final updates before CRAN

* test updates

* skipping some tests on CRAN

* skpiping tests on CRAN

* vignette updates

* Increment version number

* doc updates

* clearing cache

* Update cran-comments.md

.github/workflows/R-CMD-check.yaml

@@ -67,8 +67,8 @@ jobs:
         uses: actions/cache@v1
         with:
           path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-r-${{ matrix.config.r }}-1-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-1-
+          key: ${{ runner.os }}-r-${{ matrix.config.r }}-2-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-r-${{ matrix.config.r }}-2-
 
       - name: Install system dependencies
         if: runner.os == 'Linux'

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: gtsummary
 Title: Presentation-Ready Data Summary and Analytic Result
     Tables
-Version: 1.3.0.9019
+Version: 1.3.1
 Authors@R: 
     c(person(given = "Daniel D.",
              family = "Sjoberg",

NEWS.md

@@ -1,4 +1,4 @@
-# gtsummary (development version)
+# gtsummary 1.3.1
 
 ### New Functions
 

codemeta.json

@@ -10,14 +10,14 @@
   "codeRepository": "https://github.com/ddsjoberg/gtsummary",
   "issueTracker": "https://github.com/ddsjoberg/gtsummary/issues",
   "license": "https://spdx.org/licenses/MIT",
-  "version": "1.3.0.9014",
+  "version": "1.3.1",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
-    "version": "3.6.1",
+    "version": "4.0.0",
     "url": "https://r-project.org"
   },
-  "runtimePlatform": "R version 3.6.1 (2019-07-05)",
+  "runtimePlatform": "R version 4.0.0 (2020-04-24)",
   "provider": {
     "@id": "https://cran.r-project.org",
     "@type": "Organization",
@@ -256,7 +256,7 @@
       "@type": "SoftwareApplication",
       "identifier": "broom",
       "name": "broom",
-      "version": ">= 0.5.5",
+      "version": ">= 0.5.6",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -269,7 +269,7 @@
       "@type": "SoftwareApplication",
       "identifier": "broom.mixed",
       "name": "broom.mixed",
-      "version": ">= 0.2.4",
+      "version": ">= 0.2.6",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -334,7 +334,7 @@
       "@type": "SoftwareApplication",
       "identifier": "gt",
       "name": "gt",
-      "version": ">= 0.2.0.5",
+      "version": ">= 0.2.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -399,7 +399,7 @@
       "@type": "SoftwareApplication",
       "identifier": "purrr",
       "name": "purrr",
-      "version": ">= 0.3.3",
+      "version": ">= 0.3.4",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -412,7 +412,7 @@
       "@type": "SoftwareApplication",
       "identifier": "rlang",
       "name": "rlang",
-      "version": ">= 0.4.5",
+      "version": ">= 0.4.6",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -450,7 +450,7 @@
       "@type": "SoftwareApplication",
       "identifier": "tibble",
       "name": "tibble",
-      "version": ">= 3.0.0",
+      "version": ">= 3.0.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -463,7 +463,7 @@
       "@type": "SoftwareApplication",
       "identifier": "tidyr",
       "name": "tidyr",
-      "version": ">= 1.0.2",
+      "version": ">= 1.0.3",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -476,7 +476,7 @@
       "@type": "SoftwareApplication",
       "identifier": "tidyselect",
       "name": "tidyselect",
-      "version": ">= 1.0.0",
+      "version": ">= 1.1.0",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -489,7 +489,7 @@
       "@type": "SoftwareApplication",
       "identifier": "usethis",
       "name": "usethis",
-      "version": ">= 1.5.1",
+      "version": ">= 1.6.1",
       "provider": {
         "@id": "https://cran.r-project.org",
         "@type": "Organization",
@@ -499,9 +499,9 @@
       "sameAs": "https://CRAN.R-project.org/package=usethis"
     }
   ],
-  "releaseNotes": "https://github.com/ddsjoberg/gtsummary/blob/master/NEWS.md",
-  "readme": "https://github.com/ddsjoberg/gtsummary/blob/master/README.md",
-  "fileSize": "2944.833KB",
+  "releaseNotes": "https://github.com/oranwutang/gtsummary/blob/master/NEWS.md",
+  "readme": "https://github.com/oranwutang/gtsummary/blob/master/README.md",
+  "fileSize": "3100.021KB",
   "contIntegration": [
     "https://travis-ci.org/ddsjoberg/gtsummary",
     "https://ci.appveyor.com/project/ddsjoberg/gtsummary",

cran-comments.md

@@ -1,5 +1,5 @@
 ## Test environments
-* Windows 10 (local), R 3.6.3
+* Windows 10 (local), 3.6, 4.0
 * Ubuntu 16.04.6 LTS (on github actions), 3.4, 3.5, 3.6, 4.0
 * Windows Server 2019 (on github actions), 4.0
 * macOS (on github actions), 4.0, devel

tests/testthat/test-add_global_p.R

@@ -1,4 +1,5 @@
 context("test-add_global_p")
+testthat::skip_on_cran()
 
 test_that("no errors/warnings with standard use after tbl_regression", {
   mod1 <- lm(hp ~ factor(cyl) + mpg + factor(am), mtcars) %>% tbl_regression()

tests/testthat/test-add_n.R

@@ -1,4 +1,5 @@
 context("test-add_n")
+testthat::skip_on_cran()
 
 t1 <- trial %>% tbl_summary()
 t2 <- trial %>% tbl_summary(by = trt)

tests/testthat/test-add_nevent.R

@@ -1,4 +1,5 @@
 context("test-add_nevent")
+testthat::skip_on_cran()
 
 library(survival)
 fit_cox <- coxph(Surv(time, status) ~ sex, lung)

tests/testthat/test-add_overall.R

@@ -1,4 +1,5 @@
 context("test-add_overall")
+testthat::skip_on_cran()
 library(survival)
 
 test_that("no errors/warnings with standard use", {
@@ -22,5 +23,4 @@ test_that("no errors/warnings with missing data", {
 
 test_that("no errors/warnings with missing data in by variable", {
   expect_error(trial %>% tbl_summary(by = response) %>% add_overall(), NA)
-
 })

tests/testthat/test-add_p.R

@@ -1,4 +1,5 @@
 context("test-add_p.tbl_summary")
+testthat::skip_on_cran()
 
 test_that("add_p creates output without error/warning", {
   expect_error(

tests/testthat/test-as_gt.R

@@ -1,31 +1,31 @@
 context("test-as_gt")
+testthat::skip_on_cran()
 
-if (requireNamespace("gt", quietly = TRUE)) {
-  test_that("tbl_summary", {
-    expect_error(tbl_summary(trial) %>% as_gt(), NA)
-    expect_warning(tbl_summary(trial) %>% as_gt(), NA)
-  })
+test_that("tbl_summary", {
+  expect_error(tbl_summary(trial) %>% as_gt(), NA)
+  expect_warning(tbl_summary(trial) %>% as_gt(), NA)
+})
 
-  test_that("tbl_summary", {
-    expect_error(tbl_summary(trial) %>% as_gt(return_calls = TRUE), NA)
-    expect_warning(tbl_summary(trial) %>% as_gt(return_calls = TRUE), NA)
-  })
+test_that("tbl_summary", {
+  expect_error(tbl_summary(trial) %>% as_gt(return_calls = TRUE), NA)
+  expect_warning(tbl_summary(trial) %>% as_gt(return_calls = TRUE), NA)
+})
 
-  test_that("tbl_regression", {
-    expect_error(lm(marker ~ age, trial) %>% tbl_regression() %>% as_gt(), NA)
-    expect_warning(lm(marker ~ age, trial) %>% tbl_regression() %>% as_gt(), NA)
-  })
+test_that("tbl_regression", {
+  expect_error(lm(marker ~ age, trial) %>% tbl_regression() %>% as_gt(), NA)
+  expect_warning(lm(marker ~ age, trial) %>% tbl_regression() %>% as_gt(), NA)
+})
 
-  test_that("tbl_uvregression", {
-    expect_error(trial %>% tbl_uvregression(method = lm, y = age) %>% as_gt(), NA)
-    expect_warning(trial %>% tbl_uvregression(method = lm, y = age) %>% as_gt(), NA)
-  })
+test_that("tbl_uvregression", {
+  expect_error(trial %>% tbl_uvregression(method = lm, y = age) %>% as_gt(), NA)
+  expect_warning(trial %>% tbl_uvregression(method = lm, y = age) %>% as_gt(), NA)
+})
 
-  test_that("tbl_survfit", {
-    library(survival)
-    fit1 <- survfit(Surv(ttdeath, death) ~ trt, trial)
+test_that("tbl_survfit", {
+  library(survival)
+  fit1 <- survfit(Surv(ttdeath, death) ~ trt, trial)
+
+  expect_error(tbl_survfit(fit1, times = c(12, 24), label = "{time} Months") %>% as_gt(), NA)
+  expect_warning(tbl_survfit(fit1, times = c(12, 24), label = "{time} Months") %>% as_gt(), NA)
+})
 
-    expect_error(tbl_survfit(fit1, times = c(12, 24), label = "{time} Months") %>% as_gt(), NA)
-    expect_warning(tbl_survfit(fit1, times = c(12, 24), label = "{time} Months") %>% as_gt(), NA)
-  })
-}

tests/testthat/test-combine_terms.R

@@ -1,4 +1,6 @@
 context("test-combine_terms")
+testthat::skip_on_cran()
+
 library(Hmisc)
 mod1 <- lm(age ~ marker + I(marker^2) + stage,
            trial[c("age", "marker", "stage")] %>% na.omit())

tests/testthat/test-inline_text.R

@@ -1,4 +1,5 @@
 context("test-inline_text")
+testthat::skip_on_cran()
 
 
 # inline_text.tbl_summary tests --------------
@@ -82,11 +83,14 @@ test_that("inline_text.tbl_summary: with by -  expect errors", {
 })
 
 test_that("inline_text.tbl_summary: no errors with empty string selection", {
-  trial %>%
-    select(grade) %>%
-    mutate(grade = ifelse(grade == "I", "", as.character(grade))) %>%
-    tbl_summary() %>%
-    inline_text(variable = grade, level = "III")
+  expect_error(
+    trial %>%
+      select(grade) %>%
+      mutate(grade = ifelse(grade == "I", "", as.character(grade))) %>%
+      tbl_summary() %>%
+      inline_text(variable = grade, level = "III"),
+    NA
+  )
 })
 
 

tests/testthat/test-tbl_cross.R

@@ -1,4 +1,5 @@
 context("test-tbl_cross")
+testthat::skip_on_cran()
 
 test_that("tbl_cross- throws error if both `col` and `row`` are not specified", {
   expect_error(

tests/testthat/test-tbl_merge.R

@@ -1,4 +1,5 @@
 context("test-tbl_merge")
+testthat::skip_on_cran()
 
 library(survival)
 library(purrr)

tests/testthat/test-tbl_regression.R

@@ -1,4 +1,5 @@
 context("test-tbl_regression")
+testthat::skip_on_cran()
 library(survival)
 library(lme4)
 

tests/testthat/test-tbl_stack.R

@@ -1,4 +1,5 @@
 context("test-tbl_stack")
+testthat::skip_on_cran()
 library(survival)
 t1 <-
   glm(response ~ trt, trial, family = binomial) %>%

tests/testthat/test-tbl_summary.R

@@ -1,4 +1,5 @@
 context("test-tbl_summary")
+testthat::skip_on_cran()
 
 test_that("tbl_summary creates output without error/warning (no by var)", {
   expect_error(

tests/testthat/test-tbl_survfit.R

@@ -1,4 +1,5 @@
 context("test-tbl_survfit")
+testthat::skip_on_cran()
 library(survival)
 
 test_that("no errors/warnings with stratified variable", {

tests/testthat/test-tbl_survival.R

@@ -1,4 +1,5 @@
 context("test-tbl_survival")
+testthat::skip_on_cran()
 library(survival)
 
 test_that("no errors/warnings with stratified variable", {

tests/testthat/test-tbl_uvregression.R

@@ -1,4 +1,5 @@
 context("test-tbl_uvregression")
+testthat::skip_on_cran()
 library(survival)
 library(lme4)
 

tests/testthat/test-vetted_models-clogit.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models")
+testthat::skip_on_cran()
 library(dplyr)
 library(survival)
 

tests/testthat/test-vetted_models-coxph.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models-coxph")
+testthat::skip_on_cran()
 library(dplyr)
 library(survival)
 

tests/testthat/test-vetted_models-geeglm.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models")
+testthat::skip_on_cran()
 library(dplyr)
 
 # geeglm() --------------------------------------------------------------------

tests/testthat/test-vetted_models-glm.R

@@ -22,6 +22,7 @@
 
 
 context("test-vetted_models-glm")
+testthat::skip_on_cran()
 library(dplyr)
 
 # glm() ------------------------------------------------------------------------

tests/testthat/test-vetted_models-glmer.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models-glmer")
+testthat::skip_on_cran()
 library(dplyr)
 
 # glmer() --------------------------------------------------------------------

tests/testthat/test-vetted_models-lm.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models-lm")
+testthat::skip_on_cran()
 library(dplyr)
 
 # lm() ------------------------------------------------------------------------

tests/testthat/test-vetted_models-lmer.R

@@ -21,6 +21,7 @@
 #       - works with add_global_p(), add_nevent(), add_q()
 
 context("test-vetted_models-lmer")
+testthat::skip_on_cran()
 library(dplyr)
 
 # lmer() -----------------------------------------------------------------------

tests/testthat/test-vetted_models-survreg.R

@@ -30,6 +30,7 @@
 # survival::clogit()    DONE
 
 context("test-vetted_models-survreg")
+testthat::skip_on_cran()
 library(dplyr)
 library(survival)
 

vignettes/gallery.Rmd

@@ -192,7 +192,8 @@ gt_eventn <-
     statistic = all_categorical() ~ "{n}",
     label = list(stage ~ "T Stage", grade ~ "Grade")
   ) %>%
-  modify_header(stat_0 ~ "**Event N**")
+  modify_header(stat_0 ~ "**Event N**") %>%
+  modify_footnote(everything() ~ NA_character_)
 
 tbl_merge(list(gt_eventn, gt_model)) %>%
   bold_labels() %>%