From 18a1c5bf28413773dc0d91696c7fa859be6c7ae3 Mon Sep 17 00:00:00 2001 From: Will Beasley Date: Thu, 11 Aug 2022 22:52:58 -0500 Subject: [PATCH] follow lintr suggestions --- R/table-nih-enrollment.R | 40 +++++++++++++--------- tests/testthat/test-table-nih-enrollment.R | 20 ++++++++--- vignettes/nih-enrollment-html.Rmd | 4 +-- 3 files changed, 42 insertions(+), 22 deletions(-) diff --git a/R/table-nih-enrollment.R b/R/table-nih-enrollment.R index 9f4d57d..aa815bd 100644 --- 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 index 45d5561..601a359 100644 --- 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 index 33e773f..dda39db 100644 --- 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),