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pharmaverse · Sep 5, 2024 · 8b58650 · 8b58650
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diff --git a/R/derive_vars_cat.R b/R/derive_vars_cat.R
@@ -10,18 +10,41 @@
 #'
 #' @examples
 #'
-#' advs <- pharmaverseadam::advs
+#' advs <- tibble::tribble(
+#'   ~USUBJID, ~VSTEST, ~AVAL,
+#'   "01-701-1015", "Height", 147.32,
+#'   "01-701-1015", "Weight", 53.98,
+#'   "01-701-1023", "Height", 162.56,
+#'   "01-701-1023", "Weight", 78.47,
+#'   "01-701-1028", "Height", 177.8,
+#'   "01-701-1028", "Weight", 98.88,
+#'   "01-701-1033", "Height", 175.26,
+#'   "01-701-1033", "Weight", 88.45,
+#'   "01-701-1034", "Height", 154.94,
+#'   "01-701-1034", "Weight", 63.5,
+#'   "01-701-1047", "Height", 148.59,
+#'   "01-701-1047", "Weight", 66.23,
+#'   "01-701-1097", "Height", 168.91,
+#'   "01-701-1097", "Weight", 78.02,
+#'   "01-701-1111", "Height", 158.24,
+#'   "01-701-1111", "Weight", 60.33,
+#'   "01-701-1115", "Height", 181.61,
+#'   "01-701-1115", "Weight", 78.7,
+#'   "01-701-1118", "Height", 180.34,
+#'   "01-701-1118", "Weight", 71.67
+#' )
 #'
 #' definition <- exprs(
-#'   ~condition,  ~AVALCAT1,  ~AVALCA1N, ~NEWCOL,
-#'   VSTESTCD == "Height" & AVAL > 140,  ">140 cm",          1,  "extra1",
-#'   VSTESTCD == "Height" & AVAL <= 140, "<=140 cm",         2,  "extra2"
+#'   ~condition, ~AVALCAT1, ~AVALCA1N, ~NEWCOL,
+#'   VSTESTCD == "Height" & AVAL > 140, ">140 cm", 1, "extra1",
+#'   VSTESTCD == "Height" & AVAL <= 140, "<=140 cm", 2, "extra2"
 #' )
 #'
-#' derive_vars_cat(dataset = advs %>% filter(VSTESTCD == "Height"),
-#'                 definition = definition) %>%
+#' derive_vars_cat(
+#'   dataset = advs %>% filter(VSTESTCD == "Height"),
+#'   definition = definition
+#' ) %>%
 #'   select(USUBJID, VSTESTCD, AVAL, AVALCA1N, AVALCAT1)
-
 derive_vars_cat <- function(dataset,
                             definition) {
   # assertions
@@ -36,7 +59,7 @@ derive_vars_cat <- function(dataset,
 
 
   # extract new variable names and conditions
-  new_col_names <- names(definition) [!names(definition) == "condition"]
+  new_col_names <- names(definition)[!names(definition) == "condition"]
   condition <- definition[["condition"]] # could also be outside of the function
 
   # (re)apply the function for each new variable name and iteratively derive the categories

diff --git a/tests/testthat/_snaps/derive_vars_cat.md b/tests/testthat/_snaps/derive_vars_cat.md
@@ -3,7 +3,7 @@
     Code
       result
     Output
-      # A tibble: 254 x 5
+      # A tibble: 10 x 5
          USUBJID     VSTEST  AVAL AVALCAT1 AVALCA1N
          <chr>       <chr>  <dbl> <chr>       <dbl>
        1 01-701-1015 Height  147. <160            2
@@ -16,7 +16,6 @@
        8 01-701-1111 Height  158. <160            2
        9 01-701-1115 Height  182. >=160           1
       10 01-701-1118 Height  180. >=160           1
-      # i 244 more rows
 
 # derive_vars_cat Test 2: Error when dataset is not a dataframe
 
@@ -35,7 +34,7 @@
     Code
       result
     Output
-      # A tibble: 254 x 5
+      # A tibble: 10 x 5
          USUBJID     VSTEST  AVAL AVALCAT1 AVALCA1N
          <chr>       <chr>  <dbl> <chr>       <dbl>
        1 01-701-1015 Height  147. <NA>           NA
@@ -48,14 +47,13 @@
        8 01-701-1111 Height  158. <NA>           NA
        9 01-701-1115 Height  182. <NA>           NA
       10 01-701-1118 Height  180. <NA>           NA
-      # i 244 more rows
 
 # derive_vars_cat Test 6: Overlapping conditions handled correctly
 
     Code
       result
     Output
-      # A tibble: 254 x 5
+      # A tibble: 10 x 5
          USUBJID     VSTEST  AVAL AVALCAT1 AVALCA1N
          <chr>       <chr>  <dbl> <chr>       <dbl>
        1 01-701-1015 Height  147. <NA>           NA
@@ -68,14 +66,13 @@
        8 01-701-1111 Height  158. >155            2
        9 01-701-1115 Height  182. >=160           1
       10 01-701-1118 Height  180. >=160           1
-      # i 244 more rows
 
 # derive_vars_cat Test 7: Handles missing values in dataset correctly
 
     Code
       result
     Output
-      # A tibble: 254 x 5
+      # A tibble: 10 x 5
          USUBJID     VSTEST  AVAL AVALCAT1 AVALCA1N
          <chr>       <chr>  <dbl> <chr>       <dbl>
        1 01-701-1015 Height   NA  <NA>           NA
@@ -88,9 +85,8 @@
        8 01-701-1111 Height  158. <160            2
        9 01-701-1115 Height  182. >=160           1
       10 01-701-1118 Height  180. >=160           1
-      # i 244 more rows
 
-# derive_vars_cat Test 8: Error when condition is missing from exprs() definition object
+# derive_vars_cat Test 8: Error when condition is missing from `definition`
 
     Required variable `condition` is missing in `definition`
 
@@ -99,27 +95,36 @@
     Code
       result
     Output
-      # A tibble: 2,493 x 5
-         USUBJID     VSTEST  AVAL AVALCAT1       AVALCA1N
-         <chr>       <chr>  <dbl> <chr>             <dbl>
-       1 01-701-1015 Height 147.  Height < 160          2
-       2 01-701-1015 Weight  54.0 Weight < 66.68        4
-       3 01-701-1015 Weight  54.4 Weight < 66.68        4
-       4 01-701-1015 Weight  53.1 Weight < 66.68        4
-       5 01-701-1015 Weight  54.0 Weight < 66.68        4
-       6 01-701-1015 Weight  53.1 Weight < 66.68        4
-       7 01-701-1015 Weight  53.1 Weight < 66.68        4
-       8 01-701-1015 Weight  53.1 Weight < 66.68        4
-       9 01-701-1015 Weight  53.1 Weight < 66.68        4
-      10 01-701-1015 Weight  53.1 Weight < 66.68        4
-      # i 2,483 more rows
+      # A tibble: 20 x 5
+         USUBJID     VSTEST  AVAL AVALCAT1        AVALCA1N
+         <chr>       <chr>  <dbl> <chr>              <dbl>
+       1 01-701-1015 Height 147.  Height < 160           2
+       2 01-701-1015 Weight  54.0 Weight < 66.68         4
+       3 01-701-1023 Height 163.  Height >= 160          1
+       4 01-701-1023 Weight  78.5 Weight >= 66.68        3
+       5 01-701-1028 Height 178.  Height >= 160          1
+       6 01-701-1028 Weight  98.9 Weight >= 66.68        3
+       7 01-701-1033 Height 175.  Height >= 160          1
+       8 01-701-1033 Weight  88.4 Weight >= 66.68        3
+       9 01-701-1034 Height 155.  Height < 160           2
+      10 01-701-1034 Weight  63.5 Weight < 66.68         4
+      11 01-701-1047 Height 149.  Height < 160           2
+      12 01-701-1047 Weight  66.2 Weight < 66.68         4
+      13 01-701-1097 Height 169.  Height >= 160          1
+      14 01-701-1097 Weight  78.0 Weight >= 66.68        3
+      15 01-701-1111 Height 158.  Height < 160           2
+      16 01-701-1111 Weight  60.3 Weight < 66.68         4
+      17 01-701-1115 Height 182.  Height >= 160          1
+      18 01-701-1115 Weight  78.7 Weight >= 66.68        3
+      19 01-701-1118 Height 180.  Height >= 160          1
+      20 01-701-1118 Weight  71.7 Weight >= 66.68        3
 
 # derive_vars_cat Test 10: Adding an extra variable (flag) to the dataset
 
     Code
       result
     Output
-      # A tibble: 254 x 6
+      # A tibble: 10 x 6
          USUBJID     VSTEST  AVAL AVALCAT1 AVALCA1N extra_var
          <chr>       <chr>  <dbl> <chr>       <dbl> <lgl>    
        1 01-701-1015 Height  147. <160            2 FALSE    
@@ -132,5 +137,4 @@
        8 01-701-1111 Height  158. <160            2 FALSE    
        9 01-701-1115 Height  182. >=160           1 TRUE     
       10 01-701-1118 Height  180. >=160           1 TRUE     
-      # i 244 more rows
 
diff --git a/tests/testthat/test-derive_vars_cat.R b/tests/testthat/test-derive_vars_cat.R
@@ -1,5 +1,27 @@
 # Load the advs dataset
-advs <- pharmaverseadam::advs
+advs <- tibble::tribble(
+  ~USUBJID, ~VSTEST, ~AVAL,
+  "01-701-1015", "Height", 147.32,
+  "01-701-1015", "Weight", 53.98,
+  "01-701-1023", "Height", 162.56,
+  "01-701-1023", "Weight", 78.47,
+  "01-701-1028", "Height", 177.8,
+  "01-701-1028", "Weight", 98.88,
+  "01-701-1033", "Height", 175.26,
+  "01-701-1033", "Weight", 88.45,
+  "01-701-1034", "Height", 154.94,
+  "01-701-1034", "Weight", 63.5,
+  "01-701-1047", "Height", 148.59,
+  "01-701-1047", "Weight", 66.23,
+  "01-701-1097", "Height", 168.91,
+  "01-701-1097", "Weight", 78.02,
+  "01-701-1111", "Height", 158.24,
+  "01-701-1111", "Weight", 60.33,
+  "01-701-1115", "Height", 181.61,
+  "01-701-1115", "Weight", 78.7,
+  "01-701-1118", "Height", 180.34,
+  "01-701-1118", "Weight", 71.67
+)
 
 ## Test 1: Basic functionality with advs dataset ----
 test_that("derive_vars_cat Test 1: Basic functionality with advs dataset", {