Merge branch 'main' into 1069_lt10_format@main

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.0.9008
-Date: 2023-10-02
+Version: 0.9.1.9000
+Date: 2023-10-04
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "[email protected]", role = "aut"),
@@ -21,7 +21,7 @@ URL: https://github.com/insightsengineering/tern
 BugReports: https://github.com/insightsengineering/tern/issues
 Depends:
     R (>= 3.6),
-    rtables (>= 0.6.3)
+    rtables (>= 0.6.4)
 Imports:
     broom,
     car,
@@ -30,7 +30,7 @@ Imports:
     dplyr,
     emmeans (>= 1.4.5),
     forcats (>= 1.0.0),
-    formatters (>= 0.5.2),
+    formatters (>= 0.5.3),
     ggplot2 (>= 3.4.0),
     grid,
     gridExtra,

NEWS.md

@@ -1,4 +1,6 @@
-# tern 0.9.0.9008
+# tern 0.9.1.9000
+
+# tern 0.9.1
 ### New Features
 * Added `imputation_rule` function to apply imputation rule to data.
 * Added new format function `format_sigfig` to allow for numeric value formatting by a specified number of significant figures.

tests/testthat/_snaps/summarize_glm_count.md

@@ -129,16 +129,6 @@
       Intervals are back-transformed from the log scale 
       
 
----
-
-    Code
-      res
-    Output
-                     rate asymp.LCL asymp.UCL            ARM
-      A: Drug X      3.07  2.836527   3.32269      A: Drug X
-      B: Placebo     3.07  2.836527   3.32269     B: Placebo
-      C: Combination 3.07  2.836527   3.32269 C: Combination
-
 # s_glm_count works with healthy input
 
     Code
@@ -148,12 +138,12 @@
       [1] 73
       
       $rate
-      [1] 3.486005
+      [1] 14.11838
       attr(,"label")
       [1] "Adjusted Rate"
       
       $rate_ci
-      [1] 3.047667 3.987387
+      [1] 11.81189 16.87525
       attr(,"label")
       [1] "95% CI"
       
@@ -182,12 +172,12 @@
       [1] 73
       
       $rate
-      [1] 3.486005
+      [1] 14.11838
       attr(,"label")
       [1] "Adjusted Rate"
       
       $rate_ci
-      [1] 3.047667 3.987387
+      [1] 11.81189 16.87525
       attr(,"label")
       [1] "95% CI"
       

tests/testthat/test-summarize_glm_count.R

@@ -188,15 +188,14 @@ testthat::test_that("h_ppmeans works with healthy input", {
   testthat::expect_snapshot(fits2)
 
   # XXX ppmeans fails snapshot diff in integration tests
-  result <- h_ppmeans(
-    obj = fits$glm_fit,
-    .df_row = anl,
-    arm = "ARM",
-    conf_level = 0.95
+  testthat::expect_silent(
+    result <- h_ppmeans(
+      obj = fits$glm_fit,
+      .df_row = anl,
+      arm = "ARM",
+      conf_level = 0.95
+    ) # diff
   )
-
-  res <- testthat::expect_silent(result)
-  testthat::expect_snapshot(res) # diff
 })
 
 testthat::test_that("s_glm_count works with healthy input", {

tests/testthat/test-utils_default_stats_formats_labels.R

@@ -72,8 +72,6 @@ testthat::test_that("get_formats_from_stats works as expected", {
   res <- testthat::expect_silent(get_formats_from_stats(sts))
   testthat::expect_equal(names(res), sts)
   testthat::expect_equal(res[[1]], "xx.")
-  testthat::expect_equal(res[[2]], format_count_fraction_fixed_dp)
-  testthat::expect_equal(res[[3]], format_fraction_fixed_dp)
 
   testthat::expect_null(get_formats_from_stats(c("nothing", "n"))[["nothing"]])
 
@@ -151,7 +149,6 @@ testthat::test_that("summary_formats works as expected", {
   result <- summary_formats(type = "counts", include_pval = TRUE)
   testthat::expect_true(all(result[c("n", "count", "n_blq")] == "xx."))
   testthat::expect_identical(result[["pval_counts"]], "x.xxxx | (<0.0001)")
-  expect_identical(result[["count_fraction"]], format_count_fraction)
 })
 
 testthat::test_that("summary_labels works as expected", {