From 93a8890a9a1b3fc133862af161b1798f4a9ff830 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 14 May 2026 11:07:07 +0200 Subject: [PATCH 1/7] Add a new table to test further changes on cards --- DESCRIPTION | 2 +- tests/testthat/test-custom.R | 45 ++++++++++++++++++++++++++++++++++++ 2 files changed, 46 insertions(+), 1 deletion(-) create mode 100644 tests/testthat/test-custom.R diff --git a/DESCRIPTION b/DESCRIPTION index 05367c3d..9ad6a577 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -8,7 +8,7 @@ Authors@R: Description: R package with implementation of Safety Tables and Figures issued by FDA. License: Apache License (>= 2) -URL: https://github.com/pharmaverse/cardinal/ +URL: https://github.com/pharmaverse/cardinal/, https://pharmaverse.github.io/cardinal/ BugReports: https://github.com/pharmaverse/cardinal/issues Depends: R (>= 4.2) diff --git a/tests/testthat/test-custom.R b/tests/testthat/test-custom.R new file mode 100644 index 00000000..e8109aa3 --- /dev/null +++ b/tests/testthat/test-custom.R @@ -0,0 +1,45 @@ +test_that("custom table works", { + + skip_if_not_installed("dplyr") + skip_if_not_installed("cards") + skip_if_not_installed("gtsummary") + skip_if_not_installed("pharmaverseadam") + skip_if_not_installed("forcats") + skip_if_not_installed("crane") + + library("dplyr") + library("gtsummary") + library("forcats") + library("crane") + + adam_db <- list( + adsl = pharmaverseadam::adsl, + adae = pharmaverseadam::adae + ) + # data pre-processing ---------------------------------------------------------- + df_aet02 <- + adam_db$adae |> + mutate( + # convert hierarchy variables to factor and set an explicit NA level + across( + c(AEBODSYS, AEDECOD), + ~ .x |> fct_na_value_to_level(level = "No Coding Available") + ) + ) + + # build AET02 ------------------------------------------------------------------ + expect_silent( + df_aet02 |> + tbl_hierarchical_rate_and_count( + by = "TRT01A", + variables = c(AEBODSYS, AEDECOD), + denominator = adam_db$adsl, + label = list( + AEBODSYS ~ "MedDRA System Organ Class", + AEDECOD ~ "MedDRA Preferred Term" + ), + # sort by descending rate at the SOC and AE levels + sort = "descending" + ) + ) +}) From eac45e9226def58e4a5538b049b228de78145a3d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 14 May 2026 11:07:42 +0200 Subject: [PATCH 2/7] Small update to latest roxygen2 --- DESCRIPTION | 2 +- man/cardinal-package.Rd | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 9ad6a577..4761d712 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -39,4 +39,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.3 +RoxygenNote: 8.0.0 diff --git a/man/cardinal-package.Rd b/man/cardinal-package.Rd index 99d0ef19..4c5a74ec 100644 --- a/man/cardinal-package.Rd +++ b/man/cardinal-package.Rd @@ -12,6 +12,7 @@ Implementation of FDA Safety Tables and Figures Useful links: \itemize{ \item \url{https://github.com/pharmaverse/cardinal/} + \item \url{https://pharmaverse.github.io/cardinal/} \item Report bugs at \url{https://github.com/pharmaverse/cardinal/issues} } @@ -19,5 +20,10 @@ Useful links: \author{ \strong{Maintainer}: Pawel Rucki \email{pawel.rucki@roche.com} +Authors: +\itemize{ + \item Pawel Rucki \email{pawel.rucki@roche.com} +} + } \keyword{internal} From 3d42f375badd816d9f9f961e256b0c4e1bb40062 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 14 May 2026 11:22:51 +0200 Subject: [PATCH 3/7] Fix lintr issue --- tests/testthat/test-custom.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat/test-custom.R b/tests/testthat/test-custom.R index e8109aa3..afd17b08 100644 --- a/tests/testthat/test-custom.R +++ b/tests/testthat/test-custom.R @@ -15,7 +15,7 @@ test_that("custom table works", { adam_db <- list( adsl = pharmaverseadam::adsl, adae = pharmaverseadam::adae - ) + ) # data pre-processing ---------------------------------------------------------- df_aet02 <- adam_db$adae |> From 033c83921caf746428ed8ed6ab7b408897c7a25f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 14 May 2026 11:33:39 +0200 Subject: [PATCH 4/7] Add remotes to check the version from github for the thightly coupled packages --- DESCRIPTION | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/DESCRIPTION b/DESCRIPTION index 4761d712..4297408f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,6 +34,13 @@ Suggests: testthat (>= 3.3.2), tidyr (>= 1.3.2), withr (>= 3.0.2) +Remotes: + insightsengineering/cards, + insightsengineering/cardx, + insightsengineering/crane, + ddsjoberg/gtsummary, + pharmaverse/pharmaverseadam, + insightsengineering/random.cdisc.data Config/testthat/edition: 3 Encoding: UTF-8 Language: en-US From dd35a051ae677159a1980332fc615c8a2694cfc7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 21 May 2026 10:18:00 +0200 Subject: [PATCH 5/7] Detect new warnings --- tests/testthat.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/testthat.R b/tests/testthat.R index a95aa9ce..c9e38f50 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,6 +1,6 @@ if (requireNamespace("testthat", quietly = TRUE)) { library(testthat) - + options(warn = 2) # Warnings become errors pkg_name <- "cardinal" library(pkg_name, character.only = TRUE) testthat::test_check(pkg_name) From 1096793680cedf047f5a89350fb7a79b13423517 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Thu, 21 May 2026 10:20:08 +0200 Subject: [PATCH 6/7] Update snapshots --- tests/testthat/_snaps/fda-table_03.md | 104 +++--- tests/testthat/_snaps/fda-table_07.md | 463 +++++++++++++---------- tests/testthat/_snaps/fda-table_08.md | 208 +++++------ tests/testthat/_snaps/fda-table_10.md | 52 +-- tests/testthat/_snaps/fda-table_12.md | 84 ++--- tests/testthat/_snaps/fda-table_15.md | 104 +++--- tests/testthat/_snaps/fda-table_33.md | 130 ++++--- tests/testthat/_snaps/fda-table_34.md | 78 ++-- tests/testthat/_snaps/fda-table_44.md | 78 ++-- tests/testthat/_snaps/fda-table_45.md | 78 ++-- tests/testthat/_snaps/fda-table_50.md | 520 +++++++++++++------------- tests/testthat/test-custom.R | 4 +- 12 files changed, 1039 insertions(+), 864 deletions(-) diff --git a/tests/testthat/_snaps/fda-table_03.md b/tests/testthat/_snaps/fda-table_03.md index 4223bc72..e643e058 100644 --- a/tests/testthat/_snaps/fda-table_03.md +++ b/tests/testthat/_snaps/fda-table_03.md @@ -113,58 +113,58 @@ Code as.data.frame(ard[[2]]$tbl_hierarchical)[1:25, ] Output - variable variable_level context stat_name - 1 ..ard_hierarchical_overall.. TRUE hierarchical n - 2 ..ard_hierarchical_overall.. TRUE hierarchical N - 3 ..ard_hierarchical_overall.. TRUE hierarchical p - 4 SCRNFRS 3 hierarchical n - 5 SCRNFRS 3 hierarchical N - 6 SCRNFRS 3 hierarchical p - 7 SCRNFRS 1 hierarchical n - 8 SCRNFRS 1 hierarchical N - 9 SCRNFRS 1 hierarchical p - 10 SCRNFRS 4 hierarchical n - 11 SCRNFRS 4 hierarchical N - 12 SCRNFRS 4 hierarchical p - 13 SCRNFRS 2 hierarchical n - 14 SCRNFRS 2 hierarchical N - 15 SCRNFRS 2 hierarchical p - 16 ..ard_total_n.. NULL total_n N - NA NULL - NA.1 NULL - NA.2 NULL - NA.3 NULL - NA.4 NULL - NA.5 NULL - NA.6 NULL - NA.7 NULL - NA.8 NULL - stat_label stat stat_fmt - 1 n 52 52 - 2 N 306 306 - 3 % 0.1699346 17 - 4 n 11 11 - 5 N 306 306 - 6 % 0.03594771 3.6 - 7 n 17 17 - 8 N 306 306 - 9 % 0.05555556 5.6 - 10 n 7 7 - 11 N 306 306 - 12 % 0.02287582 2.3 - 13 n 17 17 - 14 N 306 306 - 15 % 0.05555556 5.6 - 16 N 306 306 - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL - NA.7 NULL NULL - NA.8 NULL NULL + variable variable_level + 1 ..ard_hierarchical_overall.. TRUE + 2 ..ard_hierarchical_overall.. TRUE + 3 ..ard_hierarchical_overall.. TRUE + 4 SCRNFRS Consent withdrawn + 5 SCRNFRS Consent withdrawn + 6 SCRNFRS Consent withdrawn + 7 SCRNFRS Inclusion/exclusion criteria not met + 8 SCRNFRS Inclusion/exclusion criteria not met + 9 SCRNFRS Inclusion/exclusion criteria not met + 10 SCRNFRS Other + 11 SCRNFRS Other + 12 SCRNFRS Other + 13 SCRNFRS Subject noncompliance + 14 SCRNFRS Subject noncompliance + 15 SCRNFRS Subject noncompliance + 16 ..ard_total_n.. NULL + NA NULL + NA.1 NULL + NA.2 NULL + NA.3 NULL + NA.4 NULL + NA.5 NULL + NA.6 NULL + NA.7 NULL + NA.8 NULL + context stat_name stat_label stat stat_fmt + 1 hierarchical n n 52 52 + 2 hierarchical N N 306 306 + 3 hierarchical p % 0.1699346 17 + 4 hierarchical n n 11 11 + 5 hierarchical N N 306 306 + 6 hierarchical p % 0.03594771 3.6 + 7 hierarchical n n 17 17 + 8 hierarchical N N 306 306 + 9 hierarchical p % 0.05555556 5.6 + 10 hierarchical n n 7 7 + 11 hierarchical N N 306 306 + 12 hierarchical p % 0.02287582 2.3 + 13 hierarchical n n 17 17 + 14 hierarchical N N 306 306 + 15 hierarchical p % 0.05555556 5.6 + 16 total_n N N 306 306 + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL + NA.7 NULL NULL + NA.8 NULL NULL 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, , ...) diff --git a/tests/testthat/_snaps/fda-table_07.md b/tests/testthat/_snaps/fda-table_07.md index cbfdba8e..d83007cf 100644 --- a/tests/testthat/_snaps/fda-table_07.md +++ b/tests/testthat/_snaps/fda-table_07.md @@ -13,12 +13,12 @@ 7 NULL TRT01A Xanomeline Low Dose tabulate 8 NULL TRT01A Xanomeline Low Dose tabulate 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Xanomeline High Dose AESER 1 hierarchical - 11 TRT01A Xanomeline High Dose AESER 1 hierarchical - 12 TRT01A Xanomeline High Dose AESER 1 hierarchical - 13 TRT01A Xanomeline Low Dose AESER 1 hierarchical - 14 TRT01A Xanomeline Low Dose AESER 1 hierarchical - 15 TRT01A Xanomeline Low Dose AESER 1 hierarchical + 10 TRT01A Xanomeline High Dose AESER SAE hierarchical + 11 TRT01A Xanomeline High Dose AESER SAE hierarchical + 12 TRT01A Xanomeline High Dose AESER SAE hierarchical + 13 TRT01A Xanomeline Low Dose AESER SAE hierarchical + 14 TRT01A Xanomeline Low Dose AESER SAE hierarchical + 15 TRT01A Xanomeline Low Dose AESER SAE hierarchical stat_name stat_label stat stat_fmt 1 n n 86 86 2 N N 254 254 @@ -83,12 +83,12 @@ 7 NULL TRT01A Xanomeline Low Dose tabulate 8 NULL TRT01A Xanomeline Low Dose tabulate 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Placebo AESDTH 1 hierarchical - 11 TRT01A Placebo AESDTH 1 hierarchical - 12 TRT01A Placebo AESDTH 1 hierarchical - 13 TRT01A Xanomeline Low Dose AESDTH 1 hierarchical - 14 TRT01A Xanomeline Low Dose AESDTH 1 hierarchical - 15 TRT01A Xanomeline Low Dose AESDTH 1 hierarchical + 10 TRT01A Placebo AESDTH Death hierarchical + 11 TRT01A Placebo AESDTH Death hierarchical + 12 TRT01A Placebo AESDTH Death hierarchical + 13 TRT01A Xanomeline Low Dose AESDTH Death hierarchical + 14 TRT01A Xanomeline Low Dose AESDTH Death hierarchical + 15 TRT01A Xanomeline Low Dose AESDTH Death hierarchical stat_name stat_label stat stat_fmt 1 n n 86 86 2 N N 254 254 @@ -153,12 +153,12 @@ 7 NULL TRT01A Xanomeline Low Dose tabulate 8 NULL TRT01A Xanomeline Low Dose tabulate 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Placebo AESLIFE 1 hierarchical - 11 TRT01A Placebo AESLIFE 1 hierarchical - 12 TRT01A Placebo AESLIFE 1 hierarchical - 13 TRT01A Xanomeline Low Dose AESLIFE 1 hierarchical - 14 TRT01A Xanomeline Low Dose AESLIFE 1 hierarchical - 15 TRT01A Xanomeline Low Dose AESLIFE 1 hierarchical + 10 TRT01A Placebo AESLIFE Life-threatening hierarchical + 11 TRT01A Placebo AESLIFE Life-threatening hierarchical + 12 TRT01A Placebo AESLIFE Life-threatening hierarchical + 13 TRT01A Xanomeline Low Dose AESLIFE Life-threatening hierarchical + 14 TRT01A Xanomeline Low Dose AESLIFE Life-threatening hierarchical + 15 TRT01A Xanomeline Low Dose AESLIFE Life-threatening hierarchical stat_name stat_label stat stat_fmt 1 n n 86 86 2 N N 254 254 @@ -213,44 +213,44 @@ Code as.data.frame(ard[[1]][[4]]$tbl_hierarchical) Output - group1 group1_level variable variable_level context - 1 NULL TRT01A Placebo tabulate - 2 NULL TRT01A Placebo tabulate - 3 NULL TRT01A Placebo tabulate - 4 NULL TRT01A Xanomeline High Dose tabulate - 5 NULL TRT01A Xanomeline High Dose tabulate - 6 NULL TRT01A Xanomeline High Dose tabulate - 7 NULL TRT01A Xanomeline Low Dose tabulate - 8 NULL TRT01A Xanomeline Low Dose tabulate - 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Placebo AESHOSP 1 hierarchical - 11 TRT01A Placebo AESHOSP 1 hierarchical - 12 TRT01A Placebo AESHOSP 1 hierarchical - 13 TRT01A Xanomeline High Dose AESHOSP 1 hierarchical - 14 TRT01A Xanomeline High Dose AESHOSP 1 hierarchical - 15 TRT01A Xanomeline High Dose AESHOSP 1 hierarchical - 16 TRT01A Xanomeline Low Dose AESHOSP 1 hierarchical - 17 TRT01A Xanomeline Low Dose AESHOSP 1 hierarchical - 18 TRT01A Xanomeline Low Dose AESHOSP 1 hierarchical - stat_name stat_label stat stat_fmt - 1 n n 86 86 - 2 N N 254 254 - 3 p % 0.3385827 33.9 - 4 n n 72 72 - 5 N N 254 254 - 6 p % 0.2834646 28.3 - 7 n n 96 96 - 8 N N 254 254 - 9 p % 0.3779528 37.8 - 10 n n 5 5 - 11 N N 86 86 - 12 p % 0.05813953 5.8 - 13 n n 7 7 - 14 N N 72 72 - 15 p % 0.09722222 9.7 - 16 n n 7 7 - 17 N N 96 96 - 18 p % 0.07291667 7.3 + group1 group1_level variable variable_level + 1 NULL TRT01A Placebo + 2 NULL TRT01A Placebo + 3 NULL TRT01A Placebo + 4 NULL TRT01A Xanomeline High Dose + 5 NULL TRT01A Xanomeline High Dose + 6 NULL TRT01A Xanomeline High Dose + 7 NULL TRT01A Xanomeline Low Dose + 8 NULL TRT01A Xanomeline Low Dose + 9 NULL TRT01A Xanomeline Low Dose + 10 TRT01A Placebo AESHOSP Initial or prolonged hospitalization + 11 TRT01A Placebo AESHOSP Initial or prolonged hospitalization + 12 TRT01A Placebo AESHOSP Initial or prolonged hospitalization + 13 TRT01A Xanomeline High Dose AESHOSP Initial or prolonged hospitalization + 14 TRT01A Xanomeline High Dose AESHOSP Initial or prolonged hospitalization + 15 TRT01A Xanomeline High Dose AESHOSP Initial or prolonged hospitalization + 16 TRT01A Xanomeline Low Dose AESHOSP Initial or prolonged hospitalization + 17 TRT01A Xanomeline Low Dose AESHOSP Initial or prolonged hospitalization + 18 TRT01A Xanomeline Low Dose AESHOSP Initial or prolonged hospitalization + context stat_name stat_label stat stat_fmt + 1 tabulate n n 86 86 + 2 tabulate N N 254 254 + 3 tabulate p % 0.3385827 33.9 + 4 tabulate n n 72 72 + 5 tabulate N N 254 254 + 6 tabulate p % 0.2834646 28.3 + 7 tabulate n n 96 96 + 8 tabulate N N 254 254 + 9 tabulate p % 0.3779528 37.8 + 10 hierarchical n n 5 5 + 11 hierarchical N N 86 86 + 12 hierarchical p % 0.05813953 5.8 + 13 hierarchical n n 7 7 + 14 hierarchical N N 72 72 + 15 hierarchical p % 0.09722222 9.7 + 16 hierarchical n n 7 7 + 17 hierarchical N N 96 96 + 18 hierarchical p % 0.07291667 7.3 fmt_fun 1 0 2 0 @@ -295,32 +295,32 @@ Code as.data.frame(ard[[1]][[5]]$tbl_hierarchical) Output - group1 group1_level variable variable_level context - 1 NULL TRT01A Placebo tabulate - 2 NULL TRT01A Placebo tabulate - 3 NULL TRT01A Placebo tabulate - 4 NULL TRT01A Xanomeline High Dose tabulate - 5 NULL TRT01A Xanomeline High Dose tabulate - 6 NULL TRT01A Xanomeline High Dose tabulate - 7 NULL TRT01A Xanomeline Low Dose tabulate - 8 NULL TRT01A Xanomeline Low Dose tabulate - 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Xanomeline Low Dose AESDISAB 1 hierarchical - 11 TRT01A Xanomeline Low Dose AESDISAB 1 hierarchical - 12 TRT01A Xanomeline Low Dose AESDISAB 1 hierarchical - stat_name stat_label stat stat_fmt - 1 n n 86 86 - 2 N N 254 254 - 3 p % 0.3385827 33.9 - 4 n n 72 72 - 5 N N 254 254 - 6 p % 0.2834646 28.3 - 7 n n 96 96 - 8 N N 254 254 - 9 p % 0.3779528 37.8 - 10 n n 1 1 - 11 N N 96 96 - 12 p % 0.01041667 1.0 + group1 group1_level variable variable_level + 1 NULL TRT01A Placebo + 2 NULL TRT01A Placebo + 3 NULL TRT01A Placebo + 4 NULL TRT01A Xanomeline High Dose + 5 NULL TRT01A Xanomeline High Dose + 6 NULL TRT01A Xanomeline High Dose + 7 NULL TRT01A Xanomeline Low Dose + 8 NULL TRT01A Xanomeline Low Dose + 9 NULL TRT01A Xanomeline Low Dose + 10 TRT01A Xanomeline Low Dose AESDISAB Disability or permanent damage + 11 TRT01A Xanomeline Low Dose AESDISAB Disability or permanent damage + 12 TRT01A Xanomeline Low Dose AESDISAB Disability or permanent damage + context stat_name stat_label stat stat_fmt + 1 tabulate n n 86 86 + 2 tabulate N N 254 254 + 3 tabulate p % 0.3385827 33.9 + 4 tabulate n n 72 72 + 5 tabulate N N 254 254 + 6 tabulate p % 0.2834646 28.3 + 7 tabulate n n 96 96 + 8 tabulate N N 254 254 + 9 tabulate p % 0.3779528 37.8 + 10 hierarchical n n 1 1 + 11 hierarchical N N 96 96 + 12 hierarchical p % 0.01041667 1.0 fmt_fun 1 0 2 0 @@ -353,38 +353,54 @@ Code as.data.frame(ard[[2]]$tbl_hierarchical) Output - group1 group1_level variable variable_level context - 1 NULL TRT01A Placebo tabulate - 2 NULL TRT01A Placebo tabulate - 3 NULL TRT01A Placebo tabulate - 4 NULL TRT01A Xanomeline High Dose tabulate - 5 NULL TRT01A Xanomeline High Dose tabulate - 6 NULL TRT01A Xanomeline High Dose tabulate - 7 NULL TRT01A Xanomeline Low Dose tabulate - 8 NULL TRT01A Xanomeline Low Dose tabulate - 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Xanomeline High Dose AEDISC 1 hierarchical - 11 TRT01A Xanomeline High Dose AEDISC 1 hierarchical - 12 TRT01A Xanomeline High Dose AEDISC 1 hierarchical - 13 TRT01A Xanomeline Low Dose AEDISC 1 hierarchical - 14 TRT01A Xanomeline Low Dose AEDISC 1 hierarchical - 15 TRT01A Xanomeline Low Dose AEDISC 1 hierarchical - stat_name stat_label stat stat_fmt - 1 n n 86 86 - 2 N N 254 254 - 3 p % 0.3385827 33.9 - 4 n n 72 72 - 5 N N 254 254 - 6 p % 0.2834646 28.3 - 7 n n 96 96 - 8 N N 254 254 - 9 p % 0.3779528 37.8 - 10 n n 1 1 - 11 N N 72 72 - 12 p % 0.01388889 1.4 - 13 n n 2 2 - 14 N N 96 96 - 15 p % 0.02083333 2.1 + group1 group1_level variable + 1 NULL TRT01A + 2 NULL TRT01A + 3 NULL TRT01A + 4 NULL TRT01A + 5 NULL TRT01A + 6 NULL TRT01A + 7 NULL TRT01A + 8 NULL TRT01A + 9 NULL TRT01A + 10 TRT01A Xanomeline High Dose AEDISC + 11 TRT01A Xanomeline High Dose AEDISC + 12 TRT01A Xanomeline High Dose AEDISC + 13 TRT01A Xanomeline Low Dose AEDISC + 14 TRT01A Xanomeline Low Dose AEDISC + 15 TRT01A Xanomeline Low Dose AEDISC + variable_level context stat_name + 1 Placebo tabulate n + 2 Placebo tabulate N + 3 Placebo tabulate p + 4 Xanomeline High Dose tabulate n + 5 Xanomeline High Dose tabulate N + 6 Xanomeline High Dose tabulate p + 7 Xanomeline Low Dose tabulate n + 8 Xanomeline Low Dose tabulate N + 9 Xanomeline Low Dose tabulate p + 10 AE leading to permanent discontinuation of treatment hierarchical n + 11 AE leading to permanent discontinuation of treatment hierarchical N + 12 AE leading to permanent discontinuation of treatment hierarchical p + 13 AE leading to permanent discontinuation of treatment hierarchical n + 14 AE leading to permanent discontinuation of treatment hierarchical N + 15 AE leading to permanent discontinuation of treatment hierarchical p + stat_label stat stat_fmt + 1 n 86 86 + 2 N 254 254 + 3 % 0.3385827 33.9 + 4 n 72 72 + 5 N 254 254 + 6 % 0.2834646 28.3 + 7 n 96 96 + 8 N 254 254 + 9 % 0.3779528 37.8 + 10 n 1 1 + 11 N 72 72 + 12 % 0.01388889 1.4 + 13 n 2 2 + 14 N 96 96 + 15 % 0.02083333 2.1 fmt_fun 1 0 2 0 @@ -478,61 +494,116 @@ 52 TRT01A Xanomeline Low Dose AEACN 53 TRT01A Xanomeline Low Dose AEACN 54 TRT01A Xanomeline Low Dose AEACN - variable_level context stat_name stat_label stat stat_fmt - 1 Placebo tabulate n n 86 86 - 2 Placebo tabulate N N 254 254 - 3 Placebo tabulate p % 0.3385827 33.9 - 4 Xanomeline High Dose tabulate n n 72 72 - 5 Xanomeline High Dose tabulate N N 254 254 - 6 Xanomeline High Dose tabulate p % 0.2834646 28.3 - 7 Xanomeline Low Dose tabulate n n 96 96 - 8 Xanomeline Low Dose tabulate N N 254 254 - 9 Xanomeline Low Dose tabulate p % 0.3779528 37.8 - 10 TRUE hierarchical n n 69 69 - 11 TRUE hierarchical N N 86 86 - 12 TRUE hierarchical p % 0.8023256 80 - 13 TRUE hierarchical n n 70 70 - 14 TRUE hierarchical N N 72 72 - 15 TRUE hierarchical p % 0.9722222 97 - 16 TRUE hierarchical n n 86 86 - 17 TRUE hierarchical N N 96 96 - 18 TRUE hierarchical p % 0.8958333 90 - 19 1 hierarchical n n 42 42 - 20 1 hierarchical N N 86 86 - 21 1 hierarchical p % 0.4883721 49 - 22 1 hierarchical n n 51 51 - 23 1 hierarchical N N 72 72 - 24 1 hierarchical p % 0.7083333 71 - 25 1 hierarchical n n 53 53 - 26 1 hierarchical N N 96 96 - 27 1 hierarchical p % 0.5520833 55 - 28 2 hierarchical n n 44 44 - 29 2 hierarchical N N 86 86 - 30 2 hierarchical p % 0.5116279 51 - 31 2 hierarchical n n 55 55 - 32 2 hierarchical N N 72 72 - 33 2 hierarchical p % 0.7638889 76 - 34 2 hierarchical n n 65 65 - 35 2 hierarchical N N 96 96 - 36 2 hierarchical p % 0.6770833 68 - 37 3 hierarchical n n 50 50 - 38 3 hierarchical N N 86 86 - 39 3 hierarchical p % 0.5813953 58 - 40 3 hierarchical n n 54 54 - 41 3 hierarchical N N 72 72 - 42 3 hierarchical p % 0.75 75 - 43 3 hierarchical n n 56 56 - 44 3 hierarchical N N 96 96 - 45 3 hierarchical p % 0.5833333 58 - 46 4 hierarchical n n 35 35 - 47 4 hierarchical N N 86 86 - 48 4 hierarchical p % 0.4069767 41 - 49 4 hierarchical n n 50 50 - 50 4 hierarchical N N 72 72 - 51 4 hierarchical p % 0.6944444 69 - 52 4 hierarchical n n 61 61 - 53 4 hierarchical N N 96 96 - 54 4 hierarchical p % 0.6354167 64 + variable_level context stat_name stat_label + 1 Placebo tabulate n n + 2 Placebo tabulate N N + 3 Placebo tabulate p % + 4 Xanomeline High Dose tabulate n n + 5 Xanomeline High Dose tabulate N N + 6 Xanomeline High Dose tabulate p % + 7 Xanomeline Low Dose tabulate n n + 8 Xanomeline Low Dose tabulate N N + 9 Xanomeline Low Dose tabulate p % + 10 TRUE hierarchical n n + 11 TRUE hierarchical N N + 12 TRUE hierarchical p % + 13 TRUE hierarchical n n + 14 TRUE hierarchical N N + 15 TRUE hierarchical p % + 16 TRUE hierarchical n n + 17 TRUE hierarchical N N + 18 TRUE hierarchical p % + 19 AE leading to dose delay of study drug hierarchical n n + 20 AE leading to dose delay of study drug hierarchical N N + 21 AE leading to dose delay of study drug hierarchical p % + 22 AE leading to dose delay of study drug hierarchical n n + 23 AE leading to dose delay of study drug hierarchical N N + 24 AE leading to dose delay of study drug hierarchical p % + 25 AE leading to dose delay of study drug hierarchical n n + 26 AE leading to dose delay of study drug hierarchical N N + 27 AE leading to dose delay of study drug hierarchical p % + 28 AE leading to interruption of study drug hierarchical n n + 29 AE leading to interruption of study drug hierarchical N N + 30 AE leading to interruption of study drug hierarchical p % + 31 AE leading to interruption of study drug hierarchical n n + 32 AE leading to interruption of study drug hierarchical N N + 33 AE leading to interruption of study drug hierarchical p % + 34 AE leading to interruption of study drug hierarchical n n + 35 AE leading to interruption of study drug hierarchical N N + 36 AE leading to interruption of study drug hierarchical p % + 37 AE leading to reduction of study drug hierarchical n n + 38 AE leading to reduction of study drug hierarchical N N + 39 AE leading to reduction of study drug hierarchical p % + 40 AE leading to reduction of study drug hierarchical n n + 41 AE leading to reduction of study drug hierarchical N N + 42 AE leading to reduction of study drug hierarchical p % + 43 AE leading to reduction of study drug hierarchical n n + 44 AE leading to reduction of study drug hierarchical N N + 45 AE leading to reduction of study drug hierarchical p % + 46 Other hierarchical n n + 47 Other hierarchical N N + 48 Other hierarchical p % + 49 Other hierarchical n n + 50 Other hierarchical N N + 51 Other hierarchical p % + 52 Other hierarchical n n + 53 Other hierarchical N N + 54 Other hierarchical p % + stat stat_fmt + 1 86 86 + 2 254 254 + 3 0.3385827 33.9 + 4 72 72 + 5 254 254 + 6 0.2834646 28.3 + 7 96 96 + 8 254 254 + 9 0.3779528 37.8 + 10 69 69 + 11 86 86 + 12 0.8023256 80 + 13 70 70 + 14 72 72 + 15 0.9722222 97 + 16 86 86 + 17 96 96 + 18 0.8958333 90 + 19 42 42 + 20 86 86 + 21 0.4883721 49 + 22 51 51 + 23 72 72 + 24 0.7083333 71 + 25 53 53 + 26 96 96 + 27 0.5520833 55 + 28 44 44 + 29 86 86 + 30 0.5116279 51 + 31 55 55 + 32 72 72 + 33 0.7638889 76 + 34 65 65 + 35 96 96 + 36 0.6770833 68 + 37 50 50 + 38 86 86 + 39 0.5813953 58 + 40 54 54 + 41 72 72 + 42 0.75 75 + 43 56 56 + 44 96 96 + 45 0.5833333 58 + 46 35 35 + 47 86 86 + 48 0.4069767 41 + 49 50 50 + 50 72 72 + 51 0.6944444 69 + 52 61 61 + 53 96 96 + 54 0.6354167 64 fmt_fun 1 0 2 0 @@ -714,33 +785,33 @@ 16 TRUE hierarchical n n 86 86 17 TRUE hierarchical N N 96 96 18 TRUE hierarchical p % 0.8958333 90 - 19 1 hierarchical n n 60 60 - 20 1 hierarchical N N 86 86 - 21 1 hierarchical p % 0.6976744 70 - 22 1 hierarchical n n 66 66 - 23 1 hierarchical N N 72 72 - 24 1 hierarchical p % 0.9166667 92 - 25 1 hierarchical n n 65 65 - 26 1 hierarchical N N 96 96 - 27 1 hierarchical p % 0.6770833 68 - 28 2 hierarchical n n 28 28 - 29 2 hierarchical N N 86 86 - 30 2 hierarchical p % 0.3255814 33 - 31 2 hierarchical n n 48 48 - 32 2 hierarchical N N 72 72 - 33 2 hierarchical p % 0.6666667 67 - 34 2 hierarchical n n 60 60 - 35 2 hierarchical N N 96 96 - 36 2 hierarchical p % 0.625 63 - 37 3 hierarchical n n 7 7 - 38 3 hierarchical N N 86 86 - 39 3 hierarchical p % 0.08139535 8.1 - 40 3 hierarchical n n 8 8 - 41 3 hierarchical N N 72 72 - 42 3 hierarchical p % 0.1111111 11 - 43 3 hierarchical n n 16 16 - 44 3 hierarchical N N 96 96 - 45 3 hierarchical p % 0.1666667 17 + 19 MILD hierarchical n n 60 60 + 20 MILD hierarchical N N 86 86 + 21 MILD hierarchical p % 0.6976744 70 + 22 MILD hierarchical n n 66 66 + 23 MILD hierarchical N N 72 72 + 24 MILD hierarchical p % 0.9166667 92 + 25 MILD hierarchical n n 65 65 + 26 MILD hierarchical N N 96 96 + 27 MILD hierarchical p % 0.6770833 68 + 28 MODERATE hierarchical n n 28 28 + 29 MODERATE hierarchical N N 86 86 + 30 MODERATE hierarchical p % 0.3255814 33 + 31 MODERATE hierarchical n n 48 48 + 32 MODERATE hierarchical N N 72 72 + 33 MODERATE hierarchical p % 0.6666667 67 + 34 MODERATE hierarchical n n 60 60 + 35 MODERATE hierarchical N N 96 96 + 36 MODERATE hierarchical p % 0.625 63 + 37 SEVERE hierarchical n n 7 7 + 38 SEVERE hierarchical N N 86 86 + 39 SEVERE hierarchical p % 0.08139535 8.1 + 40 SEVERE hierarchical n n 8 8 + 41 SEVERE hierarchical N N 72 72 + 42 SEVERE hierarchical p % 0.1111111 11 + 43 SEVERE hierarchical n n 16 16 + 44 SEVERE hierarchical N N 96 96 + 45 SEVERE hierarchical p % 0.1666667 17 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_08.md b/tests/testthat/_snaps/fda-table_08.md index 37ef7d49..e29260de 100644 --- a/tests/testthat/_snaps/fda-table_08.md +++ b/tests/testthat/_snaps/fda-table_08.md @@ -3,58 +3,58 @@ Code as.data.frame(ard[[1]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level variable variable_level - 1 NULL TRT01A Placebo - 2 NULL TRT01A Placebo - 3 NULL TRT01A Placebo - 4 NULL TRT01A Xanomeline High Dose - 5 NULL TRT01A Xanomeline High Dose - 6 NULL TRT01A Xanomeline High Dose - 7 NULL TRT01A Xanomeline Low Dose - 8 NULL TRT01A Xanomeline Low Dose - 9 NULL TRT01A Xanomeline Low Dose - 10 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 11 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 12 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 13 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 14 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 15 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 16 TRT01A Placebo DTHCAUS 1 - 17 TRT01A Placebo DTHCAUS 1 - 18 TRT01A Placebo DTHCAUS 1 - 19 TRT01A Xanomeline Low Dose DTHCAUS 1 - 20 TRT01A Xanomeline Low Dose DTHCAUS 1 - 21 TRT01A Xanomeline Low Dose DTHCAUS 1 - 22 TRT01A Placebo DTHCAUS 2 - 23 TRT01A Placebo DTHCAUS 2 - 24 TRT01A Placebo DTHCAUS 2 - 25 TRT01A Xanomeline Low Dose DTHCAUS 2 - context stat_name stat_label stat stat_fmt - 1 tabulate n n 86 86 - 2 tabulate N N 254 254 - 3 tabulate p % 0.3385827 33.9 - 4 tabulate n n 72 72 - 5 tabulate N N 254 254 - 6 tabulate p % 0.2834646 28.3 - 7 tabulate n n 96 96 - 8 tabulate N N 254 254 - 9 tabulate p % 0.3779528 37.8 - 10 hierarchical n n 2 2 - 11 hierarchical N N 86 86 - 12 hierarchical p % 0.02325581 2.3 - 13 hierarchical n n 1 1 - 14 hierarchical N N 96 96 - 15 hierarchical p % 0.01041667 1.0 - 16 hierarchical n n 1 1 - 17 hierarchical N N 86 86 - 18 hierarchical p % 0.01162791 1.2 - 19 hierarchical n n 0 0 - 20 hierarchical N N 96 96 - 21 hierarchical p % 0 0 - 22 hierarchical n n 1 1 - 23 hierarchical N N 86 86 - 24 hierarchical p % 0.01162791 1.2 - 25 hierarchical n n 0 0 + group1 group1_level variable + 1 NULL TRT01A + 2 NULL TRT01A + 3 NULL TRT01A + 4 NULL TRT01A + 5 NULL TRT01A + 6 NULL TRT01A + 7 NULL TRT01A + 8 NULL TRT01A + 9 NULL TRT01A + 10 TRT01A Placebo ..ard_hierarchical_overall.. + 11 TRT01A Placebo ..ard_hierarchical_overall.. + 12 TRT01A Placebo ..ard_hierarchical_overall.. + 13 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 14 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 15 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 16 TRT01A Placebo DTHCAUS + 17 TRT01A Placebo DTHCAUS + 18 TRT01A Placebo DTHCAUS + 19 TRT01A Xanomeline Low Dose DTHCAUS + 20 TRT01A Xanomeline Low Dose DTHCAUS + 21 TRT01A Xanomeline Low Dose DTHCAUS + 22 TRT01A Placebo DTHCAUS + 23 TRT01A Placebo DTHCAUS + 24 TRT01A Placebo DTHCAUS + 25 TRT01A Xanomeline Low Dose DTHCAUS + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 86 86 + 2 Placebo tabulate N N 254 254 + 3 Placebo tabulate p % 0.3385827 33.9 + 4 Xanomeline High Dose tabulate n n 72 72 + 5 Xanomeline High Dose tabulate N N 254 254 + 6 Xanomeline High Dose tabulate p % 0.2834646 28.3 + 7 Xanomeline Low Dose tabulate n n 96 96 + 8 Xanomeline Low Dose tabulate N N 254 254 + 9 Xanomeline Low Dose tabulate p % 0.3779528 37.8 + 10 TRUE hierarchical n n 2 2 + 11 TRUE hierarchical N N 86 86 + 12 TRUE hierarchical p % 0.02325581 2.3 + 13 TRUE hierarchical n n 1 1 + 14 TRUE hierarchical N N 96 96 + 15 TRUE hierarchical p % 0.01041667 1.0 + 16 COMPLETED SUICIDE hierarchical n n 1 1 + 17 COMPLETED SUICIDE hierarchical N N 86 86 + 18 COMPLETED SUICIDE hierarchical p % 0.01162791 1.2 + 19 COMPLETED SUICIDE hierarchical n n 0 0 + 20 COMPLETED SUICIDE hierarchical N N 96 96 + 21 COMPLETED SUICIDE hierarchical p % 0 0 + 22 MYOCARDIAL INFARCTION hierarchical n n 1 1 + 23 MYOCARDIAL INFARCTION hierarchical N N 86 86 + 24 MYOCARDIAL INFARCTION hierarchical p % 0.01162791 1.2 + 25 MYOCARDIAL INFARCTION hierarchical n n 0 0 fmt_fun 1 0 2 0 @@ -113,58 +113,58 @@ Code as.data.frame(ard[[2]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level variable variable_level - 1 NULL TRT01A Placebo - 2 NULL TRT01A Placebo - 3 NULL TRT01A Placebo - 4 NULL TRT01A Xanomeline High Dose - 5 NULL TRT01A Xanomeline High Dose - 6 NULL TRT01A Xanomeline High Dose - 7 NULL TRT01A Xanomeline Low Dose - 8 NULL TRT01A Xanomeline Low Dose - 9 NULL TRT01A Xanomeline Low Dose - 10 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 11 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 12 TRT01A Placebo ..ard_hierarchical_overall.. TRUE - 13 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 14 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 15 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. TRUE - 16 TRT01A Placebo AEDECOD 1 - 17 TRT01A Placebo AEDECOD 1 - 18 TRT01A Placebo AEDECOD 1 - 19 TRT01A Xanomeline Low Dose AEDECOD 1 - 20 TRT01A Xanomeline Low Dose AEDECOD 1 - 21 TRT01A Xanomeline Low Dose AEDECOD 1 - 22 TRT01A Placebo AEDECOD 2 - 23 TRT01A Placebo AEDECOD 2 - 24 TRT01A Placebo AEDECOD 2 - 25 TRT01A Xanomeline Low Dose AEDECOD 2 - context stat_name stat_label stat stat_fmt - 1 tabulate n n 86 86 - 2 tabulate N N 254 254 - 3 tabulate p % 0.3385827 33.9 - 4 tabulate n n 72 72 - 5 tabulate N N 254 254 - 6 tabulate p % 0.2834646 28.3 - 7 tabulate n n 96 96 - 8 tabulate N N 254 254 - 9 tabulate p % 0.3779528 37.8 - 10 hierarchical n n 2 2 - 11 hierarchical N N 86 86 - 12 hierarchical p % 0.02325581 2.3 - 13 hierarchical n n 1 1 - 14 hierarchical N N 96 96 - 15 hierarchical p % 0.01041667 1.0 - 16 hierarchical n n 1 1 - 17 hierarchical N N 86 86 - 18 hierarchical p % 0.01162791 1.2 - 19 hierarchical n n 0 0 - 20 hierarchical N N 96 96 - 21 hierarchical p % 0 0 - 22 hierarchical n n 1 1 - 23 hierarchical N N 86 86 - 24 hierarchical p % 0.01162791 1.2 - 25 hierarchical n n 0 0 + group1 group1_level variable + 1 NULL TRT01A + 2 NULL TRT01A + 3 NULL TRT01A + 4 NULL TRT01A + 5 NULL TRT01A + 6 NULL TRT01A + 7 NULL TRT01A + 8 NULL TRT01A + 9 NULL TRT01A + 10 TRT01A Placebo ..ard_hierarchical_overall.. + 11 TRT01A Placebo ..ard_hierarchical_overall.. + 12 TRT01A Placebo ..ard_hierarchical_overall.. + 13 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 14 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 15 TRT01A Xanomeline Low Dose ..ard_hierarchical_overall.. + 16 TRT01A Placebo AEDECOD + 17 TRT01A Placebo AEDECOD + 18 TRT01A Placebo AEDECOD + 19 TRT01A Xanomeline Low Dose AEDECOD + 20 TRT01A Xanomeline Low Dose AEDECOD + 21 TRT01A Xanomeline Low Dose AEDECOD + 22 TRT01A Placebo AEDECOD + 23 TRT01A Placebo AEDECOD + 24 TRT01A Placebo AEDECOD + 25 TRT01A Xanomeline Low Dose AEDECOD + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 86 86 + 2 Placebo tabulate N N 254 254 + 3 Placebo tabulate p % 0.3385827 33.9 + 4 Xanomeline High Dose tabulate n n 72 72 + 5 Xanomeline High Dose tabulate N N 254 254 + 6 Xanomeline High Dose tabulate p % 0.2834646 28.3 + 7 Xanomeline Low Dose tabulate n n 96 96 + 8 Xanomeline Low Dose tabulate N N 254 254 + 9 Xanomeline Low Dose tabulate p % 0.3779528 37.8 + 10 TRUE hierarchical n n 2 2 + 11 TRUE hierarchical N N 86 86 + 12 TRUE hierarchical p % 0.02325581 2.3 + 13 TRUE hierarchical n n 1 1 + 14 TRUE hierarchical N N 96 96 + 15 TRUE hierarchical p % 0.01041667 1.0 + 16 COMPLETED SUICIDE hierarchical n n 1 1 + 17 COMPLETED SUICIDE hierarchical N N 86 86 + 18 COMPLETED SUICIDE hierarchical p % 0.01162791 1.2 + 19 COMPLETED SUICIDE hierarchical n n 0 0 + 20 COMPLETED SUICIDE hierarchical N N 96 96 + 21 COMPLETED SUICIDE hierarchical p % 0 0 + 22 MYOCARDIAL INFARCTION hierarchical n n 1 1 + 23 MYOCARDIAL INFARCTION hierarchical N N 86 86 + 24 MYOCARDIAL INFARCTION hierarchical p % 0.01162791 1.2 + 25 MYOCARDIAL INFARCTION hierarchical n n 0 0 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_10.md b/tests/testthat/_snaps/fda-table_10.md index d3e932b7..6cec5f52 100644 --- a/tests/testthat/_snaps/fda-table_10.md +++ b/tests/testthat/_snaps/fda-table_10.md @@ -55,32 +55,32 @@ 23 NULL 24 NULL 25 AESOC NERVOUS SYSTEM DISORDERS - tbl_hierarchical.variable tbl_hierarchical.variable_level - 1 TRT01A Placebo - 2 TRT01A Placebo - 3 TRT01A Placebo - 4 TRT01A Screen Failure - 5 TRT01A Screen Failure - 6 TRT01A Screen Failure - 7 TRT01A Xanomeline High Dose - 8 TRT01A Xanomeline High Dose - 9 TRT01A Xanomeline High Dose - 10 TRT01A Xanomeline Low Dose - 11 TRT01A Xanomeline Low Dose - 12 TRT01A Xanomeline Low Dose - 13 ..ard_hierarchical_overall.. TRUE - 14 ..ard_hierarchical_overall.. TRUE - 15 ..ard_hierarchical_overall.. TRUE - 16 ..ard_hierarchical_overall.. TRUE - 17 ..ard_hierarchical_overall.. TRUE - 18 ..ard_hierarchical_overall.. TRUE - 19 AESOC NERVOUS SYSTEM DISORDERS - 20 AESOC NERVOUS SYSTEM DISORDERS - 21 AESOC NERVOUS SYSTEM DISORDERS - 22 AESOC NERVOUS SYSTEM DISORDERS - 23 AESOC NERVOUS SYSTEM DISORDERS - 24 AESOC NERVOUS SYSTEM DISORDERS - 25 AEDECOD 1 + tbl_hierarchical.variable tbl_hierarchical.variable_level + 1 TRT01A Placebo + 2 TRT01A Placebo + 3 TRT01A Placebo + 4 TRT01A Screen Failure + 5 TRT01A Screen Failure + 6 TRT01A Screen Failure + 7 TRT01A Xanomeline High Dose + 8 TRT01A Xanomeline High Dose + 9 TRT01A Xanomeline High Dose + 10 TRT01A Xanomeline Low Dose + 11 TRT01A Xanomeline Low Dose + 12 TRT01A Xanomeline Low Dose + 13 ..ard_hierarchical_overall.. TRUE + 14 ..ard_hierarchical_overall.. TRUE + 15 ..ard_hierarchical_overall.. TRUE + 16 ..ard_hierarchical_overall.. TRUE + 17 ..ard_hierarchical_overall.. TRUE + 18 ..ard_hierarchical_overall.. TRUE + 19 AESOC NERVOUS SYSTEM DISORDERS + 20 AESOC NERVOUS SYSTEM DISORDERS + 21 AESOC NERVOUS SYSTEM DISORDERS + 22 AESOC NERVOUS SYSTEM DISORDERS + 23 AESOC NERVOUS SYSTEM DISORDERS + 24 AESOC NERVOUS SYSTEM DISORDERS + 25 AEDECOD PARTIAL SEIZURES WITH SECONDARY GENERALISATION tbl_hierarchical.context tbl_hierarchical.stat_name 1 tabulate n 2 tabulate N diff --git a/tests/testthat/_snaps/fda-table_12.md b/tests/testthat/_snaps/fda-table_12.md index 0c384a3f..028873c3 100644 --- a/tests/testthat/_snaps/fda-table_12.md +++ b/tests/testthat/_snaps/fda-table_12.md @@ -3,42 +3,42 @@ Code as.data.frame(ard$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable - 1 NULL NULL TRT01A - 2 NULL NULL TRT01A - 3 NULL NULL TRT01A - 4 NULL NULL TRT01A - 5 NULL NULL TRT01A - 6 NULL NULL TRT01A - 7 NULL NULL TRT01A - 8 NULL NULL TRT01A - 9 NULL NULL TRT01A - 10 TRT01A 1 NULL ..ard_hierarchical_overall.. - 11 TRT01A 1 NULL ..ard_hierarchical_overall.. - 12 TRT01A 1 NULL ..ard_hierarchical_overall.. - 13 TRT01A 2 NULL ..ard_hierarchical_overall.. - 14 TRT01A 2 NULL ..ard_hierarchical_overall.. - 15 TRT01A 2 NULL ..ard_hierarchical_overall.. - 16 TRT01A 3 NULL ..ard_hierarchical_overall.. - 17 TRT01A 3 NULL ..ard_hierarchical_overall.. - 18 TRT01A 3 NULL ..ard_hierarchical_overall.. - 19 TRT01A 1 NULL AEBODSYS - 20 TRT01A 1 NULL AEBODSYS - 21 TRT01A 1 NULL AEBODSYS - 22 TRT01A 2 NULL AEBODSYS - 23 TRT01A 2 NULL AEBODSYS - 24 TRT01A 2 NULL AEBODSYS - 25 TRT01A 3 NULL AEBODSYS + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A A: Drug X NULL ..ard_hierarchical_overall.. + 11 TRT01A A: Drug X NULL ..ard_hierarchical_overall.. + 12 TRT01A A: Drug X NULL ..ard_hierarchical_overall.. + 13 TRT01A B: Placebo NULL ..ard_hierarchical_overall.. + 14 TRT01A B: Placebo NULL ..ard_hierarchical_overall.. + 15 TRT01A B: Placebo NULL ..ard_hierarchical_overall.. + 16 TRT01A C: Combination NULL ..ard_hierarchical_overall.. + 17 TRT01A C: Combination NULL ..ard_hierarchical_overall.. + 18 TRT01A C: Combination NULL ..ard_hierarchical_overall.. + 19 TRT01A A: Drug X NULL AEBODSYS + 20 TRT01A A: Drug X NULL AEBODSYS + 21 TRT01A A: Drug X NULL AEBODSYS + 22 TRT01A B: Placebo NULL AEBODSYS + 23 TRT01A B: Placebo NULL AEBODSYS + 24 TRT01A B: Placebo NULL AEBODSYS + 25 TRT01A C: Combination NULL AEBODSYS variable_level context stat_name stat_label stat stat_fmt - 1 1 tabulate n n 134 134 - 2 1 tabulate N N 400 400 - 3 1 tabulate p % 0.335 33.5 - 4 2 tabulate n n 134 134 - 5 2 tabulate N N 400 400 - 6 2 tabulate p % 0.335 33.5 - 7 3 tabulate n n 132 132 - 8 3 tabulate N N 400 400 - 9 3 tabulate p % 0.33 33.0 + 1 A: Drug X tabulate n n 134 134 + 2 A: Drug X tabulate N N 400 400 + 3 A: Drug X tabulate p % 0.335 33.5 + 4 B: Placebo tabulate n n 134 134 + 5 B: Placebo tabulate N N 400 400 + 6 B: Placebo tabulate p % 0.335 33.5 + 7 C: Combination tabulate n n 132 132 + 8 C: Combination tabulate N N 400 400 + 9 C: Combination tabulate p % 0.33 33.0 10 TRUE hierarchical n n 86 86 11 TRUE hierarchical N N 134 134 12 TRUE hierarchical p % 0.641791 64 @@ -48,13 +48,13 @@ 16 TRUE hierarchical n n 90 90 17 TRUE hierarchical N N 132 132 18 TRUE hierarchical p % 0.6818182 68 - 19 1 hierarchical n n 53 53 - 20 1 hierarchical N N 134 134 - 21 1 hierarchical p % 0.3955224 40 - 22 1 hierarchical n n 55 55 - 23 1 hierarchical N N 134 134 - 24 1 hierarchical p % 0.4104478 41 - 25 1 hierarchical n n 69 69 + 19 cl A.1 hierarchical n n 53 53 + 20 cl A.1 hierarchical N N 134 134 + 21 cl A.1 hierarchical p % 0.3955224 40 + 22 cl A.1 hierarchical n n 55 55 + 23 cl A.1 hierarchical N N 134 134 + 24 cl A.1 hierarchical p % 0.4104478 41 + 25 cl A.1 hierarchical n n 69 69 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_15.md b/tests/testthat/_snaps/fda-table_15.md index 052534c3..df5f21e9 100644 --- a/tests/testthat/_snaps/fda-table_15.md +++ b/tests/testthat/_snaps/fda-table_15.md @@ -3,58 +3,58 @@ Code as.data.frame(ard$tbl_hierarchical)[1:25, ] Output - group1 group1_level variable variable_level context - 1 NULL TRT01A Placebo tabulate - 2 NULL TRT01A Placebo tabulate - 3 NULL TRT01A Placebo tabulate - 4 NULL TRT01A Xanomeline High Dose tabulate - 5 NULL TRT01A Xanomeline High Dose tabulate - 6 NULL TRT01A Xanomeline High Dose tabulate - 7 NULL TRT01A Xanomeline Low Dose tabulate - 8 NULL TRT01A Xanomeline Low Dose tabulate - 9 NULL TRT01A Xanomeline Low Dose tabulate - 10 TRT01A Placebo AEDECOD 12 hierarchical - 11 TRT01A Placebo AEDECOD 12 hierarchical - 12 TRT01A Placebo AEDECOD 12 hierarchical - 13 TRT01A Xanomeline High Dose AEDECOD 12 hierarchical - 14 TRT01A Xanomeline High Dose AEDECOD 12 hierarchical - 15 TRT01A Xanomeline High Dose AEDECOD 12 hierarchical - 16 TRT01A Xanomeline Low Dose AEDECOD 12 hierarchical - 17 TRT01A Xanomeline Low Dose AEDECOD 12 hierarchical - 18 TRT01A Xanomeline Low Dose AEDECOD 12 hierarchical - 19 TRT01A Placebo AEDECOD 16 hierarchical - 20 TRT01A Placebo AEDECOD 16 hierarchical - 21 TRT01A Placebo AEDECOD 16 hierarchical - 22 TRT01A Xanomeline High Dose AEDECOD 16 hierarchical - 23 TRT01A Xanomeline High Dose AEDECOD 16 hierarchical - 24 TRT01A Xanomeline High Dose AEDECOD 16 hierarchical - 25 TRT01A Xanomeline Low Dose AEDECOD 16 hierarchical - stat_name stat_label stat stat_fmt - 1 n n 86 86 - 2 N N 254 254 - 3 p % 0.3385827 33.9 - 4 n n 72 72 - 5 N N 254 254 - 6 p % 0.2834646 28.3 - 7 n n 96 96 - 8 N N 254 254 - 9 p % 0.3779528 37.8 - 10 n n 5 5 - 11 N N 86 86 - 12 p % 0.05813953 5.8 - 13 n n 7 7 - 14 N N 72 72 - 15 p % 0.09722222 9.7 - 16 n n 9 9 - 17 N N 96 96 - 18 p % 0.09375 9.4 - 19 n n 3 3 - 20 N N 86 86 - 21 p % 0.03488372 3.5 - 22 n n 14 14 - 23 N N 72 72 - 24 p % 0.1944444 19 - 25 n n 13 13 + group1 group1_level variable variable_level + 1 NULL TRT01A Placebo + 2 NULL TRT01A Placebo + 3 NULL TRT01A Placebo + 4 NULL TRT01A Xanomeline High Dose + 5 NULL TRT01A Xanomeline High Dose + 6 NULL TRT01A Xanomeline High Dose + 7 NULL TRT01A Xanomeline Low Dose + 8 NULL TRT01A Xanomeline Low Dose + 9 NULL TRT01A Xanomeline Low Dose + 10 TRT01A Placebo AEDECOD APPLICATION SITE DERMATITIS + 11 TRT01A Placebo AEDECOD APPLICATION SITE DERMATITIS + 12 TRT01A Placebo AEDECOD APPLICATION SITE DERMATITIS + 13 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE DERMATITIS + 14 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE DERMATITIS + 15 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE DERMATITIS + 16 TRT01A Xanomeline Low Dose AEDECOD APPLICATION SITE DERMATITIS + 17 TRT01A Xanomeline Low Dose AEDECOD APPLICATION SITE DERMATITIS + 18 TRT01A Xanomeline Low Dose AEDECOD APPLICATION SITE DERMATITIS + 19 TRT01A Placebo AEDECOD APPLICATION SITE ERYTHEMA + 20 TRT01A Placebo AEDECOD APPLICATION SITE ERYTHEMA + 21 TRT01A Placebo AEDECOD APPLICATION SITE ERYTHEMA + 22 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE ERYTHEMA + 23 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE ERYTHEMA + 24 TRT01A Xanomeline High Dose AEDECOD APPLICATION SITE ERYTHEMA + 25 TRT01A Xanomeline Low Dose AEDECOD APPLICATION SITE ERYTHEMA + context stat_name stat_label stat stat_fmt + 1 tabulate n n 86 86 + 2 tabulate N N 254 254 + 3 tabulate p % 0.3385827 33.9 + 4 tabulate n n 72 72 + 5 tabulate N N 254 254 + 6 tabulate p % 0.2834646 28.3 + 7 tabulate n n 96 96 + 8 tabulate N N 254 254 + 9 tabulate p % 0.3779528 37.8 + 10 hierarchical n n 5 5 + 11 hierarchical N N 86 86 + 12 hierarchical p % 0.05813953 5.8 + 13 hierarchical n n 7 7 + 14 hierarchical N N 72 72 + 15 hierarchical p % 0.09722222 9.7 + 16 hierarchical n n 9 9 + 17 hierarchical N N 96 96 + 18 hierarchical p % 0.09375 9.4 + 19 hierarchical n n 3 3 + 20 hierarchical N N 86 86 + 21 hierarchical p % 0.03488372 3.5 + 22 hierarchical n n 14 14 + 23 hierarchical N N 72 72 + 24 hierarchical p % 0.1944444 19 + 25 hierarchical n n 13 13 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_33.md b/tests/testthat/_snaps/fda-table_33.md index af1a4c33..1da18f1a 100644 --- a/tests/testthat/_snaps/fda-table_33.md +++ b/tests/testthat/_snaps/fda-table_33.md @@ -3,58 +3,84 @@ Code as.data.frame(ard$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable - 1 NULL NULL TRT01A - 2 NULL NULL TRT01A - 3 NULL NULL TRT01A - 4 NULL NULL TRT01A - 5 NULL NULL TRT01A - 6 NULL NULL TRT01A - 7 NULL NULL TRT01A - 8 NULL NULL TRT01A - 9 NULL NULL TRT01A - 10 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 11 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 12 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 13 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 14 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 15 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 16 TRT01A Xanomeline Low Dose OCMQ01NAM 1 AEDECOD - 17 TRT01A Xanomeline Low Dose OCMQ01NAM 1 AEDECOD - 18 TRT01A Xanomeline Low Dose OCMQ01NAM 1 AEDECOD - 19 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 20 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 21 TRT01A Placebo OCMQ01NAM 1 AEDECOD - 22 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 23 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 24 TRT01A Xanomeline High Dose OCMQ01NAM 1 AEDECOD - 25 TRT01A Xanomeline Low Dose OCMQ01NAM 1 AEDECOD - variable_level context stat_name stat_label stat stat_fmt - 1 Placebo tabulate n n 6 6 - 2 Placebo tabulate N N 29 29 - 3 Placebo tabulate p % 0.2068966 20.7 - 4 Xanomeline High Dose tabulate n n 12 12 - 5 Xanomeline High Dose tabulate N N 29 29 - 6 Xanomeline High Dose tabulate p % 0.4137931 41.4 - 7 Xanomeline Low Dose tabulate n n 11 11 - 8 Xanomeline Low Dose tabulate N N 29 29 - 9 Xanomeline Low Dose tabulate p % 0.3793103 37.9 - 10 1 hierarchical n n 0 0 - 11 1 hierarchical N N 6 6 - 12 1 hierarchical p % 0 0 - 13 1 hierarchical n n 6 6 - 14 1 hierarchical N N 12 12 - 15 1 hierarchical p % 0.5 50 - 16 1 hierarchical n n 8 8 - 17 1 hierarchical N N 11 11 - 18 1 hierarchical p % 0.7272727 73 - 19 2 hierarchical n n 1 1 - 20 2 hierarchical N N 6 6 - 21 2 hierarchical p % 0.1666667 17 - 22 2 hierarchical n n 0 0 - 23 2 hierarchical N N 12 12 - 24 2 hierarchical p % 0 0 - 25 2 hierarchical n n 0 0 + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 11 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 12 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 13 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 14 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 15 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 16 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 17 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 18 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 19 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 20 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 21 TRT01A Placebo OCMQ01NAM Erectile Dysfunction AEDECOD + 22 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 23 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 24 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD + 25 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD + variable_level context stat_name stat_label stat + 1 Placebo tabulate n n 6 + 2 Placebo tabulate N N 29 + 3 Placebo tabulate p % 0.2068966 + 4 Xanomeline High Dose tabulate n n 12 + 5 Xanomeline High Dose tabulate N N 29 + 6 Xanomeline High Dose tabulate p % 0.4137931 + 7 Xanomeline Low Dose tabulate n n 11 + 8 Xanomeline Low Dose tabulate N N 29 + 9 Xanomeline Low Dose tabulate p % 0.3793103 + 10 APPLICATION SITE ERYTHEMA hierarchical n n 0 + 11 APPLICATION SITE ERYTHEMA hierarchical N N 6 + 12 APPLICATION SITE ERYTHEMA hierarchical p % 0 + 13 APPLICATION SITE ERYTHEMA hierarchical n n 6 + 14 APPLICATION SITE ERYTHEMA hierarchical N N 12 + 15 APPLICATION SITE ERYTHEMA hierarchical p % 0.5 + 16 APPLICATION SITE ERYTHEMA hierarchical n n 8 + 17 APPLICATION SITE ERYTHEMA hierarchical N N 11 + 18 APPLICATION SITE ERYTHEMA hierarchical p % 0.7272727 + 19 COLD SWEAT hierarchical n n 1 + 20 COLD SWEAT hierarchical N N 6 + 21 COLD SWEAT hierarchical p % 0.1666667 + 22 COLD SWEAT hierarchical n n 0 + 23 COLD SWEAT hierarchical N N 12 + 24 COLD SWEAT hierarchical p % 0 + 25 COLD SWEAT hierarchical n n 0 + stat_fmt + 1 6 + 2 29 + 3 20.7 + 4 12 + 5 29 + 6 41.4 + 7 11 + 8 29 + 9 37.9 + 10 0 + 11 6 + 12 0 + 13 6 + 14 12 + 15 50 + 16 8 + 17 11 + 18 73 + 19 1 + 20 6 + 21 17 + 22 0 + 23 12 + 24 0 + 25 0 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_34.md b/tests/testthat/_snaps/fda-table_34.md index 2ba67103..642cd8dc 100644 --- a/tests/testthat/_snaps/fda-table_34.md +++ b/tests/testthat/_snaps/fda-table_34.md @@ -29,32 +29,58 @@ 23 TRT01A Xanomeline High Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD 24 TRT01A Xanomeline High Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD 25 TRT01A Xanomeline Low Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD - variable_level context stat_name stat_label stat stat_fmt - 1 Placebo tabulate n n 9 9 - 2 Placebo tabulate N N 33 33 - 3 Placebo tabulate p % 0.2727273 27.3 - 4 Xanomeline High Dose tabulate n n 13 13 - 5 Xanomeline High Dose tabulate N N 33 33 - 6 Xanomeline High Dose tabulate p % 0.3939394 39.4 - 7 Xanomeline Low Dose tabulate n n 11 11 - 8 Xanomeline Low Dose tabulate N N 33 33 - 9 Xanomeline Low Dose tabulate p % 0.3333333 33.3 - 10 1 hierarchical n n 2 2 - 11 1 hierarchical N N 9 9 - 12 1 hierarchical p % 0.2222222 22 - 13 1 hierarchical n n 1 1 - 14 1 hierarchical N N 13 13 - 15 1 hierarchical p % 0.07692308 7.7 - 16 1 hierarchical n n 1 1 - 17 1 hierarchical N N 11 11 - 18 1 hierarchical p % 0.09090909 9.1 - 19 2 hierarchical n n 0 0 - 20 2 hierarchical N N 9 9 - 21 2 hierarchical p % 0 0 - 22 2 hierarchical n n 2 2 - 23 2 hierarchical N N 13 13 - 24 2 hierarchical p % 0.1538462 15 - 25 2 hierarchical n n 1 1 + variable_level context stat_name stat_label stat + 1 Placebo tabulate n n 9 + 2 Placebo tabulate N N 33 + 3 Placebo tabulate p % 0.2727273 + 4 Xanomeline High Dose tabulate n n 13 + 5 Xanomeline High Dose tabulate N N 33 + 6 Xanomeline High Dose tabulate p % 0.3939394 + 7 Xanomeline Low Dose tabulate n n 11 + 8 Xanomeline Low Dose tabulate N N 33 + 9 Xanomeline Low Dose tabulate p % 0.3333333 + 10 APPLICATION SITE IRRITATION hierarchical n n 2 + 11 APPLICATION SITE IRRITATION hierarchical N N 9 + 12 APPLICATION SITE IRRITATION hierarchical p % 0.2222222 + 13 APPLICATION SITE IRRITATION hierarchical n n 1 + 14 APPLICATION SITE IRRITATION hierarchical N N 13 + 15 APPLICATION SITE IRRITATION hierarchical p % 0.07692308 + 16 APPLICATION SITE IRRITATION hierarchical n n 1 + 17 APPLICATION SITE IRRITATION hierarchical N N 11 + 18 APPLICATION SITE IRRITATION hierarchical p % 0.09090909 + 19 APPLICATION SITE PRURITUS hierarchical n n 0 + 20 APPLICATION SITE PRURITUS hierarchical N N 9 + 21 APPLICATION SITE PRURITUS hierarchical p % 0 + 22 APPLICATION SITE PRURITUS hierarchical n n 2 + 23 APPLICATION SITE PRURITUS hierarchical N N 13 + 24 APPLICATION SITE PRURITUS hierarchical p % 0.1538462 + 25 APPLICATION SITE PRURITUS hierarchical n n 1 + stat_fmt + 1 9 + 2 33 + 3 27.3 + 4 13 + 5 33 + 6 39.4 + 7 11 + 8 33 + 9 33.3 + 10 2 + 11 9 + 12 22 + 13 1 + 14 13 + 15 7.7 + 16 1 + 17 11 + 18 9.1 + 19 0 + 20 9 + 21 0 + 22 2 + 23 13 + 24 15 + 25 1 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_44.md b/tests/testthat/_snaps/fda-table_44.md index 77b1dbce..a71db3fb 100644 --- a/tests/testthat/_snaps/fda-table_44.md +++ b/tests/testthat/_snaps/fda-table_44.md @@ -29,32 +29,58 @@ 23 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD 24 TRT01A Xanomeline High Dose OCMQ01NAM Erectile Dysfunction AEDECOD 25 TRT01A Xanomeline Low Dose OCMQ01NAM Erectile Dysfunction AEDECOD - variable_level context stat_name stat_label stat stat_fmt - 1 Placebo tabulate n n 3 3 - 2 Placebo tabulate N N 18 18 - 3 Placebo tabulate p % 0.1666667 16.7 - 4 Xanomeline High Dose tabulate n n 8 8 - 5 Xanomeline High Dose tabulate N N 18 18 - 6 Xanomeline High Dose tabulate p % 0.4444444 44.4 - 7 Xanomeline Low Dose tabulate n n 7 7 - 8 Xanomeline Low Dose tabulate N N 18 18 - 9 Xanomeline Low Dose tabulate p % 0.3888889 38.9 - 10 1 hierarchical n n 0 0 - 11 1 hierarchical N N 3 3 - 12 1 hierarchical p % 0 0 - 13 1 hierarchical n n 3 3 - 14 1 hierarchical N N 8 8 - 15 1 hierarchical p % 0.375 38 - 16 1 hierarchical n n 3 3 - 17 1 hierarchical N N 7 7 - 18 1 hierarchical p % 0.4285714 43 - 19 2 hierarchical n n 1 1 - 20 2 hierarchical N N 3 3 - 21 2 hierarchical p % 0.3333333 33 - 22 2 hierarchical n n 3 3 - 23 2 hierarchical N N 8 8 - 24 2 hierarchical p % 0.375 38 - 25 2 hierarchical n n 0 0 + variable_level context stat_name stat_label stat + 1 Placebo tabulate n n 3 + 2 Placebo tabulate N N 18 + 3 Placebo tabulate p % 0.1666667 + 4 Xanomeline High Dose tabulate n n 8 + 5 Xanomeline High Dose tabulate N N 18 + 6 Xanomeline High Dose tabulate p % 0.4444444 + 7 Xanomeline Low Dose tabulate n n 7 + 8 Xanomeline Low Dose tabulate N N 18 + 9 Xanomeline Low Dose tabulate p % 0.3888889 + 10 APPLICATION SITE ERYTHEMA hierarchical n n 0 + 11 APPLICATION SITE ERYTHEMA hierarchical N N 3 + 12 APPLICATION SITE ERYTHEMA hierarchical p % 0 + 13 APPLICATION SITE ERYTHEMA hierarchical n n 3 + 14 APPLICATION SITE ERYTHEMA hierarchical N N 8 + 15 APPLICATION SITE ERYTHEMA hierarchical p % 0.375 + 16 APPLICATION SITE ERYTHEMA hierarchical n n 3 + 17 APPLICATION SITE ERYTHEMA hierarchical N N 7 + 18 APPLICATION SITE ERYTHEMA hierarchical p % 0.4285714 + 19 COUGH hierarchical n n 1 + 20 COUGH hierarchical N N 3 + 21 COUGH hierarchical p % 0.3333333 + 22 COUGH hierarchical n n 3 + 23 COUGH hierarchical N N 8 + 24 COUGH hierarchical p % 0.375 + 25 COUGH hierarchical n n 0 + stat_fmt + 1 3 + 2 18 + 3 16.7 + 4 8 + 5 18 + 6 44.4 + 7 7 + 8 18 + 9 38.9 + 10 0 + 11 3 + 12 0 + 13 3 + 14 8 + 15 38 + 16 3 + 17 7 + 18 43 + 19 1 + 20 3 + 21 33 + 22 3 + 23 8 + 24 38 + 25 0 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_45.md b/tests/testthat/_snaps/fda-table_45.md index 1dfb0830..dd24a6fa 100644 --- a/tests/testthat/_snaps/fda-table_45.md +++ b/tests/testthat/_snaps/fda-table_45.md @@ -29,32 +29,58 @@ 23 TRT01A Xanomeline High Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD 24 TRT01A Xanomeline High Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD 25 TRT01A Xanomeline Low Dose OCMQ01NAM Abnormal Uterine Bleeding AEDECOD - variable_level context stat_name stat_label stat stat_fmt - 1 Placebo tabulate n n 7 7 - 2 Placebo tabulate N N 40 40 - 3 Placebo tabulate p % 0.175 17.5 - 4 Xanomeline High Dose tabulate n n 13 13 - 5 Xanomeline High Dose tabulate N N 40 40 - 6 Xanomeline High Dose tabulate p % 0.325 32.5 - 7 Xanomeline Low Dose tabulate n n 20 20 - 8 Xanomeline Low Dose tabulate N N 40 40 - 9 Xanomeline Low Dose tabulate p % 0.5 50.0 - 10 1 hierarchical n n 1 1 - 11 1 hierarchical N N 7 7 - 12 1 hierarchical p % 0.1428571 14 - 13 1 hierarchical n n 1 1 - 14 1 hierarchical N N 13 13 - 15 1 hierarchical p % 0.07692308 7.7 - 16 1 hierarchical n n 1 1 - 17 1 hierarchical N N 20 20 - 18 1 hierarchical p % 0.05 5.0 - 19 2 hierarchical n n 0 0 - 20 2 hierarchical N N 7 7 - 21 2 hierarchical p % 0 0 - 22 2 hierarchical n n 3 3 - 23 2 hierarchical N N 13 13 - 24 2 hierarchical p % 0.2307692 23 - 25 2 hierarchical n n 2 2 + variable_level context stat_name stat_label stat + 1 Placebo tabulate n n 7 + 2 Placebo tabulate N N 40 + 3 Placebo tabulate p % 0.175 + 4 Xanomeline High Dose tabulate n n 13 + 5 Xanomeline High Dose tabulate N N 40 + 6 Xanomeline High Dose tabulate p % 0.325 + 7 Xanomeline Low Dose tabulate n n 20 + 8 Xanomeline Low Dose tabulate N N 40 + 9 Xanomeline Low Dose tabulate p % 0.5 + 10 APPLICATION SITE IRRITATION hierarchical n n 1 + 11 APPLICATION SITE IRRITATION hierarchical N N 7 + 12 APPLICATION SITE IRRITATION hierarchical p % 0.1428571 + 13 APPLICATION SITE IRRITATION hierarchical n n 1 + 14 APPLICATION SITE IRRITATION hierarchical N N 13 + 15 APPLICATION SITE IRRITATION hierarchical p % 0.07692308 + 16 APPLICATION SITE IRRITATION hierarchical n n 1 + 17 APPLICATION SITE IRRITATION hierarchical N N 20 + 18 APPLICATION SITE IRRITATION hierarchical p % 0.05 + 19 APPLICATION SITE PRURITUS hierarchical n n 0 + 20 APPLICATION SITE PRURITUS hierarchical N N 7 + 21 APPLICATION SITE PRURITUS hierarchical p % 0 + 22 APPLICATION SITE PRURITUS hierarchical n n 3 + 23 APPLICATION SITE PRURITUS hierarchical N N 13 + 24 APPLICATION SITE PRURITUS hierarchical p % 0.2307692 + 25 APPLICATION SITE PRURITUS hierarchical n n 2 + stat_fmt + 1 7 + 2 40 + 3 17.5 + 4 13 + 5 40 + 6 32.5 + 7 20 + 8 40 + 9 50.0 + 10 1 + 11 7 + 12 14 + 13 1 + 14 13 + 15 7.7 + 16 1 + 17 20 + 18 5.0 + 19 0 + 20 7 + 21 0 + 22 3 + 23 13 + 24 23 + 25 2 fmt_fun 1 0 2 0 diff --git a/tests/testthat/_snaps/fda-table_50.md b/tests/testthat/_snaps/fda-table_50.md index c202ee1b..81742624 100644 --- a/tests/testthat/_snaps/fda-table_50.md +++ b/tests/testthat/_snaps/fda-table_50.md @@ -3,58 +3,58 @@ Code as.data.frame(ard[[1]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level variable variable_level context stat_name - 1 NULL TRT01A 1 tabulate n - 2 NULL TRT01A 1 tabulate N - 3 NULL TRT01A 1 tabulate p - 4 NULL TRT01A 2 tabulate n - 5 NULL TRT01A 2 tabulate N - 6 NULL TRT01A 2 tabulate p - 7 NULL TRT01A 3 tabulate n - 8 NULL TRT01A 3 tabulate N - 9 NULL TRT01A 3 tabulate p - 10 TRT01A 1 AESER 1 hierarchical n - 11 TRT01A 1 AESER 1 hierarchical N - 12 TRT01A 1 AESER 1 hierarchical p - 13 TRT01A 2 AESER 1 hierarchical n - 14 TRT01A 2 AESER 1 hierarchical N - 15 TRT01A 2 AESER 1 hierarchical p - 16 TRT01A 3 AESER 1 hierarchical n - 17 TRT01A 3 AESER 1 hierarchical N - 18 TRT01A 3 AESER 1 hierarchical p - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL - stat_label stat stat_fmt - 1 n 86 86 - 2 N 254 254 - 3 % 0.3385827 33.9 - 4 n 72 72 - 5 N 254 254 - 6 % 0.2834646 28.3 - 7 n 96 96 - 8 N 254 254 - 9 % 0.3779528 37.8 - 10 n 0 0 - 11 N 86 86 - 12 % 0 0 - 13 n 1 1 - 14 N 72 72 - 15 % 0.01388889 1.4 - 16 n 2 2 - 17 N 96 96 - 18 % 0.02083333 2.1 - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL + group1 group1_level variable variable_level context + 1 NULL TRT01A Placebo tabulate + 2 NULL TRT01A Placebo tabulate + 3 NULL TRT01A Placebo tabulate + 4 NULL TRT01A Xanomeline High Dose tabulate + 5 NULL TRT01A Xanomeline High Dose tabulate + 6 NULL TRT01A Xanomeline High Dose tabulate + 7 NULL TRT01A Xanomeline Low Dose tabulate + 8 NULL TRT01A Xanomeline Low Dose tabulate + 9 NULL TRT01A Xanomeline Low Dose tabulate + 10 TRT01A Placebo AESER Any SAE, n(%) hierarchical + 11 TRT01A Placebo AESER Any SAE, n(%) hierarchical + 12 TRT01A Placebo AESER Any SAE, n(%) hierarchical + 13 TRT01A Xanomeline High Dose AESER Any SAE, n(%) hierarchical + 14 TRT01A Xanomeline High Dose AESER Any SAE, n(%) hierarchical + 15 TRT01A Xanomeline High Dose AESER Any SAE, n(%) hierarchical + 16 TRT01A Xanomeline Low Dose AESER Any SAE, n(%) hierarchical + 17 TRT01A Xanomeline Low Dose AESER Any SAE, n(%) hierarchical + 18 TRT01A Xanomeline Low Dose AESER Any SAE, n(%) hierarchical + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL + stat_name stat_label stat stat_fmt + 1 n n 86 86 + 2 N N 254 254 + 3 p % 0.3385827 33.9 + 4 n n 72 72 + 5 N N 254 254 + 6 p % 0.2834646 28.3 + 7 n n 96 96 + 8 N N 254 254 + 9 p % 0.3779528 37.8 + 10 n n 0 0 + 11 N N 86 86 + 12 p % 0 0 + 13 n n 1 1 + 14 N N 72 72 + 15 p % 0.01388889 1.4 + 16 n n 2 2 + 17 N N 96 96 + 18 p % 0.02083333 2.1 + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL fmt_fun 1 0 2 0 @@ -113,58 +113,58 @@ Code as.data.frame(ard[[2]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable variable_level context - 1 NULL NULL TRT01A 1 tabulate - 2 NULL NULL TRT01A 1 tabulate - 3 NULL NULL TRT01A 1 tabulate - 4 NULL NULL TRT01A 2 tabulate - 5 NULL NULL TRT01A 2 tabulate - 6 NULL NULL TRT01A 2 tabulate - 7 NULL NULL TRT01A 3 tabulate - 8 NULL NULL TRT01A 3 tabulate - 9 NULL NULL TRT01A 3 tabulate - 10 TRT01A 1 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 11 TRT01A 1 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 12 TRT01A 1 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 13 TRT01A 2 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 14 TRT01A 2 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 15 TRT01A 2 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 16 TRT01A 3 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 17 TRT01A 3 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 18 TRT01A 3 SEXGR Sex, n (%) SEXGR1 1 hierarchical - 19 TRT01A 1 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 20 TRT01A 1 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 21 TRT01A 1 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 22 TRT01A 2 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 23 TRT01A 2 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 24 TRT01A 2 SEXGR Sex, n (%) SEXGR1 2 hierarchical - 25 TRT01A 3 SEXGR Sex, n (%) SEXGR1 2 hierarchical - stat_name stat_label stat stat_fmt - 1 n n 0 0 - 2 N N 3 3 - 3 p % 0 0.0 - 4 n n 1 1 - 5 N N 3 3 - 6 p % 0.3333333 33.3 - 7 n n 2 2 - 8 N N 3 3 - 9 p % 0.6666667 66.7 - 10 n n 0 0 - 11 N N 0 0 - 12 p % NaN NA - 13 n n 1 1 - 14 N N 1 1 - 15 p % 1 100 - 16 n n 1 1 - 17 N N 2 2 - 18 p % 0.5 50 - 19 n n 0 0 - 20 N N 0 0 - 21 p % NaN NA - 22 n n 0 0 - 23 N N 1 1 - 24 p % 0 0 - 25 n n 1 1 + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 11 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 12 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 13 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 14 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 15 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 16 TRT01A Xanomeline Low Dose SEXGR Sex, n (%) SEXGR1 + 17 TRT01A Xanomeline Low Dose SEXGR Sex, n (%) SEXGR1 + 18 TRT01A Xanomeline Low Dose SEXGR Sex, n (%) SEXGR1 + 19 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 20 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 21 TRT01A Placebo SEXGR Sex, n (%) SEXGR1 + 22 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 23 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 24 TRT01A Xanomeline High Dose SEXGR Sex, n (%) SEXGR1 + 25 TRT01A Xanomeline Low Dose SEXGR Sex, n (%) SEXGR1 + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 0 0 + 2 Placebo tabulate N N 3 3 + 3 Placebo tabulate p % 0 0.0 + 4 Xanomeline High Dose tabulate n n 1 1 + 5 Xanomeline High Dose tabulate N N 3 3 + 6 Xanomeline High Dose tabulate p % 0.3333333 33.3 + 7 Xanomeline Low Dose tabulate n n 2 2 + 8 Xanomeline Low Dose tabulate N N 3 3 + 9 Xanomeline Low Dose tabulate p % 0.6666667 66.7 + 10 F hierarchical n n 0 0 + 11 F hierarchical N N 0 0 + 12 F hierarchical p % NaN NA + 13 F hierarchical n n 1 1 + 14 F hierarchical N N 1 1 + 15 F hierarchical p % 1 100 + 16 F hierarchical n n 1 1 + 17 F hierarchical N N 2 2 + 18 F hierarchical p % 0.5 50 + 19 M hierarchical n n 0 0 + 20 M hierarchical N N 0 0 + 21 M hierarchical p % NaN NA + 22 M hierarchical n n 0 0 + 23 M hierarchical N N 1 1 + 24 M hierarchical p % 0 0 + 25 M hierarchical n n 1 1 fmt_fun 1 0 2 0 @@ -223,58 +223,58 @@ Code as.data.frame(ard[[3]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable variable_level - 1 NULL NULL TRT01A 1 - 2 NULL NULL TRT01A 1 - 3 NULL NULL TRT01A 1 - 4 NULL NULL TRT01A 2 - 5 NULL NULL TRT01A 2 - 6 NULL NULL TRT01A 2 - 7 NULL NULL TRT01A 3 - 8 NULL NULL TRT01A 3 - 9 NULL NULL TRT01A 3 - 10 TRT01A 1 AGEGR Age group, years, n(%) AGEGR1 1 - 11 TRT01A 1 AGEGR Age group, years, n(%) AGEGR1 1 - 12 TRT01A 1 AGEGR Age group, years, n(%) AGEGR1 1 - 13 TRT01A 2 AGEGR Age group, years, n(%) AGEGR1 1 - 14 TRT01A 2 AGEGR Age group, years, n(%) AGEGR1 1 - 15 TRT01A 2 AGEGR Age group, years, n(%) AGEGR1 1 - 16 TRT01A 3 AGEGR Age group, years, n(%) AGEGR1 1 - 17 TRT01A 3 AGEGR Age group, years, n(%) AGEGR1 1 - 18 TRT01A 3 AGEGR Age group, years, n(%) AGEGR1 1 - NA NULL NULL NULL - NA.1 NULL NULL NULL - NA.2 NULL NULL NULL - NA.3 NULL NULL NULL - NA.4 NULL NULL NULL - NA.5 NULL NULL NULL - NA.6 NULL NULL NULL - context stat_name stat_label stat stat_fmt - 1 tabulate n n 0 0 - 2 tabulate N N 3 3 - 3 tabulate p % 0 0.0 - 4 tabulate n n 1 1 - 5 tabulate N N 3 3 - 6 tabulate p % 0.3333333 33.3 - 7 tabulate n n 2 2 - 8 tabulate N N 3 3 - 9 tabulate p % 0.6666667 66.7 - 10 hierarchical n n 0 0 - 11 hierarchical N N 0 0 - 12 hierarchical p % NaN NA - 13 hierarchical n n 1 1 - 14 hierarchical N N 1 1 - 15 hierarchical p % 1 100 - 16 hierarchical n n 2 2 - 17 hierarchical N N 2 2 - 18 hierarchical p % 1 100 - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A Placebo AGEGR Age group, years, n(%) AGEGR1 + 11 TRT01A Placebo AGEGR Age group, years, n(%) AGEGR1 + 12 TRT01A Placebo AGEGR Age group, years, n(%) AGEGR1 + 13 TRT01A Xanomeline High Dose AGEGR Age group, years, n(%) AGEGR1 + 14 TRT01A Xanomeline High Dose AGEGR Age group, years, n(%) AGEGR1 + 15 TRT01A Xanomeline High Dose AGEGR Age group, years, n(%) AGEGR1 + 16 TRT01A Xanomeline Low Dose AGEGR Age group, years, n(%) AGEGR1 + 17 TRT01A Xanomeline Low Dose AGEGR Age group, years, n(%) AGEGR1 + 18 TRT01A Xanomeline Low Dose AGEGR Age group, years, n(%) AGEGR1 + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 0 0 + 2 Placebo tabulate N N 3 3 + 3 Placebo tabulate p % 0 0.0 + 4 Xanomeline High Dose tabulate n n 1 1 + 5 Xanomeline High Dose tabulate N N 3 3 + 6 Xanomeline High Dose tabulate p % 0.3333333 33.3 + 7 Xanomeline Low Dose tabulate n n 2 2 + 8 Xanomeline Low Dose tabulate N N 3 3 + 9 Xanomeline Low Dose tabulate p % 0.6666667 66.7 + 10 >64 hierarchical n n 0 0 + 11 >64 hierarchical N N 0 0 + 12 >64 hierarchical p % NaN NA + 13 >64 hierarchical n n 1 1 + 14 >64 hierarchical N N 1 1 + 15 >64 hierarchical p % 1 100 + 16 >64 hierarchical n n 2 2 + 17 >64 hierarchical N N 2 2 + 18 >64 hierarchical p % 1 100 + NA NULL NULL NULL + NA.1 NULL NULL NULL + NA.2 NULL NULL NULL + NA.3 NULL NULL NULL + NA.4 NULL NULL NULL + NA.5 NULL NULL NULL + NA.6 NULL NULL NULL fmt_fun 1 0 2 0 @@ -333,58 +333,58 @@ Code as.data.frame(ard[[4]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable variable_level - 1 NULL NULL TRT01A 1 - 2 NULL NULL TRT01A 1 - 3 NULL NULL TRT01A 1 - 4 NULL NULL TRT01A 2 - 5 NULL NULL TRT01A 2 - 6 NULL NULL TRT01A 2 - 7 NULL NULL TRT01A 3 - 8 NULL NULL TRT01A 3 - 9 NULL NULL TRT01A 3 - 10 TRT01A 1 RACEGR Race, n(%) RACEGR1 1 - 11 TRT01A 1 RACEGR Race, n(%) RACEGR1 1 - 12 TRT01A 1 RACEGR Race, n(%) RACEGR1 1 - 13 TRT01A 2 RACEGR Race, n(%) RACEGR1 1 - 14 TRT01A 2 RACEGR Race, n(%) RACEGR1 1 - 15 TRT01A 2 RACEGR Race, n(%) RACEGR1 1 - 16 TRT01A 3 RACEGR Race, n(%) RACEGR1 1 - 17 TRT01A 3 RACEGR Race, n(%) RACEGR1 1 - 18 TRT01A 3 RACEGR Race, n(%) RACEGR1 1 - NA NULL NULL NULL - NA.1 NULL NULL NULL - NA.2 NULL NULL NULL - NA.3 NULL NULL NULL - NA.4 NULL NULL NULL - NA.5 NULL NULL NULL - NA.6 NULL NULL NULL - context stat_name stat_label stat stat_fmt - 1 tabulate n n 0 0 - 2 tabulate N N 3 3 - 3 tabulate p % 0 0.0 - 4 tabulate n n 1 1 - 5 tabulate N N 3 3 - 6 tabulate p % 0.3333333 33.3 - 7 tabulate n n 2 2 - 8 tabulate N N 3 3 - 9 tabulate p % 0.6666667 66.7 - 10 hierarchical n n 0 0 - 11 hierarchical N N 0 0 - 12 hierarchical p % NaN NA - 13 hierarchical n n 1 1 - 14 hierarchical N N 1 1 - 15 hierarchical p % 1 100 - 16 hierarchical n n 2 2 - 17 hierarchical N N 2 2 - 18 hierarchical p % 1 100 - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A Placebo RACEGR Race, n(%) RACEGR1 + 11 TRT01A Placebo RACEGR Race, n(%) RACEGR1 + 12 TRT01A Placebo RACEGR Race, n(%) RACEGR1 + 13 TRT01A Xanomeline High Dose RACEGR Race, n(%) RACEGR1 + 14 TRT01A Xanomeline High Dose RACEGR Race, n(%) RACEGR1 + 15 TRT01A Xanomeline High Dose RACEGR Race, n(%) RACEGR1 + 16 TRT01A Xanomeline Low Dose RACEGR Race, n(%) RACEGR1 + 17 TRT01A Xanomeline Low Dose RACEGR Race, n(%) RACEGR1 + 18 TRT01A Xanomeline Low Dose RACEGR Race, n(%) RACEGR1 + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 0 0 + 2 Placebo tabulate N N 3 3 + 3 Placebo tabulate p % 0 0.0 + 4 Xanomeline High Dose tabulate n n 1 1 + 5 Xanomeline High Dose tabulate N N 3 3 + 6 Xanomeline High Dose tabulate p % 0.3333333 33.3 + 7 Xanomeline Low Dose tabulate n n 2 2 + 8 Xanomeline Low Dose tabulate N N 3 3 + 9 Xanomeline Low Dose tabulate p % 0.6666667 66.7 + 10 White hierarchical n n 0 0 + 11 White hierarchical N N 0 0 + 12 White hierarchical p % NaN NA + 13 White hierarchical n n 1 1 + 14 White hierarchical N N 1 1 + 15 White hierarchical p % 1 100 + 16 White hierarchical n n 2 2 + 17 White hierarchical N N 2 2 + 18 White hierarchical p % 1 100 + NA NULL NULL NULL + NA.1 NULL NULL NULL + NA.2 NULL NULL NULL + NA.3 NULL NULL NULL + NA.4 NULL NULL NULL + NA.5 NULL NULL NULL + NA.6 NULL NULL NULL fmt_fun 1 0 2 0 @@ -443,58 +443,58 @@ Code as.data.frame(ard[[5]]$tbl_hierarchical)[1:25, ] Output - group1 group1_level group2 group2_level variable variable_level - 1 NULL NULL TRT01A 1 - 2 NULL NULL TRT01A 1 - 3 NULL NULL TRT01A 1 - 4 NULL NULL TRT01A 2 - 5 NULL NULL TRT01A 2 - 6 NULL NULL TRT01A 2 - 7 NULL NULL TRT01A 3 - 8 NULL NULL TRT01A 3 - 9 NULL NULL TRT01A 3 - 10 TRT01A 1 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 11 TRT01A 1 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 12 TRT01A 1 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 13 TRT01A 2 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 14 TRT01A 2 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 15 TRT01A 2 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 16 TRT01A 3 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 17 TRT01A 3 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - 18 TRT01A 3 ETHNICGR Ethnicity, n(%) ETHNICGR1 1 - NA NULL NULL NULL - NA.1 NULL NULL NULL - NA.2 NULL NULL NULL - NA.3 NULL NULL NULL - NA.4 NULL NULL NULL - NA.5 NULL NULL NULL - NA.6 NULL NULL NULL - context stat_name stat_label stat stat_fmt - 1 tabulate n n 0 0 - 2 tabulate N N 3 3 - 3 tabulate p % 0 0.0 - 4 tabulate n n 1 1 - 5 tabulate N N 3 3 - 6 tabulate p % 0.3333333 33.3 - 7 tabulate n n 2 2 - 8 tabulate N N 3 3 - 9 tabulate p % 0.6666667 66.7 - 10 hierarchical n n 0 0 - 11 hierarchical N N 0 0 - 12 hierarchical p % NaN NA - 13 hierarchical n n 1 1 - 14 hierarchical N N 1 1 - 15 hierarchical p % 1 100 - 16 hierarchical n n 2 2 - 17 hierarchical N N 2 2 - 18 hierarchical p % 1 100 - NA NULL NULL - NA.1 NULL NULL - NA.2 NULL NULL - NA.3 NULL NULL - NA.4 NULL NULL - NA.5 NULL NULL - NA.6 NULL NULL + group1 group1_level group2 group2_level variable + 1 NULL NULL TRT01A + 2 NULL NULL TRT01A + 3 NULL NULL TRT01A + 4 NULL NULL TRT01A + 5 NULL NULL TRT01A + 6 NULL NULL TRT01A + 7 NULL NULL TRT01A + 8 NULL NULL TRT01A + 9 NULL NULL TRT01A + 10 TRT01A Placebo ETHNICGR Ethnicity, n(%) ETHNICGR1 + 11 TRT01A Placebo ETHNICGR Ethnicity, n(%) ETHNICGR1 + 12 TRT01A Placebo ETHNICGR Ethnicity, n(%) ETHNICGR1 + 13 TRT01A Xanomeline High Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + 14 TRT01A Xanomeline High Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + 15 TRT01A Xanomeline High Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + 16 TRT01A Xanomeline Low Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + 17 TRT01A Xanomeline Low Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + 18 TRT01A Xanomeline Low Dose ETHNICGR Ethnicity, n(%) ETHNICGR1 + NA NULL NULL + NA.1 NULL NULL + NA.2 NULL NULL + NA.3 NULL NULL + NA.4 NULL NULL + NA.5 NULL NULL + NA.6 NULL NULL + variable_level context stat_name stat_label stat stat_fmt + 1 Placebo tabulate n n 0 0 + 2 Placebo tabulate N N 3 3 + 3 Placebo tabulate p % 0 0.0 + 4 Xanomeline High Dose tabulate n n 1 1 + 5 Xanomeline High Dose tabulate N N 3 3 + 6 Xanomeline High Dose tabulate p % 0.3333333 33.3 + 7 Xanomeline Low Dose tabulate n n 2 2 + 8 Xanomeline Low Dose tabulate N N 3 3 + 9 Xanomeline Low Dose tabulate p % 0.6666667 66.7 + 10 WHITE hierarchical n n 0 0 + 11 WHITE hierarchical N N 0 0 + 12 WHITE hierarchical p % NaN NA + 13 WHITE hierarchical n n 1 1 + 14 WHITE hierarchical N N 1 1 + 15 WHITE hierarchical p % 1 100 + 16 WHITE hierarchical n n 2 2 + 17 WHITE hierarchical N N 2 2 + 18 WHITE hierarchical p % 1 100 + NA NULL NULL NULL + NA.1 NULL NULL NULL + NA.2 NULL NULL NULL + NA.3 NULL NULL NULL + NA.4 NULL NULL NULL + NA.5 NULL NULL NULL + NA.6 NULL NULL NULL fmt_fun 1 0 2 0 diff --git a/tests/testthat/test-custom.R b/tests/testthat/test-custom.R index afd17b08..ba6aaa92 100644 --- a/tests/testthat/test-custom.R +++ b/tests/testthat/test-custom.R @@ -28,8 +28,8 @@ test_that("custom table works", { ) # build AET02 ------------------------------------------------------------------ - expect_silent( - df_aet02 |> + expect_no_warning( + df_aet02 |> tbl_hierarchical_rate_and_count( by = "TRT01A", variables = c(AEBODSYS, AEDECOD), From 4ffa7667f5e27ae3bdfee1961fbbeafc07226140 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Llu=C3=ADs=20Revilla?= Date: Fri, 19 Jun 2026 17:05:11 +0200 Subject: [PATCH 7/7] Remove unnecessary field --- DESCRIPTION | 7 ------- 1 file changed, 7 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index ed9c115c..ce94de86 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -34,13 +34,6 @@ Suggests: testthat (>= 3.3), tidyr (>= 1.3), withr (>= 3.0.2) -Remotes: - insightsengineering/cards, - insightsengineering/cardx, - insightsengineering/crane, - ddsjoberg/gtsummary, - pharmaverse/pharmaverseadam, - insightsengineering/random.cdisc.data Config/testthat/edition: 3 Encoding: UTF-8 Language: en-US