gtsummary"))
 
 # add_glance_source_note() -----------------------------------------------------

diff --git a/tests/testthat/test-add_global_p.R b/tests/testthat/test-add_global_p.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 test_that("add_global_p() works", {
   expect_error(
     lm(age ~ trt, trial) |>

diff --git a/tests/testthat/test-add_n.tbl_regression.R b/tests/testthat/test-add_n.tbl_regression.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_n.tbl_regression() works", {
   tbl <-
     glm(response ~ grade + age, trial, family = binomial) %>%

diff --git a/tests/testthat/test-add_n.tbl_summary.R b/tests/testthat/test-add_n.tbl_summary.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_n.tbl_summary() works", {
   # with stratifying variable
   expect_error(

diff --git a/tests/testthat/test-add_n.tbl_survfit.R b/tests/testthat/test-add_n.tbl_survfit.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_n.tbl_survfit() works", {
   # add_n.tbl_survfit works
   fit1 <- survival::survfit(survival::Surv(ttdeath, death) ~ 1, trial)

diff --git a/tests/testthat/test-add_n.tbl_svysummary.R b/tests/testthat/test-add_n.tbl_svysummary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("survey", reference_pkg = "gtsummary"))
 
 svy_trial <- survey::svydesign(~1, data = trial, weights = ~1)

diff --git a/tests/testthat/test-add_n.tbl_uvregression.R b/tests/testthat/test-add_n.tbl_uvregression.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom.helpers", "broom"), reference_pkg = "gtsummary"))
 
 test_that("add_n.tbl_uvregression() works", {

diff --git a/tests/testthat/test-add_nevent.tbl_regression.R b/tests/testthat/test-add_nevent.tbl_regression.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 test_that("add_nevent.tbl_regression() works", {
   tbl <-
     glm(response ~ grade + age, trial, family = binomial) %>%

diff --git a/tests/testthat/test-add_nevent.tbl_survfit.R b/tests/testthat/test-add_nevent.tbl_survfit.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_nevent.tbl_survfit() works", {
   tbl <- trial |>
     tbl_survfit(

diff --git a/tests/testthat/test-add_nevent.tbl_uvregression.R b/tests/testthat/test-add_nevent.tbl_uvregression.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom.helpers", "broom"), reference_pkg = "gtsummary"))
 
 test_that("add_nevent.tbl_uvregression() works", {

diff --git a/tests/testthat/test-add_overall.tbl_continuous.R b/tests/testthat/test-add_overall.tbl_continuous.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 test_that("add_overall.tbl_continuous() works", {
   # typical usage works
   expect_error(

diff --git a/tests/testthat/test-add_overall.tbl_svysummary.R b/tests/testthat/test-add_overall.tbl_svysummary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("survey", reference_pkg = "gtsummary"))
 
 svy_mtcars <- survey::svydesign(~1, data = mtcars, weights = ~1)

diff --git a/tests/testthat/test-add_p.tbl_continuous.R b/tests/testthat/test-add_p.tbl_continuous.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
 
 test_that("add_p.tbl_continuous() works", {

diff --git a/tests/testthat/test-add_p.tbl_cross.R b/tests/testthat/test-add_p.tbl_cross.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
+
 test_that("add_p.tbl_cross() works", {
   expect_silent(
     out <- trial |>

diff --git a/tests/testthat/test-add_p.tbl_summary.R b/tests/testthat/test-add_p.tbl_summary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom", "lme4", "broom.helpers"), reference_pkg = "cardx"))
 
 test_that("add_p.tbl_summary() snapshots of common outputs", {

diff --git a/tests/testthat/test-add_p.tbl_survfit.R b/tests/testthat/test-add_p.tbl_survfit.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("cardx", "survival"), reference_pkg = "cardx"))
+
 test_that("add_p.tbl_survfit() works", {
   tbl <- trial |>
     tbl_survfit(

diff --git a/tests/testthat/test-add_q.R b/tests/testthat/test-add_q.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_q() works after add_p()", {
   table1 <- trial %>%
     tbl_summary(by = trt) %>%

diff --git a/tests/testthat/test-add_stat.R b/tests/testthat/test-add_stat.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
 
 my_ttest <- function(data, variable, by, ...) {

diff --git a/tests/testthat/test-add_stat_label.R b/tests/testthat/test-add_stat_label.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("add_stat_label(location='row') standard use", {
   tbl <- trial |> tbl_summary(by = trt)
 

diff --git a/tests/testthat/test-add_stat_label.tbl_svysummary.R b/tests/testthat/test-add_stat_label.tbl_svysummary.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("survey", reference_pkg = "gtsummary"))
 
 svy_trial <- survey::svydesign(~1, data = trial, weights = ~1)

diff --git a/tests/testthat/test-add_vif.R b/tests/testthat/test-add_vif.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("car", "broom.helpers", "cardx"), reference_pkg = "gtsummary"))
 
 test_that("add_vif(x)", {

diff --git a/tests/testthat/test-bold_italicize_labels_levels.R b/tests/testthat/test-bold_italicize_labels_levels.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 tbl <- tbl_summary(trial, include = age)
 
 test_that("bold_labels() works", {

diff --git a/tests/testthat/test-bold_p.R b/tests/testthat/test-bold_p.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
+
 test_that("bold_p() works", {
   expect_equal(
     trial |>

diff --git a/tests/testthat/test-custom_tidiers.R b/tests/testthat/test-custom_tidiers.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom.helpers", "cardx"), reference_pkg = "gtsummary"))
 
 test_that("tidy_standardize()", {

diff --git a/tests/testthat/test-gather_ard.R b/tests/testthat/test-gather_ard.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
 
 test_that("gather_ard(x) works with `tbl_*()` functions", {

diff --git a/tests/testthat/test-inline_text.R b/tests/testthat/test-inline_text.R
@@ -1,4 +1,5 @@
-skip_if_not(broom.helpers::.assert_package("survival", pkg_search = "gtsummary", boolean = TRUE))
+skip_on_cran()
+skip_if_not(is_pkg_installed("survival", reference_pkg = "gtsummary"))
 
 # inline_text.tbl_summary tests ------------------------------------------------
 test_inline1 <- trial |> tbl_summary()

diff --git a/tests/testthat/test-label_style.R b/tests/testthat/test-label_style.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("withr", reference_pkg = "gtsummary"))
 
 test_that("label_style_*()", {

diff --git a/tests/testthat/test-modify_caption.R b/tests/testthat/test-modify_caption.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("modify_caption(caption) works", {
   expect_equal(
     tbl_summary(trial, include = marker) |>

diff --git a/tests/testthat/test-modify_column_alignment.R b/tests/testthat/test-modify_column_alignment.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("modify_column_alignment() works", {
   tbl <-
     lm(age ~ marker + grade, trial) |>

diff --git a/tests/testthat/test-modify_column_hide.R b/tests/testthat/test-modify_column_hide.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("modify_column_hide() works", {
   expect_snapshot(
     lm(age ~ marker + grade, trial) |>

diff --git a/tests/testthat/test-modify_column_indent.R b/tests/testthat/test-modify_column_indent.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 # begin with deprecation messaging
 test_that("modify_column_indent() deprecations", {
   lifecycle::expect_deprecated(

diff --git a/tests/testthat/test-modify_column_merge.R b/tests/testthat/test-modify_column_merge.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("broom.helpers", "cardx"), reference_pkg = "gtsummary"))
+
 mod <- lm(marker ~ age + grade, trial) |> tbl_regression()
 
 test_that("modify_column_merge() works", {

diff --git a/tests/testthat/test-modify_fmt_fun.R b/tests/testthat/test-modify_fmt_fun.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("broom.helpers", "cardx"), reference_pkg = "gtsummary"))
+
 test_that("modify_fmt_fun() works", {
   expect_error(
     tbl <- lm(age ~ marker + grade, trial) |>

diff --git a/tests/testthat/test-modify_footnote.R b/tests/testthat/test-modify_footnote.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 
 # first, testing deprecation
 test_that("modify_footnote(update,quiet) are deprecated", {

diff --git a/tests/testthat/test-modify_header.R b/tests/testthat/test-modify_header.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 
 # first, testing deprecation
 test_that("modify_header(update,quiet) are deprecated", {

diff --git a/tests/testthat/test-modify_spanning_header.R b/tests/testthat/test-modify_spanning_header.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 
 # first, testing deprecation
 test_that("modify_spanning_header(update,quiet) are deprecated", {

diff --git a/tests/testthat/test-modify_table_body.R b/tests/testthat/test-modify_table_body.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("modify_table_body() works", {
   expect_snapshot(
     glm(response ~ trt + marker, trial, family = binomial) |>

diff --git a/tests/testthat/test-modify_table_styling.R b/tests/testthat/test-modify_table_styling.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 # starting with checks of the deprecation
 test_that("modify_table_styling(undo_text_format=logical()) deprecation", {
   withr::local_options(lifecycle_verbosity = "quiet")

diff --git a/tests/testthat/test-plot.tbl_regression.R b/tests/testthat/test-plot.tbl_regression.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("ggstats", "broom.helpers"), reference_pkg = "gtsummary"))
 
 test_that("plot.tbl_regression() works", {

diff --git a/tests/testthat/test-plot.tbl_uvregression.R b/tests/testthat/test-plot.tbl_uvregression.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("ggstats", "broom.helpers"), reference_pkg = "gtsummary"))
 
 test_that("plot.tbl_uvregression() works", {

diff --git a/tests/testthat/test-remove_row_type.R b/tests/testthat/test-remove_row_type.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("cardx", "broom.helpers"), reference_pkg = "gtsummary"))
+
 test_that("remove_row_type(type) works", {
   tbl1 <- tbl_summary(trial, include = c(response, age, grade))
   tbl2 <- lm(age ~ grade + response, trial) |> tbl_regression()

diff --git a/tests/testthat/test-scoping_gtsummary.R b/tests/testthat/test-scoping_gtsummary.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("scope_header()", {
   tbl <- trial |>
     tbl_summary(by = trt, include = age, missing = "no")

diff --git a/tests/testthat/test-select_helpers.R b/tests/testthat/test-select_helpers.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("select_helpers work", {
   tbl_sum <- trial |> tbl_summary(type = age ~ "continuous2")
   tbl_reg <-

diff --git a/tests/testthat/test-separate_p_footnotes.R b/tests/testthat/test-separate_p_footnotes.R
@@ -1,5 +1,5 @@
-skip_if_not(is_pkg_installed("cardx", reference_pkg = "gtsummary"))
-skip_if_not(is_pkg_installed("broom", reference_pkg = "cardx"))
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("cardx", "broom"), reference_pkg = "gtsummary"))
 
 test_that("separate_p_footnotes()", {
   tbl <- trial |>

diff --git a/tests/testthat/test-show_header_names.R b/tests/testthat/test-show_header_names.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("cardx", "broom.helpers"), reference_pkg = "gtsummary"))
+
 test_that("show_header_names() works with tbl_summary()", {
   expect_snapshot(
     tbl_summary(trial, include = age, by = trt, missing = "no") |>

diff --git a/tests/testthat/test-sort_filter_p.R b/tests/testthat/test-sort_filter_p.R
@@ -1,3 +1,6 @@
+skip_on_cran()
+skip_if_not(is_pkg_installed(c("cardx", "broom"), reference_pkg = "gtsummary"))
+
 test_that("sort_p() works", {
   # check the variables sort to the correct order
   expect_equal(

diff --git a/tests/testthat/test-tbl_likert.R b/tests/testthat/test-tbl_likert.R
@@ -1,3 +1,4 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed("withr", reference_pkg = "gtsummary"))
 
 levels <- c("Strongly Disagree", "Disagree", "Agree", "Strongly Agree")

diff --git a/tests/testthat/test-tbl_regression_methods.R b/tests/testthat/test-tbl_regression_methods.R
@@ -1,6 +1,6 @@
+skip_on_cran()
 skip_if_not(is_pkg_installed(c("broom.helpers", "withr"), reference_pkg = "gtsummary"))
 
-
 test_that("tbl_regression.model_fit()", {
   skip_if_not(is_pkg_installed("parsnip", reference_pkg = "gtsummary"))
 
@@ -79,7 +79,6 @@ test_that("tbl_regression.gam()", {
   )
 })
 
-
 test_that("tbl_regression.crr()", {
   skip_if_not(is_pkg_installed("cmprsk", reference_pkg = "gtsummary"))
   withr::local_package("cmprsk")

diff --git a/tests/testthat/test-tbl_split.R b/tests/testthat/test-tbl_split.R
@@ -1,3 +1,5 @@
+skip_on_cran()
+
 test_that("tbl_split()", {
   expect_silent(
     tbl <- tbl_summary(trial) |>

diff --git a/vignettes/inline_text.Rmd → vignettes/articles/inline_text.Rmd b/vignettes/inline_text.Rmd → vignettes/articles/inline_text.Rmd
@@ -1,12 +1,5 @@
 ---
 title: "inline_text() tutorial"
-date: "Last Updated: September 13, 2020"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteEncoding{UTF-8}
-  %\VignetteIndexEntry{Tutorial: inline_text}
-  %\VignetteEngine{knitr::rmarkdown}
-  chunk_output_type: console
 ---
 
 ```{r, include = FALSE}

diff --git a/vignettes/themes.Rmd → vignettes/articles/themes.Rmd b/vignettes/themes.Rmd → vignettes/articles/themes.Rmd
@@ -1,18 +1,10 @@
 ---
 title: "gtsummary themes"
-output: rmarkdown::html_vignette
-vignette: >
-  %\VignetteIndexEntry{gtsummary themes}
-  %\VignetteEncoding{UTF-8}
-  %\VignetteEngine{knitr::rmarkdown}
-editor_options: 
-  chunk_output_type: console
 ---
 
 ```{r, include = FALSE}
 knitr::opts_chunk$set(
   collapse = TRUE,
-  warning = FALSE,
   comment = "#>"
 )
 ```