resolve conflict

Author: shajoezhu

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 # R specific hooks: https://github.com/lorenzwalthert/precommit
 repos:
   - repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.3.9005
+    rev: v0.4.3.9017
     hooks:
       - id: style-files
         args: [--style_pkg=styler, --style_fun=tidyverse_style]
@@ -51,7 +51,7 @@ repos:
     hooks:
       - id: prettier
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: check-added-large-files
         args: ["--maxkb=200"]
@@ -77,6 +77,6 @@ repos:
         files: '\.Rhistory|\.RData|\.Rds|\.rds$'
         # `exclude: <regex>` to allow committing specific files.
   - repo: https://github.com/igorshubovych/markdownlint-cli
-    rev: v0.44.0
+    rev: v0.47.0
     hooks:
       - id: markdownlint

DESCRIPTION

@@ -1,18 +1,18 @@
 Type: Package
 Package: scda.test
 Title: Template Tests
-Version: 0.0.0.9097
-Date: 2025-03-11
+Version: 0.0.0.9103
+Date: 2025-12-25
 Authors@R: c(
     person("Joe", "Zhu", , "[email protected]", role = c("aut", "cre")),
-    person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@roche.com", role = "aut"),
-    person("Jana", "Stoilova", , "jana.stoilova@roche.com", role = "aut"),
-    person("Heng", "Wang", , "wang.heng@gene.com", role = "aut"),
+    person("Daniel", "Sabanés Bové", , "daniel.sabanes_bove@rconis.com", role = "aut"),
+    person("Jana", "Stoilova", , "stoilova@dnli.com", role = "aut"),
+    person("Heng", "Wang", , "Heng.Wang21@gilead.com", role = "aut"),
     person("Francois", "Collin", role = "aut"),
-    person("Adrian", "Waddell", , "adrian.waddell@gene.com", role = "aut"),
+    person("Adrian", "Waddell", , "aadrian.waddell@gmail.com", role = "aut"),
     person("Pawel", "Rucki", , "[email protected]", role = "aut"),
-    person("Chendi", "Liao", , "[email protected]", role = "aut"),
-    person("Jennifer", "Li", , "[email protected]", role = "aut"),
+    person("Chendi", "Liao", role = "aut"),
+    person("Jennifer", "Li", role = "aut"),
     person("F. Hoffmann-La Roche AG", role = c("cph", "fnd"))
   )
 Description: Tests of sample templates from TLG Catalog using data from
@@ -21,13 +21,13 @@ License: Apache License 2.0 | file LICENSE
 URL: https://github.com/insightsengineering/scda.test/
 BugReports: https://github.com/insightsengineering/scda.test/issues
 Depends:
-    formatters (>= 0.5.10.9001),
+    formatters (>= 0.5.12),
     R (>= 4.2),
-    rlistings (>= 0.2.10),
-    rtables (>= 0.6.11.9017),
-    tern (>= 0.9.7.9018)
+    rlistings (>= 0.2.13),
+    rtables (>= 0.6.15),
+    tern (>= 0.9.10)
 Imports:
-    pharmaverseadam (>= 1.1.0),
+    pharmaverseadam (>= 1.1.0.9001),
     random.cdisc.data (>= 0.3.16)
 Suggests:
     broom,
@@ -46,6 +46,7 @@ VignetteBuilder:
     knitr
 Remotes:
     insightsengineering/formatters@main,
+    insightsengineering/rlistings@main,
     insightsengineering/rtables@main,
     insightsengineering/tern@main,
     pharmaverse/pharmaverseadam@main
@@ -56,4 +57,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.2
+RoxygenNote: 7.3.3

NEWS.md

@@ -1,4 +1,4 @@
-# scda.test 0.0.0.9097
+# scda.test 0.0.0.9103
 
 ### New Features
 * Added table tests from `tern`.

man/scda.test-package.Rd

@@ -7,7 +7,7 @@
       
       ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
                                                                                           Heart Rate Result                    QT Duration Result                    RR Duration Result                 
-                                                                                  Study     (BEATS/MIN);        Heart Rate          (msec);          QT Duration          (msec);          RR Duration  
+                                                                                  Study     (beats/min);        Heart Rate           (ms);           QT Duration           (ms);           RR Duration  
       Treatment   Center/Subject ID            Age/Sex/Race             Visit      Day     Range:(40-100)     Change from BL    Range:(350-450)     Change from BL    Range:(600-1500)    Change from BL
       ——————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————————
        Placebo        701/1015                  63/F/WHITE             Baseline     1            73.67                NA            456.67/H                NA            519.00/L                NA    

tests/testthat/_snaps/listing_egl01.md

@@ -0,0 +1,21 @@
+# DMT01 variant factor with only Missing values
+
+    Code
+      res
+    Output
+                                 Placebo     Screen Failure   Xanomeline High Dose   Xanomeline Low Dose
+                                 (N=86)          (N=52)              (N=72)                (N=96)       
+      ——————————————————————————————————————————————————————————————————————————————————————————————————
+      Age (yr)                                                                                          
+        n                          86              52                  72                    96         
+        Mean (SD)              75.2 (8.6)      75.1 (9.7)          73.8 (7.9)            76.0 (8.1)     
+        Median                    76.0            76.0                75.5                  78.0        
+        Min - Max              52.0 - 89.0    50.0 - 89.0         56.0 - 88.0            51.0 - 88.0    
+      Age Group                                                                                         
+        n                          86              52                  72                    96         
+        18-40                       0              0                   0                      0         
+        41-64                  14 (16.3%)      9 (17.3%)           11 (15.3%)             8 (8.3%)      
+        >=65                   72 (83.7%)      43 (82.7%)          61 (84.7%)            88 (91.7%)     
+      Biomarker 1 Categories                                                                            
+        n                           0              0                   0                      0         
+

tests/testthat/_snaps/table_jnj_tbl1.md

@@ -190,7 +190,8 @@ advs_raw <- random.cdisc.data::cadvs
 # Data loading for pharmaverse
 
 adpp_pharmaverse <- pharmaverseadam::adpp
-adpc_pharmaverse <- pharmaverseadam::adpc
+adpc_pharmaverse <- pharmaverseadam::adpc %>%
+  filter(!is.na(AVAL))
 
 set.seed(99)
 

tests/testthat/setup.R

@@ -34,8 +34,8 @@ adsl_local <- local({
 
   adsl_f$AGEGRP <- factor(adsl_f$AGEGRP, levels = c("< 65 yrs", ">= 65 yrs"))
   adsl_f$ETHNIC <- factor(adsl_f$ETHNIC, levels = c("Ethnicity 1", "Ethnicity 2", "Unknown"))
+  # adsl_f <- df_explicit_na(adsl_f)
   # nolint end
-  adsl_f <- df_explicit_na(adsl_f)
   adsl_f
 })
 

tests/testthat/test-table_disclosures.R

@@ -112,7 +112,7 @@ testthat::test_that("DTHT01 variant 4 is produced correctly", {
     mutate(
       DTHCAUS_other = factor(ifelse(
         DTHCAT == "OTHER" & DTHCAUS != "Post-study reporting of death", as.character(DTHCAUS), NA
-      ), levels = c("LOST TO FOLLOW UP", "SUICIDE", "UNKNOWN", "MISSING")) %>% explicit_na()
+      ), levels = c("LOST TO FOLLOW UP", "SUICIDE", "UNKNOWN", "MISSING")) %>% explicit_na(label = "<Missing>")
     )
 
   lyt <- basic_table(show_colcounts = TRUE) %>%

tests/testthat/test-table_dtht01.R

@@ -0,0 +1,56 @@
+# extra special case situation to scenario from test-table_dmt01.R
+# Tests DMT01 with corner case situation to demonstrate bug in analyze is resolved with empty factor data
+# tern@1431-bug-s_summaryfactor
+set.seed(1)
+
+adsl <- pharmaverseadam::adsl
+adsl <- adsl %>%
+  mutate(BMRKR1 = rnorm(nrow(adsl), 3.5, 10)) %>%
+  mutate(STRATA1 = factor(sample(c("A", "B", "C"), nrow(adsl), TRUE)))
+
+adsl <- df_explicit_na(adsl)
+
+adsl <- adsl %>%
+  mutate(
+    SEX = factor(case_when(
+      SEX == "M" ~ "Male",
+      SEX == "F" ~ "Female",
+      SEX == "U" ~ "Unknown",
+      SEX == "UNDIFFERENTIATED" ~ "Undifferentiated"
+    )),
+    AGEGR1 = factor(
+      case_when(
+        between(AGE, 18, 40) ~ "18-40",
+        between(AGE, 41, 64) ~ "41-64",
+        AGE > 64 ~ ">=65"
+      ),
+      levels = c("18-40", "41-64", ">=65")
+    ),
+    BMRKR1_CAT = NA_character_
+  ) %>%
+  var_relabel(
+    BMRKR1_CAT = "Biomarker 1 Categories"
+  )
+
+adsl <- df_explicit_na(adsl, na_level = "<Missing>")
+
+
+testthat::test_that("DMT01 variant factor with only Missing values", {
+  vars <- c("AGE", "AGEGR1", "BMRKR1_CAT")
+  var_labels <- c(
+    "Age (yr)",
+    "Age Group",
+    "Biomarker 1 Categories"
+  )
+
+  result <- basic_table(show_colcounts = TRUE) %>%
+    split_cols_by(var = "ACTARM") %>%
+    analyze_vars(
+      vars = vars,
+      var_labels = var_labels
+    ) %>%
+    build_table(adsl)
+
+  res <- testthat::expect_silent(result)
+  testthat::expect_snapshot(res)
+})