vbump to 0.9.7, prep for release [skip vbump] (#1372)

close #1281

Author: shajoezhu

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.6.9020
+Version: 0.9.7
 Date: 2025-01-17
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),

NAMESPACE

@@ -318,6 +318,7 @@ importFrom(grid,widthDetails)
 importFrom(magrittr,"%>%")
 importFrom(methods,new)
 importFrom(nestcolor,theme_nest)
+importFrom(rlang,"%||%")
 importFrom(rlang,.data)
 importFrom(stats,complete.cases)
 importFrom(stats,pchisq)

NEWS.md

@@ -1,19 +1,19 @@
-# tern 0.9.6.9020
+# tern 0.9.7
 
 ### Enhancements
 * Added the `denom` parameter to `s_count_cumulative()`, `s_count_missed_doses()`, and `s_count_occurrences_by_grade()`.
 * Added `"N_row"` as an optional input to `denom` in `s_count_occurrences()`.
-* Refactored `a_count_occurrences_by_grade()`, `a_count_patients_with_event()`, and `a_count_patients_with_flags()` to no longer use `make_afun()`.
 * Added `rel_height_plot` parameter to `g_lineplot()` to control the line plot height relative to annotation table height.
-* Updated the `table_font_size` parameter of `g_lineplot()` to control the size of all text in the annotation table, including labels.
 * Added `as_list` parameter to `g_lineplot()` to allow users to return the line plot and annotation table elements as a list instead of stacked for more complex customization.
-* Refactored `summarize_change()` and `count_values()` to work without `make_afun()`.
 * Added vignette "Understanding `tern` functions" for future reference.
-* Refactored `analyze_vars()` and `a_summary()` to take all options from `?rtables::additional_fun_params`.
 * Added to `analyze_vars()` statistical names that are used by `rtables::as_result_df()`.
-* Merged `compare_vars()` into `analyze_vars()` as overlap was significant.
 * Added the possibility to integrate custom statistical functions to default ones in `analyze_vars()`.
-* Reworked `get_labels_from_stats()` to use a named list of levels for each statistic instead of row names.
+* Refactored `analyze_vars()` and `a_summary()` to take all options from `?rtables::additional_fun_params`.
+* Refactored `summarize_change()` and `count_values()` to work without `make_afun()`.
+* Refactored `a_count_occurrences_by_grade()`, `a_count_patients_with_event()`, and `a_count_patients_with_flags()` to no longer use `make_afun()`.
+* Refactored `get_labels_from_stats()` to use a named list of levels for each statistic instead of row names.
+* Updated the `table_font_size` parameter of `g_lineplot()` to control the size of all text in the annotation table, including labels.
+* Merged `compare_vars()` into `analyze_vars()` as overlap was significant.
 
 ### Bug Fixes
 * Fixed bug in `a_summary()` causing non-unique `row_name` values to occur when multiple statistics are selected for count variables.

R/package.R

@@ -11,7 +11,7 @@
 #' @importFrom methods new
 #' @importFrom nestcolor theme_nest
 #' @importFrom Rdpack reprompt
-#' @importFrom rlang .data
+#' @importFrom rlang .data %||%
 #' @importFrom survival coxph strata Surv
 #' @importFrom stats pchisq setNames complete.cases qnorm qt sd
 NULL

tests/testthat/test-bland-altman.R

@@ -95,10 +95,10 @@ testthat::test_that("g_bland_altman works with default settings", {
   )
   conf_level <- 0.9
 
-  withr::with_options(
+  testthat::expect_silent(g_bland_altman_res <- withr::with_options(
     opts_partial_match_old,
-    g_bland_altman <- g_bland_altman(x, y, conf_level = conf_level)
-  )
+    g_bland_altman(x, y, conf_level = conf_level)
+  ))
 
-  expect_snapshot_ggplot(title = "g_bland_altman", fig = g_bland_altman, width = 10, height = 8)
+  expect_snapshot_ggplot(title = "g_bland_altman", fig = g_bland_altman_res, width = 10, height = 8)
 })

tests/testthat/test-g_lineplot.R

@@ -67,9 +67,9 @@ testthat::test_that("g_lineplot maintains factor levels in legend", {
       caption = "caption"
     )
   ))
-
   expect_snapshot_ggplot(title = "g_lineplot_factor_levels", fig = g_lineplot_factor_levels, width = 10, height = 8)
 })
+
 testthat::test_that("g_lineplot does not produce a warning if group_var has >6 levels", {
   set.seed(1)
   adlb$FACTOR7 <- as.factor(sample(1:7, nrow(adlb), replace = TRUE))
@@ -84,7 +84,7 @@ testthat::test_that("g_lineplot does not produce a warning if group_var has >6 l
 })
 
 testthat::test_that("g_lineplot works with facet_var specified", {
-  g_lineplot_facets <- withr::with_options(
+  testthat::expect_silent(g_lineplot_facets <- withr::with_options(
     opts_partial_match_old,
     g_lineplot(
       adlb,
@@ -97,34 +97,34 @@ testthat::test_that("g_lineplot works with facet_var specified", {
       subtitle = "Laboratory Test:",
       caption = "caption"
     )
-  )
+  ))
   expect_snapshot_ggplot(title = "g_lineplot_facets", fig = g_lineplot_facets, width = 10, height = 8)
 })
 
 testthat::test_that("g_lineplot xticks, xlim, and ylim arguments work", {
-  g_lineplot_xticks_by <- withr::with_options(
+  testthat::expect_silent(g_lineplot_xticks_by <- withr::with_options(
     opts_partial_match_old,
     g_lineplot(
       adlb,
       adsl,
       variables = control_lineplot_vars(x = "AVISITN"),
       xticks = 1
     )
-  )
+  ))
   expect_snapshot_ggplot(title = "g_lineplot_xticks_by", fig = g_lineplot_xticks_by, width = 10, height = 8)
 
-  g_lineplot_xticks <- withr::with_options(
+  testthat::expect_silent(g_lineplot_xticks <- withr::with_options(
     opts_partial_match_old,
     g_lineplot(
       adlb,
       adsl,
       variables = control_lineplot_vars(x = "AVISITN"),
       xticks = c(0, 2.5, 5)
     )
-  )
+  ))
   expect_snapshot_ggplot(title = "g_lineplot_xticks", fig = g_lineplot_xticks, width = 10, height = 8)
 
-  g_lineplot_xlim_ylim <- withr::with_options(
+  testthat::expect_silent(g_lineplot_xlim_ylim <- withr::with_options(
     opts_partial_match_old,
     g_lineplot(
       adlb,
@@ -134,7 +134,7 @@ testthat::test_that("g_lineplot xticks, xlim, and ylim arguments work", {
       ylim = c(17, 21),
       xticks = 1:6
     )
-  )
+  ))
   expect_snapshot_ggplot(title = "g_lineplot_xlim_ylim", fig = g_lineplot_xlim_ylim, width = 10, height = 8)
 })