CRAN snapshot tests TO DISCUSS

CHANGELOG.md

@@ -35,6 +35,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Bump flextable and remove the skip() units tests (#193)
 - docx exporter added missing defaults (#186)
 
+
 ### Added
 
 - Added option to switch on/off the export of the csv in both `tt_to_tlgrtf()` and `export_as_docx_j()`

tests/testthat/test-a_freq_j.R

@@ -20,7 +20,7 @@ test_that("a_freq_j with label_map works in a table layout as expected", {
       )
     )
   result <- build_table(lyt, dta)
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("a_freq_j with label_map restricts the values according to row split and label_map", {
@@ -48,7 +48,7 @@ test_that("a_freq_j with label_map restricts the values according to row split a
       )
     )
   result <- build_table(lyt, dta)
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("a_freq_j_with_exclude allows to exclude row split levels from the analysis", {
@@ -78,7 +78,7 @@ test_that("a_freq_j_with_exclude allows to exclude row split levels from the ana
     )
   result <- build_table(lyt, dta) |>
     safe_prune_table(prune_func = tern::keep_rows(keep_non_null_rows))
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("a_freq_j in specific situation error for not passing alt_counts_df", {
@@ -122,22 +122,22 @@ test_that("a_freq_j in specific situation error for not passing alt_counts_df",
   )
 
   result <- build_table(lyt, adsl, alt_counts_df = adsl)
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("a_freq_j in layout with relative risk column for combined facet", {
   library(dplyr)
   trtvar <- "ARM"
   ctrl_grp <- "B: Placebo"
-  
+
   adsl <- ex_adsl |> select(c("USUBJID", "STRATA1", "EOSSTT", all_of(trtvar)))
   adsl$colspan_trt <- factor(
     ifelse(adsl[[trtvar]] == ctrl_grp, " ", "Active Study Agent"),
     levels = c("Active Study Agent", " ")
   )
   adsl$rrisk_header <- "Risk Difference (%) (95% CI)"
   adsl$rrisk_label <- paste(adsl[[trtvar]], paste("vs", ctrl_grp))
-  
+
   colspan_trt_map <- create_colspan_map(
     df = adsl,
     non_active_grp = ctrl_grp,
@@ -146,74 +146,78 @@ test_that("a_freq_j in layout with relative risk column for combined facet", {
     colspan_var = "colspan_trt",
     trt_var = trtvar
   )
-  
+
   a_freq_j_args <- list(
     .stats = "count_unique_fraction",
     ref_path = c("colspan_trt", " ", trtvar, ctrl_grp)
   )
-  
-  
+
+
   # Set up levels and label for the required combined columns
-  add_combo <- add_combo_facet("Combined",
-                               label = "Combined",
-                               levels = setdiff(unique(adsl[[trtvar]]), ctrl_grp)
+  add_combo <- add_combo_facet(
+    "Combined",
+    label = "Combined",
+    levels = setdiff(unique(adsl[[trtvar]]), ctrl_grp)
   )
-  
+
   # choose if any facets need to be removed - e.g remove the combined column for placebo
   rm_combo_from_placebo <- cond_rm_facets(
     facets = "Combined",
     ancestor_pos = NA,
     value = " ",
     split = "colspan_trt"
   )
-  
-  mysplit_comb <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))  
-  
+
+  mysplit_comb <- make_split_fun(post = list(add_combo, rm_combo_from_placebo))
+
   # choose if any facets need to be removed - e.g remove the combined column for placebo
   rm_combo_from_placebo2 <- cond_rm_facets(
     facets = ctrl_grp,
     ancestor_pos = NA,
     value = "Risk Difference (%) (95% CI)",
     split = "rrisk_header"
   )
-  add_combo2 <- add_combo_facet("Combined",
-                               label = paste0("Combined vs ", ctrl_grp),
-                               levels = setdiff(unique(adsl[[trtvar]]), ctrl_grp)
+  add_combo2 <- add_combo_facet(
+    "Combined",
+    label = paste0("Combined vs ", ctrl_grp),
+    levels = setdiff(unique(adsl[[trtvar]]), ctrl_grp)
   )
-  
+
   mysplit_comb2 <- make_split_fun(post = list(add_combo2, rm_combo_from_placebo2))
 
-    
+
   lyt <- basic_table(show_colcounts = TRUE) |>
     split_cols_by("colspan_trt", split_fun = trim_levels_to_map(map = colspan_trt_map)) |>
-    split_cols_by(trtvar, split_fun = mysplit_comb) |> 
+    split_cols_by(trtvar, split_fun = mysplit_comb) |>
     split_cols_by("rrisk_header", nested = FALSE) |>
     split_cols_by(trtvar, labels_var = "rrisk_label", split_fun = mysplit_comb2) |>
     split_rows_by("STRATA1") |>
     analyze("EOSSTT", afun = a_freq_j, extra_args = a_freq_j_args)
-  
+
 
   result <- build_table(lyt, adsl, alt_counts_df = adsl)
-  
+
   # confirm column is not NE (NE, NE) and numbers are correct
   actual_row <- result[2, ]
   actual <- cell_values(result[2, 7])
-  
+
   colcounts <- col_counts(actual_row)
-  
+
   combcols <- 1:2
   ctrlcol <- 4
   ncolcomb <- sum(colcounts[combcols])
   ncolctrl <- colcounts[ctrlcol]
-  
+
   countscomb <- sum(sapply(cell_values(actual_row[1, combcols]), function(v) v[["count_unique"]]), na.rm = TRUE)
   countsctrl <- cell_values(actual_row[1, ctrlcol])[[1]][["count_unique"]]
-  
+
   # default method for relative risk in a_freq_j is wald stat which is based upon tern function
-  expected <- tern::stat_propdiff_ci( x = list(countscomb), 
-                    y = list(countsctrl), 
-                    N_x = ncolcomb, 
-                    N_y = ncolctrl)
-
+  expected <- tern::stat_propdiff_ci(
+    x = list(countscomb),
+    y = list(countsctrl),
+    N_x = ncolcomb,
+    N_y = ncolctrl
+  )
+
   testthat::expect_equal(actual, expected, ignore_attr = TRUE)
 })

tests/testthat/test-a_summarize_aval_chg_diff.R

@@ -34,7 +34,7 @@ test_that("a_summarize_aval_chg_diff_j comp_btw_group = FALSE works as expected"
 
   tbl <- expect_silent(build_table(lyt, advs, alt_counts_df = adsl))
   expect_s4_class(tbl, "TableTree")
-  expect_snapshot(tbl)
+  expect_snapshot(cran = TRUE, tbl)
 
   # this one also ran fine prior hotfix78
   extra_args_3col2 <- list(
@@ -56,7 +56,7 @@ test_that("a_summarize_aval_chg_diff_j comp_btw_group = FALSE works as expected"
 
   tbl2 <- build_table(lyt2, advs, alt_counts_df = adsl)
   expect_s4_class(tbl2, "TableTree")
-  expect_snapshot(tbl2)
+  expect_snapshot(cran = TRUE, tbl2)
 })
 
 test_that("a_summarize_aval_chg_diff_j t-test sparse data works as expected", {
@@ -144,11 +144,11 @@ test_that("a_summarize_aval_chg_diff_j t-test sparse data works as expected", {
 
   tbl <- build_table(lyt, advs, alt_counts_df = adsl)
   expect_s4_class(tbl, "TableTree")
-  expect_snapshot(tbl)
+  expect_snapshot(cran = TRUE, tbl)
 
   tbl2 <- build_table(lyt, advs_2, alt_counts_df = adsl)
   expect_s4_class(tbl2, "TableTree")
-  expect_snapshot(tbl2)
+  expect_snapshot(cran = TRUE, tbl2)
 })
 
 

tests/testthat/test-blank_line.R

@@ -28,7 +28,7 @@ test_that("insert_blank_line works as expected", {
 
   # We expect 6 blank lines: after mean and range, for each of the
   # 3 STRATA1 levels' row splits.
-  expect_snapshot(mf_strings(matrix_form(tbl)))
+  expect_snapshot(cran = TRUE, mf_strings(matrix_form(tbl)))
 })
 
 test_that("insert_blank_line optionally uses custom table names", {

tests/testthat/test-cmhrms.R

@@ -80,7 +80,7 @@ test_that("a_cmhrms_j works in a table layout as expected", {
       )
     )
   res <- expect_silent(build_table(lyt, df = dta))
-  expect_snapshot(res)
+  expect_snapshot(cran = TRUE, res)
 })
 
 test_that("a_cmhrms_j_with_exclude works in a table layout as expected", {
@@ -107,5 +107,5 @@ test_that("a_cmhrms_j_with_exclude works in a table layout as expected", {
     )
   res <- expect_silent(build_table(lyt, df = dta)) |>
     safe_prune_table(prune_func = tern::keep_rows(keep_non_null_rows))
-  expect_snapshot(res)
+  expect_snapshot(cran = TRUE, res)
 })

tests/testthat/test-cmp_functions.R

@@ -2,7 +2,7 @@ test_that("cmp_split_fun works as expected", {
   result <- basic_table(round_type = "sas") |>
     split_cols_by("ID", split_fun = cmp_split_fun) |>
     build_table(formatters::DM)
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("cmp_cfun works correctly for expected column", {
@@ -17,7 +17,7 @@ test_that("cmp_cfun works correctly for expected column", {
     variables = list(expected = "exp", received = "rec", missing = "mis"),
     formats = list()
   )
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("cmp_cfun works correctly for received column", {
@@ -35,7 +35,7 @@ test_that("cmp_cfun works correctly for received column", {
     variables = list(expected = "exp", received = "rec", missing = "mis"),
     formats = list(count_percent = jjcsformat_count_fraction)
   )
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("cmp_cfun works correctly for missing column", {
@@ -54,5 +54,5 @@ test_that("cmp_cfun works correctly for missing column", {
     variables = list(expected = "exp", received = "rec", missing = "mis"),
     formats = list(count_percent = jjcsformat_count_fraction)
   )
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })

tests/testthat/test-colwidths.R

@@ -123,7 +123,7 @@ test_that("find_free_colspc works as expected", {
 
   suppressWarnings(result <- find_free_colspc(curposs = curdf, fullposs = full_possdf))
 
-  expect_snapshot(result)
+  expect_snapshot(cran = TRUE, result)
 })
 
 test_that("smart_colwidths_1page works as expected", {