diff --git a/DESCRIPTION b/DESCRIPTION index 6d731c85..c07eff72 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -25,7 +25,7 @@ Depends: R (>= 4.2), rlistings (>= 0.2.10), rtables (>= 0.6.11.9017), - tern (>= 0.9.7.9018) + tern (>= 0.9.9.9003) Imports: pharmaverseadam (>= 1.1.0.9001), random.cdisc.data (>= 0.3.16) @@ -56,4 +56,4 @@ Encoding: UTF-8 Language: en-US LazyData: true Roxygen: list(markdown = TRUE) -RoxygenNote: 7.3.2 +RoxygenNote: 7.3.3 diff --git a/man/scda.test-package.Rd b/man/scda.test-package.Rd index 79eca56e..d2916778 100644 --- a/man/scda.test-package.Rd +++ b/man/scda.test-package.Rd @@ -10,7 +10,7 @@ This package provides a testing suite for templates based on \code{scda} data and \code{tern} analysis methods. } \details{ -To learn mode about the package, check the documentation of \link{tern}. +To learn mode about the package, check the documentation of \link[tern:tern-package]{tern::tern}. } \seealso{ Useful links: diff --git a/tests/testthat/_snaps/table_jnj_tbl1.md b/tests/testthat/_snaps/table_jnj_tbl1.md new file mode 100644 index 00000000..cc8c92e5 --- /dev/null +++ b/tests/testthat/_snaps/table_jnj_tbl1.md @@ -0,0 +1,21 @@ +# DMT01 variant factor with only Missing values + + Code + res + Output + Placebo Screen Failure Xanomeline High Dose Xanomeline Low Dose + (N=86) (N=52) (N=72) (N=96) + —————————————————————————————————————————————————————————————————————————————————————————————————— + Age (yr) + n 86 52 72 96 + Mean (SD) 75.2 (8.6) 75.1 (9.7) 73.8 (7.9) 76.0 (8.1) + Median 76.0 76.0 75.5 78.0 + Min - Max 52.0 - 89.0 50.0 - 89.0 56.0 - 88.0 51.0 - 88.0 + Age Group + n 86 52 72 96 + 18-40 0 0 0 0 + 41-64 14 (16.3%) 9 (17.3%) 11 (15.3%) 8 (8.3%) + >=65 72 (83.7%) 43 (82.7%) 61 (84.7%) 88 (91.7%) + Biomarker 1 Categories + n 0 0 0 0 + diff --git a/tests/testthat/test-table_jnj_tbl1.R b/tests/testthat/test-table_jnj_tbl1.R new file mode 100644 index 00000000..285954d7 --- /dev/null +++ b/tests/testthat/test-table_jnj_tbl1.R @@ -0,0 +1,56 @@ +# extra special case situation to scenario from test-table_dmt01.R +# Tests DMT01 with corner case situation to demonstrate bug in analyze is resolved with empty factor data +# tern@1431-bug-s_summaryfactor +set.seed(1) + +adsl <- pharmaverseadam::adsl +adsl <- adsl %>% + mutate(BMRKR1 = rnorm(nrow(adsl), 3.5, 10)) %>% + mutate(STRATA1 = factor(sample(c("A", "B", "C"), nrow(adsl), TRUE))) + +adsl <- df_explicit_na(adsl) + +adsl <- adsl %>% + mutate( + SEX = factor(case_when( + SEX == "M" ~ "Male", + SEX == "F" ~ "Female", + SEX == "U" ~ "Unknown", + SEX == "UNDIFFERENTIATED" ~ "Undifferentiated" + )), + AGEGR1 = factor( + case_when( + between(AGE, 18, 40) ~ "18-40", + between(AGE, 41, 64) ~ "41-64", + AGE > 64 ~ ">=65" + ), + levels = c("18-40", "41-64", ">=65") + ), + BMRKR1_CAT = NA_character_ + ) %>% + var_relabel( + BMRKR1_CAT = "Biomarker 1 Categories" + ) + +adsl <- df_explicit_na(adsl, na_level = "") + + +testthat::test_that("DMT01 variant factor with only Missing values", { + vars <- c("AGE", "AGEGR1", "BMRKR1_CAT") + var_labels <- c( + "Age (yr)", + "Age Group", + "Biomarker 1 Categories" + ) + + result <- basic_table(show_colcounts = TRUE) %>% + split_cols_by(var = "ACTARM") %>% + analyze_vars( + vars = vars, + var_labels = var_labels + ) %>% + build_table(adsl) + + res <- testthat::expect_silent(result) + testthat::expect_snapshot(res) +})