Merge branch 'main' into 1238_mtx_form_indent@main

insightsengineering · May 10, 2024 · 8827f8d · 8827f8d
2 parents 2a6a83a + bfb529f
commit 8827f8d
Show file tree

Hide file tree

Showing 6 changed files with 55 additions and 15 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: tern
 Title: Create Common TLGs Used in Clinical Trials
-Version: 0.9.4.9004
-Date: 2024-04-29
+Version: 0.9.4.9005
+Date: 2024-05-10
 Authors@R: c(
     person("Joe", "Zhu", , "joe.zhu@roche.com", role = c("aut", "cre")),
     person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = "aut"),

diff --git a/NEWS.md b/NEWS.md
@@ -1,10 +1,13 @@
-# tern 0.9.4.9004
+# tern 0.9.4.9005
 
 ### Enhancements
 * Added `facet_var` to `g_lineplot` to allow plot faceting by a factor variable.
 * Updated `g_lineplot` legend to follow factor levels set by users.
 * Added examples and tests for `label_all` parameter to `extract_survival_biomarkers` and `extract_survival_subgroups`.
 
+### Bug Fixes
+* Fixed bug in `s_ancova` that prevented statistics from being printed when arm levels include special characters.
+
 ### Miscellaneous
 * Began deprecation of the unused `label_all` parameter to `tabulate_survival_biomarkers` and `tabulate_survival_subgroups`, with redirection to the same parameter in their associated `extract_*` functions.
 

diff --git a/R/summarize_ancova.R b/R/summarize_ancova.R
@@ -167,7 +167,9 @@ s_ancova <- function(df,
       adjust = "none"
     )
 
-    contrast_lvls <- gsub(paste0(" - ", .ref_group[[arm]][1], ".*"), "", sum_contrasts$contrast)
+    contrast_lvls <- gsub(
+      "^\\(|\\)$", "", gsub(paste0(" - \\(*", .ref_group[[arm]][1], ".*"), "", sum_contrasts$contrast)
+    )
     if (!is.null(interaction_item)) {
       sum_contrasts_level <- sum_contrasts[grepl(sum_level, contrast_lvls, fixed = TRUE), ]
     } else {

diff --git a/inst/WORDLIST b/inst/WORDLIST
@@ -7,7 +7,6 @@ ADTTE
 AE
 ANCOVA
 Agresti
-Bové
 Byar's
 CDISC
 CMH
@@ -27,7 +26,6 @@ Newcombe
 Pre
 Rua
 SMQ
-Sabanés
 Satterthwaite
 Schouten
 TLG

diff --git a/tests/testthat/_snaps/summarize_ancova.md b/tests/testthat/_snaps/summarize_ancova.md
@@ -109,13 +109,27 @@
     Code
       res
     Output
-                                  ARM A         ARM B (x)     ARM C 
-                                 (N=69)          (N=73)       (N=58)
-      ——————————————————————————————————————————————————————————————
-      Unadjusted comparison                                         
-        n                          552             584         464  
-        Mean                      0.01            0.01        -0.05 
-        Difference in Means       0.06            0.06              
-          95% CI              (-0.07, 0.19)   (-0.06, 0.19)         
-          p-value                0.3442          0.3186             
+                                  ARM A       ARM B (x)   ARM C 
+                                 (N=69)        (N=73)     (N=58)
+      ——————————————————————————————————————————————————————————
+      Unadjusted comparison                                     
+        n                          552           584       464  
+        Mean                      0.01          0.01      -0.05 
+        Difference in Means       0.06                          
+          95% CI              (-0.07, 0.19)                     
+          p-value                0.3442                         
+
+---
+
+    Code
+      res
+    Output
+                                       10mg/kg      20mg/kg         30mg/kg   
+      ————————————————————————————————————————————————————————————————————————
+      ARMCD                                                                   
+        n                                69           73              58      
+        Adjusted Mean                   6.30         6.75            6.16     
+        Difference in Adjusted Means                 0.45            -0.14    
+          95% CI                                 (-0.70, 1.60)   (-1.36, 1.08)
+          p-value                                   0.4433          0.8214    
 
diff --git a/tests/testthat/test-summarize_ancova.R b/tests/testthat/test-summarize_ancova.R
@@ -206,4 +206,27 @@ testthat::test_that("summarize_ancova works with irregular arm levels", {
 
   res <- testthat::expect_silent(result2)
   testthat::expect_snapshot(res)
+
+  adsl <- adsl |>
+    mutate(
+      ARMCD = case_match(
+        ARMCD,
+        "ARM A" ~ "10mg/kg",
+        "ARM B" ~ "20mg/kg",
+        "ARM C" ~ "30mg/kg"
+      ) |> factor(levels = paste0(1:3, "0mg/kg")),
+    )
+
+  result3 <- basic_table() |>
+    split_cols_by("ARMCD", ref_group = "10mg/kg") |>
+    summarize_ancova(
+      vars = "BMRKR1",
+      variables = list(arm = "ARMCD"),
+      conf_level = 0.95,
+      var_labels = "ARMCD"
+    ) |>
+    build_table(adsl)
+
+  res <- testthat::expect_silent(result3)
+  testthat::expect_snapshot(res)
 })