Update tests to use snapshots and use tern data (#813)

Closes #779
insightsengineering · Feb 2, 2023 · 914934d · 914934d
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diff --git a/NEWS.md b/NEWS.md
@@ -23,6 +23,8 @@
 * Created vignette which saves cached synthetic CDISC dataset files to the `data/` folder.
 * Added cached synthetic datasets to `data/` folder to use in tests/examples instead of `scda` data.
 * Updated examples to use datasets from the `tern` package instead of `scda` datasets.
+* Replaced all applicable tests with snapshot testing.
+* Updated all (non-table) tests to use `tern` data.
 
 ### Bug Fixes
 * Fixed bug causing incorrect ordering of numeric grade levels when missing 

diff --git a/data/tern_ex_adae.rda b/data/tern_ex_adae.rda
diff --git a/data/tern_ex_adlb.rda b/data/tern_ex_adlb.rda
diff --git a/data/tern_ex_adpp.rda b/data/tern_ex_adpp.rda
diff --git a/data/tern_ex_adrs.rda b/data/tern_ex_adrs.rda
diff --git a/data/tern_ex_adsl.rda b/data/tern_ex_adsl.rda
diff --git a/data/tern_ex_adtte.rda b/data/tern_ex_adtte.rda
diff --git a/man/ex_data.Rd b/man/ex_data.Rd
diff --git a/tests/testthat/_snaps/abnormal.md b/tests/testthat/_snaps/abnormal.md
@@ -0,0 +1,114 @@
+# s_count_abnormal works with healthy input and default arguments
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$high
+        num denom 
+          1     2 
+      attr(,"label")
+      [1] "high"
+      
+      $fraction$low
+        num denom 
+          1     2 
+      attr(,"label")
+      [1] "low"
+      
+      
+
+# s_count_abnormal works when excluding patients with abnormality at baseline
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$high
+        num denom 
+          1     2 
+      attr(,"label")
+      [1] "high"
+      
+      $fraction$low
+        num denom 
+          1     2 
+      attr(,"label")
+      [1] "low"
+      
+      
+
+# s_count_abnormal also works with tibble and custom arguments
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$high
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "high"
+      
+      $fraction$low
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "low"
+      
+      
+
+# count_abnormal works with default arguments
+
+    Code
+      res
+    Output
+              all obs 
+      ————————————————
+      low    1/2 (50%)
+      high      0/1   
+
+# count_abnormal works with custom arguments
+
+    Code
+      res
+    Output
+                all obs
+      —————————————————
+        < LLN    1 / 2 
+        > ULN    0 / 1 
+
+# count_abnormal works with default arguments and visit
+
+    Code
+      res
+    Output
+                all obs 
+      ——————————————————
+      WEEK 1            
+        low    1/2 (50%)
+        high   1/2 (50%)
+      WEEK 2            
+        low    1/2 (50%)
+        high      0/2   
+
+# s_count_abnormal works with healthy input and grouped abnormal arguments
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$high
+        num denom 
+          2     4 
+      attr(,"label")
+      [1] "high"
+      
+      $fraction$low
+        num denom 
+          2     4 
+      attr(,"label")
+      [1] "low"
+      
+      
+
diff --git a/tests/testthat/_snaps/abnormal_by_baseline.md b/tests/testthat/_snaps/abnormal_by_baseline.md
@@ -0,0 +1,162 @@
+# s_count_abnormal_by_baseline works with healthy input and default arguments
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$not_abnormal
+        num denom 
+          1     3 
+      attr(,"label")
+      [1] "Not low baseline status"
+      
+      $fraction$abnormal
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "Low baseline status"
+      
+      $fraction$total
+        num denom 
+          1     4 
+      attr(,"label")
+      [1] "Total"
+      
+      
+
+---
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$not_abnormal
+        num denom 
+          1     3 
+      attr(,"label")
+      [1] "Not high baseline status"
+      
+      $fraction$abnormal
+        num denom 
+          1     1 
+      attr(,"label")
+      [1] "High baseline status"
+      
+      $fraction$total
+        num denom 
+          2     4 
+      attr(,"label")
+      [1] "Total"
+      
+      
+
+# s_count_abnormal_by_baseline also works with tibble and custom arguments
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$not_abnormal
+        num denom 
+          2     5 
+      attr(,"label")
+      [1] "Not low baseline status"
+      
+      $fraction$abnormal
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "Low baseline status"
+      
+      $fraction$total
+        num denom 
+          2     6 
+      attr(,"label")
+      [1] "Total"
+      
+      
+
+---
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$not_abnormal
+        num denom 
+          1     5 
+      attr(,"label")
+      [1] "Not high baseline status"
+      
+      $fraction$abnormal
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "High baseline status"
+      
+      $fraction$total
+        num denom 
+          1     6 
+      attr(,"label")
+      [1] "Total"
+      
+      
+
+# count_abnormal_by_baseline throws warning with character var
+
+    Code
+      res
+    Output
+      $fraction
+      $fraction$not_abnormal
+        num denom 
+          2     4 
+      attr(,"label")
+      [1] "Not low baseline status"
+      
+      $fraction$abnormal
+        num denom 
+          0     1 
+      attr(,"label")
+      [1] "Low baseline status"
+      
+      $fraction$total
+        num denom 
+          2     5 
+      attr(,"label")
+      [1] "Total"
+      
+      
+
+# count_abnormal_by_baseline works with default arguments
+
+    Code
+      res
+    Output
+                                     all obs  
+      ————————————————————————————————————————
+      Low                                     
+        Not low baseline status    1/3 (33.3%)
+        Low baseline status            0/1    
+        Total                       1/4 (25%) 
+      High                                    
+        Not high baseline status    1/2 (50%) 
+        High baseline status        1/2 (50%) 
+        Total                       2/4 (50%) 
+
+# count_abnormal_by_baseline works with custom arguments
+
+    Code
+      res
+    Output
+                                   all obs
+      ————————————————————————————————————
+      Low                                 
+        Not low baseline status     1 / 3 
+        Low baseline status         0 / 1 
+        Total                       1 / 4 
+      High                                
+        Not high baseline status    1 / 2 
+        High baseline status        1 / 2 
+        Total                       2 / 4 
+
diff --git a/tests/testthat/_snaps/abnormal_by_marked.md b/tests/testthat/_snaps/abnormal_by_marked.md
@@ -0,0 +1,51 @@
+# s_count_abnormal_by_marked works as expected
+
+    Code
+      res
+    Output
+      $count_fraction
+      $count_fraction$`Single, not last`
+      [1] 0 0
+      
+      $count_fraction$`Last or replicated`
+      [1] 5.00000000 0.07246377
+      
+      $count_fraction$`Any Abnormality`
+      [1] 5.00000000 0.07246377
+      
+      
+
+---
+
+    Code
+      res
+    Output
+      $count_fraction
+      $count_fraction$`Single, not last`
+      [1] 0 0
+      
+      $count_fraction$`Last or replicated`
+      [1] 5.00000000 0.07246377
+      
+      $count_fraction$`Any Abnormality`
+      [1] 5.00000000 0.07246377
+      
+      
+
+# count_abnormal_by_marked works as expected
+
+    Code
+      res
+    Output
+                                ARM A      ARM B      ARM C  
+      ———————————————————————————————————————————————————————
+      CRP (n)                     69         73         58   
+        Low                                                  
+          Single, not last        0       1 (1.4%)      0    
+          Last or replicated   5 (7.2%)   2 (2.7%)   5 (8.6%)
+          Any Abnormality      5 (7.2%)   3 (4.1%)   5 (8.6%)
+        High                                                 
+          Single, not last        0          0       1 (1.7%)
+          Last or replicated   5 (7.2%)   7 (9.6%)   4 (6.9%)
+          Any Abnormality      5 (7.2%)   7 (9.6%)   5 (8.6%)
+