remove byvars reference

pharmaverse · Aug 5, 2024 · 966a393 · 966a393
1 parent a1091f2
commit 966a393
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Showing 8 changed files with 10 additions and 89 deletions.
diff --git a/R/derive_params_growth_age.R b/R/derive_params_growth_age.R
@@ -8,12 +8,6 @@
 #'   The variables specified in `sex`, `age`, `age_unit`, `parameter`, `analysis_var`
 #'   are expected to be in the dataset.
 #'
-#' @param by_vars Grouping variables
-#'
-#'   The variables from `dataset` which identifies a unique subject and their visit is expected.
-#'
-#'   *Permitted Values*: A list of variables created by `exprs()`, e.g `exprs(USUBJID, VISIT)`.
-#'
 #' @param sex Sex
 #'
 #'   A character vector is expected.
@@ -183,7 +177,6 @@
 #'
 #' derive_params_growth_age(
 #'   advs,
-#'   by_vars = exprs(STUDYID, USUBJID, VISIT),
 #'   sex = SEX,
 #'   age = AGECUR,
 #'   age_unit = AGECURU,
@@ -201,7 +194,6 @@
 #'   )
 #' )
 derive_params_growth_age <- function(dataset,
-                                     by_vars = NULL,
                                      sex,
                                      age,
                                      age_unit,
@@ -213,17 +205,13 @@ derive_params_growth_age <- function(dataset,
                                      set_values_to_sds = NULL,
                                      set_values_to_pctl = NULL) {
   # Apply assertions to each argument to ensure each object is appropriate class
-  if (is.null(by_vars)) {
-    warning("A list of variables created by `exprs()` is expected in argument `by_vars`.")
-  }
-  assert_vars(by_vars)
   sex <- assert_symbol(enexpr(sex))
   age <- assert_symbol(enexpr(age))
   age_unit <- assert_symbol(enexpr(age_unit))
   analysis_var <- assert_symbol(enexpr(analysis_var))
   assert_data_frame(
     dataset,
-    required_vars = expr_c(sex, age, age_unit, analysis_var, by_vars)
+    required_vars = expr_c(sex, age, age_unit, analysis_var)
   )
 
   assert_data_frame(meta_criteria, required_vars = exprs(SEX, AGE, AGEU, L, M, S))
@@ -279,11 +267,6 @@ derive_params_growth_age <- function(dataset,
     ) %>%
     filter(!is.na(metadata_age))
 
-  by_exprs <- enexpr(by_vars)
-  by_antijoin <- setNames(as.character(by_exprs), as.character(by_exprs))
-  # unmatched_records <- anti_join(dataset2, added_records, by = by_antijoin) %>%
-  #   filter(!!enexpr(parameter))
-
   dataset_final <- dataset
 
   # create separate records objects as appropriate depending if user specific sds and/or pctl
@@ -322,10 +305,7 @@ derive_params_growth_age <- function(dataset,
         select(-c(P95, Sigma))
     }
 
-    # unmatched_sds <- unmatched_records %>%
-    #   mutate(!!!set_values_to_sds)
-
-    dataset_final <- bind_rows(dataset, add_sds) %>% # , unmatched_sds) %>%
+    dataset_final <- bind_rows(dataset, add_sds) %>%
       select(-c(L, M, S, sex_join, ageu_join, metadata_age, temp_val, temp_z))
   }
 
@@ -364,13 +344,10 @@ derive_params_growth_age <- function(dataset,
         select(-c(P95, Sigma))
     } else {
       add_pctl <- add_pctl %>%
-        mutate(AVAL = pnorm(AVAL) * 100)
+        mutate(AVAL = pnorm(temp_z) * 100)
     }
 
-    # unmatched_pctl <- unmatched_records %>%
-    #   mutate(!!!set_values_to_pctl)
-
-    dataset_final <- bind_rows(dataset_final, add_pctl) %>% # , unmatched_pctl) %>%
+    dataset_final <- bind_rows(dataset_final, add_pctl) %>%
       select(-c(L, M, S, sex_join, ageu_join, metadata_age, temp_val, temp_z))
   }
 

diff --git a/R/derive_params_growth_height.R b/R/derive_params_growth_height.R
@@ -9,12 +9,6 @@
 #'   The variables specified in `sex`, `height`, `height_unit`, `parameter`, `analysis_var`
 #'   are expected to be in the dataset.
 #'
-#' @param by_vars Grouping variables
-#'
-#'   The variables from `dataset` which identifies a unique subject and their visit is expected.
-#'
-#'   *Permitted Values*: A list of variables created by `exprs()`, e.g `exprs(USUBJID, VISIT)`.
-#'
 #' @param sex Sex
 #'
 #'   A character vector is expected.
@@ -173,7 +167,6 @@
 #'
 #' derive_params_growth_height(
 #'   advs_under2,
-#'   by_vars = exprs(STUDYID, USUBJID, VISIT),
 #'   sex = SEX,
 #'   height = HGTTMP,
 #'   height_unit = HGTTMPU,
@@ -191,7 +184,6 @@
 #'   )
 #' )
 derive_params_growth_height <- function(dataset,
-                                        by_vars = NULL,
                                         sex,
                                         height,
                                         height_unit,
@@ -202,17 +194,13 @@ derive_params_growth_height <- function(dataset,
                                         set_values_to_sds = NULL,
                                         set_values_to_pctl = NULL) {
   # Apply assertions to each argument to ensure each object is appropriate class
-  if (is.null(by_vars)) {
-    warning("A list of variables created by `exprs()` is expected in argument `by_vars`.")
-  }
-  assert_vars(by_vars)
   sex <- assert_symbol(enexpr(sex))
   height <- assert_symbol(enexpr(height))
   height_unit <- assert_symbol(enexpr(height_unit))
   analysis_var <- assert_symbol(enexpr(analysis_var))
   assert_data_frame(
     dataset,
-    required_vars = expr_c(sex, height, height_unit, analysis_var, by_vars)
+    required_vars = expr_c(sex, height, height_unit, analysis_var)
   )
   assert_data_frame(
     meta_criteria,
@@ -266,11 +254,6 @@ derive_params_growth_height <- function(dataset,
     ) %>%
     filter(!is.na(meta_height))
 
-  by_exprs <- enexpr(by_vars)
-  by_antijoin <- setNames(as.character(by_exprs), as.character(by_exprs))
-  # unmatched_records <- anti_join(dataset2, added_records, by = by_antijoin) %>%
-  #   filter(!!enexpr(parameter))
-
   dataset_final <- dataset
 
   # create separate records objects as appropriate depending if user specific sds and/or pctl
@@ -293,10 +276,8 @@ derive_params_growth_height <- function(dataset,
           )
         )
     }
-    # unmatched_sds <- unmatched_records %>%
-    #   mutate(!!!set_values_to_sds)
 
-    dataset_final <- bind_rows(dataset, add_sds) %>% # , unmatched_sds) %>%
+    dataset_final <- bind_rows(dataset, add_sds) %>%
       select(-c(L, M, S, sex_join, heightu_join, meta_height, temp_val, temp_z))
   }
 
@@ -321,12 +302,9 @@ derive_params_growth_height <- function(dataset,
     }
 
     add_pctl <- add_pctl %>%
-      mutate(AVAL = pnorm(AVAL) * 100)
-
-    # unmatched_pctl <- unmatched_records %>%
-    #   mutate(!!!set_values_to_pctl)
+      mutate(AVAL = pnorm(temp_z) * 100)
 
-    dataset_final <- bind_rows(dataset_final, add_pctl) %>% # , unmatched_pctl) %>%
+    dataset_final <- bind_rows(dataset_final, add_pctl) %>%
       select(-c(L, M, S, sex_join, heightu_join, meta_height, temp_val, temp_z))
   }
 

diff --git a/inst/templates/ad_advs.R b/inst/templates/ad_advs.R
@@ -295,7 +295,6 @@ advs_age_wt <- advs %>%
   slice_derivation(
     derivation = derive_params_growth_age,
     args = params(
-      by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
       sex = SEX,
       age = AAGECUR,
       age_unit = AAGECURU,
@@ -329,7 +328,6 @@ advs_age_wt <- advs %>%
   slice_derivation(
     derivation = derive_params_growth_age,
     args = params(
-      by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
       sex = SEX,
       age = AAGECUR,
       age_unit = AAGECURU,
@@ -364,7 +362,6 @@ advs_age_wt <- advs %>%
 
 advs_age <- advs_age_wt %>%
   derive_params_growth_age(
-    by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
     sex = SEX,
     age = AAGECUR,
     age_unit = AAGECURU,
@@ -381,7 +378,6 @@ advs_age <- advs_age_wt %>%
     )
   ) %>%
   derive_params_growth_age(
-    by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
     sex = SEX,
     age = AAGECUR,
     age_unit = AAGECURU,
@@ -408,7 +404,6 @@ advs_ht_lgth <- advs %>%
   restrict_derivation(
     derivation = derive_params_growth_height,
     args = params(
-      by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
       sex = SEX,
       height = HGTTMP,
       height_unit = HGTTMPU,

diff --git a/man/derive_params_growth_age.Rd b/man/derive_params_growth_age.Rd
diff --git a/man/derive_params_growth_height.Rd b/man/derive_params_growth_height.Rd
diff --git a/tests/testthat/test-derive_params_growth_age.R b/tests/testthat/test-derive_params_growth_age.R
@@ -20,7 +20,6 @@ test_that("derive_params_growth_age Test 1: Weight SDS and percentile works", {
   )
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -80,7 +79,6 @@ test_that("derive_params_growth_age Test 2: Height SDS and percentile works (P50
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -139,7 +137,6 @@ test_that("derive_params_growth_age Test 3: BMI SDS and percentile works (Z-scor
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -196,7 +193,6 @@ test_that("derive_params_growth_age Test 4: Head circumference SDS and percentil
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -249,7 +245,6 @@ test_that("derive_params_growth_age Test 5: Extreme BMI value derivation works",
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -319,7 +314,6 @@ test_that("derive_params_growth_age Test 6: Test out of bound ages", {
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -357,7 +351,6 @@ test_that("derive_params_growth_age Test 7: Test missing anthropocentric values"
 
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -396,7 +389,6 @@ test_that("derive_params_growth_age Test 8: Age unit/Metadata in months works",
   )
   actual <- derive_params_growth_age(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,
@@ -446,7 +438,6 @@ test_that("derive_params_growth_age Test 8: WHO outlier adjustment works", {
 
   actual <- derive_params_growth_age(
     vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     age = AGECUR,
     age_unit = AGEU,

diff --git a/tests/testthat/test-derive_params_growth_height.R b/tests/testthat/test-derive_params_growth_height.R
@@ -21,7 +21,6 @@ test_that("derive_params_growth_height Test 1: derive_params_growth_height works
 
   actual <- derive_params_growth_height(
     dataset = vs_data,
-    by_vars = exprs(STUDYID, USUBJID, VISIT),
     sex = SEX,
     height = HEIGHT,
     height_unit = HEIGHTU,
@@ -71,7 +70,6 @@ test_that("derive_params_growth_height Test 2: derives correct z-scores/percenti
 
   out <- derive_params_growth_height(
     dataset = vs_data,
-    by_vars = exprs(USUBJID, VISIT),
     sex = SEX,
     height = HEIGHT,
     height_unit = HEIGHTU,
@@ -108,7 +106,6 @@ test_that("derive_params_growth_height Test 3: handles missing height/lengths",
 
   out <- derive_params_growth_height(
     dataset = vs_data,
-    by_vars = exprs(USUBJID, VISIT),
     sex = SEX,
     height = HEIGHT,
     height_unit = HEIGHTU,
@@ -149,7 +146,6 @@ test_that("derive_params_growth_height Test 4: returns expected error message",
   expect_error(
     derive_params_growth_height(
       dataset = vs_data,
-      by_vars = exprs(USUBJID, VISIT),
       sex = SEX,
       height = HEIGHT,
       height_unit = HEIGHTU,
@@ -176,7 +172,6 @@ test_that("derive_params_growth_height Test 6: WHO outlier adjustment works", {
 
   actual <- derive_params_growth_height(
     dataset = vs_data,
-    by_vars = exprs(USUBJID, VISIT),
     sex = SEX,
     height = HEIGHT,
     height_unit = HEIGHTU,
@@ -206,6 +201,7 @@ test_that("derive_params_growth_height Test 6: WHO outlier adjustment works", {
 
   expect_equal(
     filter(actual, PARAMCD %in% c("WGHSDS", "WGHPCTL")) %>% pull(AVAL),
-    c(expected_sds, expected_pctl)
+    c(expected_sds, expected_pctl),
+    tolerance = 0.001
   )
 })
diff --git a/vignettes/advs.Rmd b/vignettes/advs.Rmd
@@ -393,7 +393,6 @@ advs <- advs %>%
   slice_derivation(
     derivation = derive_params_growth_age,
     args = params(
-      by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
       sex = SEX,
       age = AAGECUR,
       age_unit = AAGECURU,
@@ -481,7 +480,6 @@ advs <- advs %>%
   restrict_derivation(
     derivation = derive_params_growth_height,
     args = params(
-      by_vars = c(get_admiral_option("subject_keys"), exprs(AVISIT)),
       sex = SEX,
       height = HGTTMP,
       height_unit = HGTTMPU,