diff --git a/.Rbuildignore b/.Rbuildignore index dc2055c0..7639a794 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -28,3 +28,7 @@ images ^_freeze$ ^_site$ ^.*\.qmd$ +^CRAN-SUBMISSION$ +^cran-comments.md$ + +.claude diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 00000000..5f258175 --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 0.2.0 +Date: 2026-07-13 10:47:11 UTC +SHA: ba7b2df9018fe30ec6d3098fdd23ed9e5f4ac858 diff --git a/DESCRIPTION b/DESCRIPTION index 90ee20d9..de8dd2d4 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Type: Package -Package: cardinal +Package: cardinalfda Title: FDA Safety Tables and Figures -Version: 0.1.0.9088 +Version: 0.2.0 Date: 2026-07-09 Authors@R: c( person("Pawel", "Rucki", , "pawel.rucki@roche.com", role = "ctb"), @@ -32,10 +32,11 @@ URL: https://github.com/pharmaverse/cardinal/, https://pharmaverse.github.io/cardinal/ BugReports: https://github.com/pharmaverse/cardinal/issues Depends: - R (>= 4.2) -Suggests: + R (>= 4.2), cards (>= 0.8.1), cardx (>= 0.3.4), + gtsummary (>= 2.5.1) +Suggests: cowplot (>= 1.2.0), crane (>= 0.3.1), dplyr (>= 1.2), @@ -43,7 +44,6 @@ Suggests: ggplot2 (>= 4.0), ggsurvfit (>= 1.2.0), gt (>= 1.3.0), - gtsummary (>= 2.5.1), knitr (>= 1.50), labelled (>= 2.16.0), lubridate (>= 1.9), diff --git a/NAMESPACE b/NAMESPACE index 6ae92683..b3bd0162 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -1,2 +1,5 @@ # Generated by roxygen2: do not edit by hand +importFrom(cards,ard_continuous) +importFrom(cardx,ard_continuous_ci) +importFrom(gtsummary,tbl_summary) diff --git a/NEWS.md b/NEWS.md index 00ca1fca..7239b1ab 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,3 @@ -# cardinal 0.1.0.9088 +# cardinal 0.2.0 * Initial release. diff --git a/R/cardinal.R b/R/cardinal.R index c7ca18f6..b7307c51 100644 --- a/R/cardinal.R +++ b/R/cardinal.R @@ -1,6 +1,9 @@ -#' cardinal +#' cardinalfda #' #' Implementation of FDA Safety Tables and Figures #' #' @keywords internal +#' @importFrom cards ard_continuous +#' @importFrom cardx ard_continuous_ci +#' @importFrom gtsummary tbl_summary "_PACKAGE" diff --git a/cran-comments.md b/cran-comments.md new file mode 100644 index 00000000..e69de29b diff --git a/man/cardinal-package.Rd b/man/cardinalfda-package.Rd similarity index 94% rename from man/cardinal-package.Rd rename to man/cardinalfda-package.Rd index ad94a4fa..a897062b 100644 --- a/man/cardinal-package.Rd +++ b/man/cardinalfda-package.Rd @@ -1,10 +1,10 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/cardinal.R \docType{package} -\name{cardinal-package} -\alias{cardinal} -\alias{cardinal-package} -\title{cardinal} +\name{cardinalfda-package} +\alias{cardinalfda} +\alias{cardinalfda-package} +\title{cardinalfda} \description{ Implementation of FDA Safety Tables and Figures } diff --git a/tests/testthat.R b/tests/testthat.R index e44db11f..846896f9 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,7 +1,7 @@ if (requireNamespace("testthat", quietly = TRUE)) { library(testthat) options(warn = 2) # Warnings become errors - pkg_name <- "cardinal" + pkg_name <- "cardinalfda" library(pkg_name, character.only = TRUE) testthat::test_check(pkg_name) } diff --git a/tests/testthat/_snaps/fda-table_02.md b/tests/testthat/_snaps/fda-table_02.md index 835bc550..65a804fb 100644 --- a/tests/testthat/_snaps/fda-table_02.md +++ b/tests/testthat/_snaps/fda-table_02.md @@ -4,57 +4,57 @@ as.data.frame(ard$tbl_summary)[1:25, ] Output group1 group1_level variable variable_level context - 1 TRT01A Placebo AGEGR1 18-64 tabulate - 2 TRT01A Placebo AGEGR1 18-64 tabulate - 3 TRT01A Placebo AGEGR1 18-64 tabulate - 4 TRT01A Placebo AGEGR1 >64 tabulate - 5 TRT01A Placebo AGEGR1 >64 tabulate - 6 TRT01A Placebo AGEGR1 >64 tabulate - 7 TRT01A Placebo SEX F tabulate - 8 TRT01A Placebo SEX F tabulate - 9 TRT01A Placebo SEX F tabulate - 10 TRT01A Placebo SEX M tabulate - 11 TRT01A Placebo SEX M tabulate - 12 TRT01A Placebo SEX M tabulate - 13 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate - 14 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate - 15 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate - 16 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate - 17 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate - 18 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate - 19 TRT01A Placebo RACE WHITE tabulate - 20 TRT01A Placebo RACE WHITE tabulate - 21 TRT01A Placebo RACE WHITE tabulate - 22 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate - 23 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate - 24 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate - 25 TRT01A Placebo ETHNIC NOT HISPANIC OR LATINO tabulate + 1 TRT01A Placebo SEX F tabulate + 2 TRT01A Placebo SEX F tabulate + 3 TRT01A Placebo SEX F tabulate + 4 TRT01A Placebo SEX M tabulate + 5 TRT01A Placebo SEX M tabulate + 6 TRT01A Placebo SEX M tabulate + 7 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate + 8 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate + 9 TRT01A Placebo RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate + 10 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate + 11 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate + 12 TRT01A Placebo RACE BLACK OR AFRICAN AMERICAN tabulate + 13 TRT01A Placebo RACE WHITE tabulate + 14 TRT01A Placebo RACE WHITE tabulate + 15 TRT01A Placebo RACE WHITE tabulate + 16 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate + 17 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate + 18 TRT01A Placebo ETHNIC HISPANIC OR LATINO tabulate + 19 TRT01A Placebo ETHNIC NOT HISPANIC OR LATINO tabulate + 20 TRT01A Placebo ETHNIC NOT HISPANIC OR LATINO tabulate + 21 TRT01A Placebo ETHNIC NOT HISPANIC OR LATINO tabulate + 22 TRT01A Placebo AGEGR1 18-64 tabulate + 23 TRT01A Placebo AGEGR1 18-64 tabulate + 24 TRT01A Placebo AGEGR1 18-64 tabulate + 25 TRT01A Placebo AGEGR1 >64 tabulate stat_name stat_label stat - 1 n n 14 + 1 n n 53 2 N N 86 - 3 p % 0.1627907 - 4 n n 72 + 3 p % 0.6162791 + 4 n n 33 5 N N 86 - 6 p % 0.8372093 - 7 n n 53 + 6 p % 0.3837209 + 7 n n 0 8 N N 86 - 9 p % 0.6162791 - 10 n n 33 + 9 p % 0 + 10 n n 8 11 N N 86 - 12 p % 0.3837209 - 13 n n 0 + 12 p % 0.09302326 + 13 n n 78 14 N N 86 - 15 p % 0 - 16 n n 8 + 15 p % 0.9069767 + 16 n n 3 17 N N 86 - 18 p % 0.09302326 - 19 n n 78 + 18 p % 0.03488372 + 19 n n 83 20 N N 86 - 21 p % 0.9069767 - 22 n n 3 + 21 p % 0.9651163 + 22 n n 14 23 N N 86 - 24 p % 0.03488372 - 25 n n 83 + 24 p % 0.1627907 + 25 n n 72 fmt_fun 1 function (x) , style_number(x, digits = digits, big.mark = big.mark, decimal.mark = decimal.mark, , scale = scale, prefix = prefix, suffix = suffix, na = na, , ...) 2 function (x) , style_number(x, digits = digits, big.mark = big.mark, decimal.mark = decimal.mark, , scale = scale, prefix = prefix, suffix = suffix, na = na, , ...) @@ -114,57 +114,57 @@ as.data.frame(ard$add_overall)[1:25, ] Output variable variable_level context stat_name stat_label - 1 AGEGR1 18-64 tabulate n n - 2 AGEGR1 18-64 tabulate N N - 3 AGEGR1 18-64 tabulate p % - 4 AGEGR1 >64 tabulate n n - 5 AGEGR1 >64 tabulate N N - 6 AGEGR1 >64 tabulate p % - 7 SEX F tabulate n n - 8 SEX F tabulate N N - 9 SEX F tabulate p % - 10 SEX M tabulate n n - 11 SEX M tabulate N N - 12 SEX M tabulate p % - 13 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate n n - 14 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate N N - 15 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate p % - 16 RACE BLACK OR AFRICAN AMERICAN tabulate n n - 17 RACE BLACK OR AFRICAN AMERICAN tabulate N N - 18 RACE BLACK OR AFRICAN AMERICAN tabulate p % - 19 RACE WHITE tabulate n n - 20 RACE WHITE tabulate N N - 21 RACE WHITE tabulate p % - 22 ETHNIC HISPANIC OR LATINO tabulate n n - 23 ETHNIC HISPANIC OR LATINO tabulate N N - 24 ETHNIC HISPANIC OR LATINO tabulate p % - 25 ETHNIC NOT HISPANIC OR LATINO tabulate n n + 1 SEX F tabulate n n + 2 SEX F tabulate N N + 3 SEX F tabulate p % + 4 SEX M tabulate n n + 5 SEX M tabulate N N + 6 SEX M tabulate p % + 7 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate n n + 8 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate N N + 9 RACE AMERICAN INDIAN OR ALASKA NATIVE tabulate p % + 10 RACE BLACK OR AFRICAN AMERICAN tabulate n n + 11 RACE BLACK OR AFRICAN AMERICAN tabulate N N + 12 RACE BLACK OR AFRICAN AMERICAN tabulate p % + 13 RACE WHITE tabulate n n + 14 RACE WHITE tabulate N N + 15 RACE WHITE tabulate p % + 16 ETHNIC HISPANIC OR LATINO tabulate n n + 17 ETHNIC HISPANIC OR LATINO tabulate N N + 18 ETHNIC HISPANIC OR LATINO tabulate p % + 19 ETHNIC NOT HISPANIC OR LATINO tabulate n n + 20 ETHNIC NOT HISPANIC OR LATINO tabulate N N + 21 ETHNIC NOT HISPANIC OR LATINO tabulate p % + 22 AGEGR1 18-64 tabulate n n + 23 AGEGR1 18-64 tabulate N N + 24 AGEGR1 18-64 tabulate p % + 25 AGEGR1 >64 tabulate n n stat - 1 33 + 1 143 2 254 - 3 0.1299213 - 4 221 + 3 0.5629921 + 4 111 5 254 - 6 0.8700787 - 7 143 + 6 0.4370079 + 7 1 8 254 - 9 0.5629921 - 10 111 + 9 0.003937008 + 10 23 11 254 - 12 0.4370079 - 13 1 + 12 0.09055118 + 13 230 14 254 - 15 0.003937008 - 16 23 + 15 0.9055118 + 16 12 17 254 - 18 0.09055118 - 19 230 + 18 0.04724409 + 19 242 20 254 - 21 0.9055118 - 22 12 + 21 0.9527559 + 22 33 23 254 - 24 0.04724409 - 25 242 + 24 0.1299213 + 25 221 fmt_fun 1 function (x) , style_number(x, digits = digits, big.mark = big.mark, decimal.mark = decimal.mark, , scale = scale, prefix = prefix, suffix = suffix, na = na, , ...) 2 function (x) , style_number(x, digits = digits, big.mark = big.mark, decimal.mark = decimal.mark, , scale = scale, prefix = prefix, suffix = suffix, na = na, , ...)