Merge pull request #295 from Gilead-BioStats/fix-AE_qual

update AE qualification tests for sorting updates to Flag and Summarise
Gilead-BioStats · Mar 15, 2022 · 844f3f2 · 844f3f2
2 parents 6db8dfe + 3014d47
commit 844f3f2
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Showing 4 changed files with 22 additions and 8 deletions.
diff --git a/tests/testthat/test_qual_T1_1.R b/tests/testthat/test_qual_T1_1.R
@@ -32,15 +32,19 @@ test_that("AE assessment can return a correctly assessed data frame for the pois
         is.na(Residuals) ~ NA_real_,
         is.nan(Residuals) ~ NA_real_,
         TRUE ~ 0),
-    )
+    ) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_summary <- t1_flagged %>%
     mutate(
       Assessment = "Safety",
       Label = "",
       Score = Residuals
     ) %>%
-    select(Assessment, Label, SiteID, N, Score, Flag)
+    select(Assessment, Label, SiteID, N, Score, Flag)  %>%
+    arrange(desc(abs(.data$Score))) %>%
+    arrange(match(Flag, c(1, -1, 0)))
+
 
   t1_1 <- list("strFunctionName" = "AE_Assess()",
              "lParams" = list("dfInput" = "dfInput",

diff --git a/tests/testthat/test_qual_T1_2.R b/tests/testthat/test_qual_T1_2.R
@@ -33,15 +33,18 @@ test_that("AE assessment can return a correctly assessed data frame for the pois
         is.na(Residuals) ~ NA_real_,
         is.nan(Residuals) ~ NA_real_,
         TRUE ~ 0),
-    )
+    ) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_2_summary <- t1_2_flagged %>%
     mutate(
       Assessment = "Safety",
       Label = "",
       Score = Residuals
     ) %>%
-    select(Assessment, Label, SiteID, N, Score, Flag)
+    select(Assessment, Label, SiteID, N, Score, Flag) %>%
+    arrange(desc(abs(Score))) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_2 <- list("strFunctionName" = "AE_Assess()",
                "lParams" = list("dfInput" = "dfInput",

diff --git a/tests/testthat/test_qual_T1_3.R b/tests/testthat/test_qual_T1_3.R
@@ -38,15 +38,19 @@ test_that("AE assessment can return a correctly assessed data frame for the wilc
         Flag != 0 & Estimate >= median ~ 1,
         TRUE ~ Flag)
     ) %>%
-    select(-median)
+    select(-median) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_3_summary <- t1_3_flagged %>%
     mutate(
       Assessment = "Safety",
       Label = "",
       Score = PValue
     ) %>%
-    select(Assessment, Label, SiteID, N, Score, Flag)
+    select(Assessment, Label, SiteID, N, Score, Flag) %>%
+    arrange(desc(abs(.data$Score))) %>%
+    arrange(match(Flag, c(1, -1, 0)))
+
 
   t1_3 <- list("strFunctionName" = "AE_Assess()",
              "lParams" = list("dfInput" = "dfInput",

diff --git a/tests/testthat/test_qual_T1_4.R b/tests/testthat/test_qual_T1_4.R
@@ -39,15 +39,18 @@ test_that("AE assessment can return a correctly assessed data frame for the wilc
         Flag != 0 & Estimate >= median ~ 1,
         TRUE ~ Flag)
     ) %>%
-    select(-median)
+    select(-median) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_4_summary <- t1_4_flagged %>%
     mutate(
       Assessment = "Safety",
       Label = "",
       Score = PValue
     ) %>%
-    select(Assessment, Label, SiteID, N, Score, Flag)
+    select(Assessment, Label, SiteID, N, Score, Flag) %>%
+    arrange(desc(abs(.data$Score))) %>%
+    arrange(match(Flag, c(1, -1, 0)))
 
   t1_4 <- list("strFunctionName" = "AE_Assess()",
                "lParams" = list("dfInput" = "dfInput",