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OuhscBbmc · Aug 12, 2022 · 18a1c5b · 18a1c5b
1 parent f6e7e7c
commit 18a1c5b
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Showing 3 changed files with 42 additions and 22 deletions.
diff --git a/R/table-nih-enrollment.R b/R/table-nih-enrollment.R
@@ -118,8 +118,12 @@
 #' @export
 table_nih_enrollment <- function(
   d,
-  d_lu_gender=NULL, d_lu_race=NULL, d_lu_ethnicity=NULL,
-  variable_gender="gender", variable_race="race", variable_ethnicity="ethnicity"
+  d_lu_gender         = NULL,
+  d_lu_race           = NULL,
+  d_lu_ethnicity      = NULL,
+  variable_gender     = "gender",
+  variable_race       = "race",
+  variable_ethnicity  = "ethnicity"
 ) {
   checkmate::assert_data_frame(d                  , any.missing = FALSE)
   checkmate::assert_data_frame(d_lu_gender        , any.missing = FALSE, null.ok    = TRUE)
@@ -162,34 +166,34 @@ table_nih_enrollment <- function(
       race        = !!variable_race     ,
       ethnicity   = !!variable_ethnicity
     )
-  if( !is.null(d_lu_gender) ) {
+  if (!is.null(d_lu_gender)) {
     d <- d |>
-      dplyr::left_join(d_lu_gender, by=c("gender" = "input")) |>
+      dplyr::left_join(d_lu_gender, by = c("gender" = "input")) |>
       dplyr::select(-.data$gender) |>
       dplyr::rename(gender = .data$displayed)
   }
 
-  if( !is.null(d_lu_race) ) {
+  if (!is.null(d_lu_race)) {
     d <- d |>
-      dplyr::left_join(d_lu_race, by=c("race" = "input")) |>
+      dplyr::left_join(d_lu_race, by = c("race" = "input")) |>
       dplyr::select(-.data$race) |>
       dplyr::rename(race = .data$displayed)
   }
 
-  if( !is.null(d_lu_ethnicity) ) {
+  if (!is.null(d_lu_ethnicity)) {
     d <- d |>
-      dplyr::left_join(d_lu_ethnicity, by=c("ethnicity" = "input")) |>
+      dplyr::left_join(d_lu_ethnicity, by = c("ethnicity" = "input")) |>
       dplyr::select(-.data$ethnicity) |>
       dplyr::rename(ethnicity = .data$displayed)
   }
 
-  d_count <- d |>
+  d |>
     dplyr::count(.data$gender, .data$race, .data$ethnicity) |>
     dplyr::full_join(d_possible, by = c("gender", "race", "ethnicity")) |>
     dplyr::mutate(
-      gender    = factor(.data$gender   , levels=levels_gender    ),
-      race      = factor(.data$race     , levels=levels_race      ),
-      ethnicity = factor(.data$ethnicity, levels=levels_ethnicity ),
+      gender    = factor(.data$gender   , levels = levels_gender    ),
+      race      = factor(.data$race     , levels = levels_race      ),
+      ethnicity = factor(.data$ethnicity, levels = levels_ethnicity ),
       n         = dplyr::coalesce(.data$n, 0L)
     ) |>
     dplyr::select(.data$gender, .data$race, .data$ethnicity, .data$n) |>
@@ -199,8 +203,12 @@ table_nih_enrollment <- function(
 #' @export
 table_nih_enrollment_pretty <- function(
   d,
-  d_lu_gender=NULL, d_lu_race=NULL, d_lu_ethnicity=NULL,
-  variable_gender="gender", variable_race="race", variable_ethnicity="ethnicity"
+  d_lu_gender         = NULL,
+  d_lu_race           = NULL,
+  d_lu_ethnicity      = NULL,
+  variable_gender     = "gender",
+  variable_race       = "race",
+  variable_ethnicity  = "ethnicity"
 ) {
   column_order <- c(
     "race",
@@ -223,11 +231,11 @@ table_nih_enrollment_pretty <- function(
       gender_ethnicity  = paste0(.data$gender, " by ", .data$ethnicity)
     ) |>
     dplyr::select(-.data$gender, -.data$ethnicity) |>
-    tidyr::spread(key=.data$gender_ethnicity, value=.data$n) |>
+    tidyr::spread(key = .data$gender_ethnicity, value = .data$n) |>
     dplyr::select(!!column_order) |>
     knitr::kable(
       format      = "html",
-      format.args = list(big.mark=","),
+      format.args = list(big.mark = ","),
       escape      = FALSE,
       col.names   = c(
         "Racial\nCategories",

diff --git a/tests/testthat/test-table-nih-enrollment.R b/tests/testthat/test-table-nih-enrollment.R
@@ -72,7 +72,7 @@ test_that("ds_1b --ethnicity metadata required", {
     "Unknown"   ,  "Unknown/Not Reported Ethnicity"
   )
 
-  observed <- table_nih_enrollment(d_1b, d_lu_ethnicity=d_lu_ethnicity)
+  observed <- table_nih_enrollment(d_1b, d_lu_ethnicity = d_lu_ethnicity)
   expect_equal(observed, expected_1)
 })
 
@@ -112,7 +112,13 @@ test_that("ds_1c --all metadata required", {
     "Unknown"   ,  "Unknown/Not Reported Ethnicity"
   )
 
-  observed <- table_nih_enrollment(d_1c, d_lu_gender=d_lu_gender, d_lu_race=d_lu_race, d_lu_ethnicity=d_lu_ethnicity)
+  observed <-
+    table_nih_enrollment(
+      d_1c,
+      d_lu_gender     = d_lu_gender,
+      d_lu_race       = d_lu_race,
+      d_lu_ethnicity  = d_lu_ethnicity
+    )
   expect_equal(observed, expected_1)
 })
 
@@ -121,10 +127,16 @@ test_that("ds_1d --different variable names", {
     dplyr::rename(
       vg  = gender,
       vr  = race,
-      ve  = ethnicity
+      ve  = ethnicity,
     )
 
-  observed <- table_nih_enrollment(ds_1d, variable_gender="vg", variable_race="vr", variable_ethnicity="ve")
+  observed <-
+    table_nih_enrollment(
+      ds_1d,
+      variable_gender     = "vg",
+      variable_race       = "vr",
+      variable_ethnicity  = "ve"
+    )
   expect_equal(observed, expected_1)
 })
 

diff --git a/vignettes/nih-enrollment-html.Rmd b/vignettes/nih-enrollment-html.Rmd
@@ -41,7 +41,7 @@ Local Data Source
 ### Establish Datasets
 
 ```{r local-establish}
-path <- system.file("misc/example-data-1.csv", package="codified")
+path <- system.file("misc/example-data-1.csv", package = "codified")
 col_types <- readr::cols_only(
   record_id = readr::col_integer(),
   name_last = readr::col_character(),
@@ -50,7 +50,7 @@ col_types <- readr::cols_only(
   race      = readr::col_integer(),
   ethnicity = readr::col_integer()
 )
-ds <- readr::read_csv(path, col_types=col_types) |>
+ds <- readr::read_csv(path, col_types = col_types) |>
   dplyr::mutate(
     gender     = as.character(gender),
     race       = as.character(race),