update scda.test snaps allowing key column to change (#67)

Signed-off-by: Davide Garolini <dgarolini@gmail.com> Co-authored-by: Davide Garolini <dgarolini@gmail.com> Co-authored-by: Melkiades <davide.garolini@roche.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Oct 31, 2023 · a411f2f · a411f2f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -21,11 +21,11 @@ License: Apache License 2.0 | file LICENSE
 URL: https://github.com/insightsengineering/scda.test/
 BugReports: https://github.com/insightsengineering/scda.test/issues
 Depends:
-    formatters (>= 0.5.3.9002),
-    R (>= 3.6),
-    rlistings (>= 0.2.5.9002),
-    rtables (>= 0.6.4.9003),
-    tern (>= 0.9.1.9005)
+    formatters (>= 0.5.4.9002),
+    R (>= 4.2),
+    rlistings (>= 0.2.6.9005),
+    rtables (>= 0.6.5.9004),
+    tern (>= 0.9.2.9001)
 Imports:
     scda (>= 0.1.6.9012),
     scda.2022 (>= 0.1.5.9002)

diff --git a/tests/testthat/_snaps/table_ttet01.md b/tests/testthat/_snaps/table_ttet01.md
@@ -35,6 +35,43 @@
           95% CI                                         (-11.86, 11.86)   (-20.95, 2.97)
           p-value (Z-test)                                   1.0000            0.1406    
 
+# TTET01 default variant with Placebo arm
+
+    Code
+      res
+    Output
+                                           A: Drug X      C: Combination     B: Placebo  
+                                            (N=134)          (N=132)          (N=134)    
+      ———————————————————————————————————————————————————————————————————————————————————
+      Patients with event (%)             58 (43.3%)        69 (52.3%)       58 (43.3%)  
+        Earliest contributing event                                                      
+          Death                               58                69               58      
+      Patients without event (%)          76 (56.7%)        63 (47.7%)       76 (56.7%)  
+      Time to Event (Months)                                                             
+        Median                                NA               9.4               NA      
+          95% CI                           (9.3, NA)        (7.6, NA)        (9.4, NA)   
+        25% and 75%-ile                     5.6, NA          5.0, NA          5.6, NA    
+        Range (censored)                  9.9 to 16.4      9.9 to 16.3      9.9 to 16.3  
+        Range (event)                     0.5 to 9.6        0.5 to 9.8       0.9 to 9.6  
+      Unstratified Analysis                                                              
+        p-value (log-rank)                  0.9998            0.1480                     
+        Hazard Ratio                         1.00              1.29                      
+        95% CI                           (0.69, 1.44)      (0.91, 1.83)                  
+      6 Months                                                                           
+        Patients remaining at risk            97                90               97      
+        Event Free Rate (%)                  72.39            68.18            72.39     
+        95% CI                          (64.82, 79.96)    (60.24, 76.13)   (64.82, 79.96)
+        Difference in Event Free Rate        0.00             -4.21                      
+          95% CI                        (-10.71, 10.71)   (-15.18, 6.77)                 
+          p-value (Z-test)                  1.0000            0.4525                     
+      12 Months                                                                          
+        Patients remaining at risk            49                37               48      
+        Event Free Rate (%)                  56.72            47.73            56.72     
+        95% CI                          (48.33, 65.11)    (39.21, 56.25)   (48.33, 65.11)
+        Difference in Event Free Rate        0.00             -8.99                      
+          95% CI                        (-11.86, 11.86)   (-20.95, 2.97)                 
+          p-value (Z-test)                  1.0000            0.1406                     
+
 # TTET01 variant 2: selecting sections to display
 
     Code

diff --git a/tests/testthat/test-table_aovt01.R b/tests/testthat/test-table_aovt01.R
@@ -12,7 +12,7 @@ testthat::test_that("AOVT01 variant with single endpoint is produced correctly",
     dplyr::mutate(CHG = ifelse(BMEASIFL == "Y", CHG, NA)) # only analyze evaluable population
 
   result <- basic_table() %>%
-    split_cols_by("ARMCD", ref_group = "ARM A") %>%
+    split_cols_by("ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     summarize_ancova(
       vars = "CHG",
@@ -38,7 +38,7 @@ testthat::test_that("AOVT01 variant with multiple endpoints is produced correctl
   n_per_arm <- table(adsl$ARM)
 
   result <- basic_table() %>%
-    split_cols_by("ARMCD", ref_group = "ARM A") %>%
+    split_cols_by("ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     split_rows_by("PARAMCD") %>%
     summarize_ancova(

diff --git a/tests/testthat/test-table_aovt02.R b/tests/testthat/test-table_aovt02.R
@@ -14,7 +14,7 @@ adqs_single <- adqs %>%
 
 testthat::test_that("AOVT02 is produced correctly", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by("ARMCD", ref_group = "ARM A") %>%
+    split_cols_by("ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     append_varlabels(adqs_single, "PARAM") %>%
     summarize_ancova(
       vars = "CHG",

diff --git a/tests/testthat/test-table_aovt03.R b/tests/testthat/test-table_aovt03.R
@@ -9,7 +9,7 @@ adqs_in <- adqs %>%
 
 testthat::test_that("AOVT03 is produced correctly", {
   result <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by("ARMCD", ref_group = "ARM A") %>%
+    split_cols_by("ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     split_rows_by("PARAM", split_fun = drop_split_levels) %>%
     summarize_ancova(
       vars = "CHG",

diff --git a/tests/testthat/test-table_cmht01.R b/tests/testthat/test-table_cmht01.R
@@ -14,7 +14,7 @@ testthat::test_that("CMHT01 variant 1 is produced correctly", {
     mutate(strata = interaction(STRATA1, STRATA2, drop = TRUE))
 
   lyt_01 <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     estimate_proportion(vars = "is_rsp", table_names = "est_prop") %>%
     estimate_proportion_diff(
       var_labels = "Unstratified Analysis",
@@ -68,7 +68,7 @@ testthat::test_that("CMHT01 variant 2 is produced correctly", {
   split_fun <- drop_split_levels
 
   lyt_02 <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     split_rows_by(
       var = "PARAM",
       split_fun = split_fun,

diff --git a/tests/testthat/test-table_dort01.R b/tests/testthat/test-table_dort01.R
@@ -27,7 +27,7 @@ testthat::test_that("DORT01 variant 1 is produced correctly", {
   adtte <- adtte_local
 
   result <- basic_table() %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     count_values(
       vars = "USUBJID",
@@ -82,7 +82,7 @@ testthat::test_that("DORT01 variant 2 (selecting sectons) is produced correctly"
   adtte <- adtte_local
 
   result <- basic_table() %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     count_values(
       vars = "USUBJID",
@@ -138,7 +138,7 @@ testthat::test_that("DORT01 variant 3 (modifying conftype and alpha level) is pr
   adtte <- adtte_local
 
   result <- basic_table() %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     count_values(
       vars = "USUBJID",
@@ -194,7 +194,7 @@ testthat::test_that("DORT01 variant 4 (modifying time point for the “xx durati
   adtte <- adtte_local
 
   result <- basic_table() %>%
-    split_cols_by(var = "ARM", ref_group = "A: Drug X") %>%
+    split_cols_by(var = "ARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     count_values(
       vars = "USUBJID",

diff --git a/tests/testthat/test-table_lbt11.R b/tests/testthat/test-table_lbt11.R
@@ -38,7 +38,7 @@ anl <- adsaftte %>%
 
 testthat::test_that("LBT11 variant 1 works as expected", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",
@@ -62,7 +62,7 @@ testthat::test_that("LBT11 variant 1 works as expected", {
 
 testthat::test_that("LBT11 variant 2 works as expected", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",
@@ -81,7 +81,7 @@ testthat::test_that("LBT11 variant 3 works as expected", {
   strata <- c("RACE", "SEX")
 
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",

diff --git a/tests/testthat/test-table_lbt11_bl.R b/tests/testthat/test-table_lbt11_bl.R
@@ -38,7 +38,7 @@ anl <- adsaftte %>%
 
 testthat::test_that("LBT11_BL variant 1 works as expected", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",
@@ -62,7 +62,7 @@ testthat::test_that("LBT11_BL variant 1 works as expected", {
 
 testthat::test_that("LBT11_BL variant 2 works as expected", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",
@@ -81,7 +81,7 @@ testthat::test_that("LBT11_BL variant 3 works as expected", {
   strata <- c("RACE", "SEX")
 
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     count_occurrences(vars = "event_grp") %>%
     surv_time(
       vars = "AVAL",

diff --git a/tests/testthat/test-table_ratet01.R b/tests/testthat/test-table_ratet01.R
@@ -6,7 +6,10 @@ anl <- df_explicit_na(anl)
 
 testthat::test_that("RATET01 is produced correctly", {
   lyt <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by("ARM", ref_group = "B: Placebo") %>%
+    split_cols_by("ARM",
+      ref_group = "B: Placebo",
+      split_fun = ref_group_position("first")
+    ) %>%
     analyze_vars(
       "AVAL_f",
       var_labels = "Number of exacerbations per patient",

diff --git a/tests/testthat/test-table_rmpt06.R b/tests/testthat/test-table_rmpt06.R
@@ -150,7 +150,7 @@ testthat::test_that("RMPT06 variant 2 is produced correctly", {
 
 testthat::test_that("RMPT06 variant 3 is produced correctly", {
   lyt_adsl <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by("ACTARM", ref_group = "A: Drug X") %>%
+    split_cols_by("ACTARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     estimate_proportion(
       vars = "AEFL",
       method = "clopper-pearson",
@@ -213,7 +213,7 @@ testthat::test_that("RMPT06 variant 3 is produced correctly", {
 
 testthat::test_that("RMPT06 variant 4 is produced correctly", {
   lyt_adsl <- basic_table(show_colcounts = TRUE) %>%
-    split_cols_by("ACTARM", ref_group = "A: Drug X") %>%
+    split_cols_by("ACTARM", ref_group = "A: Drug X", split_fun = ref_group_position("first")) %>%
     estimate_proportion(
       vars = "AEFL",
       conf_level = 0.90,

diff --git a/tests/testthat/test-table_rspt01.R b/tests/testthat/test-table_rspt01.R
@@ -17,7 +17,7 @@ adrs <- adrs %>%
 
 testthat::test_that("RSPT01: 1. Best Overall Response", {
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",
@@ -48,7 +48,7 @@ testthat::test_that("RSPT01: 1. Best Overall Response", {
 
 testthat::test_that("RSPT01: 2. Best Overall Response (selecting sections to display)", {
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",
@@ -77,7 +77,7 @@ testthat::test_that("RSPT01: 3. Best Overall Response (modifying settings)", {
   conf_level <- 0.90
   method_prop <- "clopper-pearson"
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",
@@ -118,7 +118,7 @@ testthat::test_that("RSPT01: 3. Best Overall Response (modifying settings)", {
 
 testthat::test_that("RSPT01: 4. Best Overall Response (with stratified analysis)", {
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",
@@ -168,7 +168,7 @@ testthat::test_that("RSPT01: 4. Best Overall Response (with stratified analysis)
 
 testthat::test_that("RSPT01: 5. Best Overall Response (modifying the definition of overall response)", {
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",
@@ -219,7 +219,7 @@ testthat::test_that("RSPT01: 6. Best Overall Response (define new sections to di
     )
 
   l <- basic_table() %>%
-    split_cols_by(var = "ARMCD", ref_group = "ARM A") %>%
+    split_cols_by(var = "ARMCD", ref_group = "ARM A", split_fun = ref_group_position("first")) %>%
     add_colcounts() %>%
     estimate_proportion(
       vars = "is_rsp",