tests/testthat/test-indicate_na.R

In tidymodels/recipes: Preprocessing and Feature Engineering Steps for Modeling

library(testthat)
library(recipes)

train <-
  tibble::tibble(
    col1 = c("a", "b", "c"),
    col2 = c(NA, "d", "e"),
    col3 = c("k", NA, "g")
  )

test <-
  tibble::tibble(
    col1 = c(NA, NA, NA),
    col2 = c("t", "d", "e"),
    col3 = c("z", "f", NA)
  )

test_that("step_indicate_na populates binaries correctly", {
  rec1 <- recipe(train) %>%
    step_indicate_na(col1) %>%
    prep(train, verbose = FALSE, retain = TRUE)

  expect_identical(
    bake(rec1, train)$na_ind_col1,
    c(0L, 0L, 0L)
  )

  expect_identical(
    bake(rec1, test)$na_ind_col1,
    c(1L, 1L, 1L)
  )

  rec2 <- recipe(train) %>%
    step_indicate_na(col2, col3) %>%
    prep(train, verbose = FALSE, retain = TRUE)

  expect_equal(bake(rec2, train)$na_ind_col2, c(1, 0, 0))
  expect_equal(bake(rec2, train)$na_ind_col3, c(0, 1, 0))

  expect_equal(bake(rec2, test)$na_ind_col2, c(0, 0, 0))
  expect_equal(bake(rec2, test)$na_ind_col3, c(0, 0, 1))
})

test_that("step_indicate_na on all columns", {
  baked <- recipe(Ozone ~ ., data = airquality) %>%
    step_indicate_na(all_predictors()) %>%
    prep(airquality, verbose = FALSE, retain = TRUE) %>%
    bake(new_data = NULL)

  expect_named(
    baked,
    c(
      "Solar.R",
      "Wind",
      "Temp",
      "Month",
      "Day",
      "Ozone",
      "na_ind_Solar.R",
      "na_ind_Wind",
      "na_ind_Temp",
      "na_ind_Month",
      "na_ind_Day"
    )
  )
})

test_that("step_indicate_na on subset of columns", {
  baked <- recipe(Ozone ~ ., data = airquality) %>%
    step_indicate_na(Ozone, Solar.R) %>%
    prep(airquality, verbose = FALSE, retain = TRUE) %>%
    bake(new_data = NULL)

  expect_named(
    baked,
    c(
      "Solar.R",
      "Wind",
      "Temp",
      "Month",
      "Day",
      "Ozone",
      "na_ind_Ozone",
      "na_ind_Solar.R"
    )
  )

  baked2 <- recipe(Ozone ~ ., data = airquality) %>%
    step_indicate_na(Solar.R) %>%
    prep(airquality, verbose = FALSE, retain = TRUE) %>%
    bake(new_data = NULL)

  expect_named(
    baked2,
    c(
      "Solar.R",
      "Wind",
      "Temp",
      "Month",
      "Day",
      "Ozone",
      "na_ind_Solar.R"
    )
  )
})

test_that("check_name() is used", {
  dat <- dplyr::as_tibble(mtcars)
  dat$na_ind_mpg <- dat$mpg

  rec <- recipe(~., data = dat) %>%
    step_indicate_na(mpg)

  expect_snapshot(
    error = TRUE,
    prep(rec, training = dat)
  )
})

test_that("sparse = 'yes' works", {
  rec <- recipe(~., data = tibble(x = c(NA, letters)))

  dense <- rec %>%
    step_indicate_na(x, sparse = "no", keep_original_cols = FALSE) %>%
    prep() %>%
    bake(NULL)
  sparse <- rec %>%
    step_indicate_na(x, sparse = "yes", keep_original_cols = FALSE) %>%
    prep() %>%
    bake(NULL)

  expect_identical(dense, sparse)

  expect_false(any(vapply(dense, sparsevctrs::is_sparse_vector, logical(1))))
  expect_true(all(vapply(sparse, sparsevctrs::is_sparse_vector, logical(1))))
})

test_that("sparse argument is backwards compatible", {
  dat <- tibble(x = c(letters))
  rec <- recipe(~., data = dat) %>%
    step_indicate_na(x) %>%
    prep()

  exp <- bake(rec, dat)

  # Simulate old recipe
  rec$steps[[1]]$sparse <- NULL

  expect_identical(
    bake(rec, dat),
    exp
  )
})

test_that(".recipes_toggle_sparse_args works", {
  rec <- recipe(~., mtcars) %>%
    step_indicate_na(all_numeric_predictors(), sparse = "auto")

  exp <- rec %>% prep() %>% bake(NULL) %>% sparsevctrs::sparsity()

  expect_equal(
    .recipes_estimate_sparsity(rec),
    exp + exp
  )
})

# Infrastructure ---------------------------------------------------------------

test_that("bake method errors when needed non-standard role columns are missing", {
  rec1 <- recipe(train) %>%
    step_indicate_na(col1) %>%
    update_role(col1, new_role = "potato") %>%
    update_role_requirements(role = "potato", bake = FALSE) %>%
    prep(train, verbose = FALSE, retain = TRUE)

  expect_snapshot(error = TRUE, bake(rec1, new_data = test[, 2:3]))
})

test_that("empty printing", {
  rec <- recipe(mpg ~ ., mtcars)
  rec <- step_indicate_na(rec)

  expect_snapshot(rec)

  rec <- prep(rec, mtcars)

  expect_snapshot(rec)
})

test_that("empty selection prep/bake is a no-op", {
  rec1 <- recipe(mpg ~ ., mtcars)
  rec2 <- step_indicate_na(rec1)

  rec1 <- prep(rec1, mtcars)
  rec2 <- prep(rec2, mtcars)

  baked1 <- bake(rec1, mtcars)
  baked2 <- bake(rec2, mtcars)

  expect_identical(baked1, baked2)
})

test_that("empty selection tidy method works", {
  rec <- recipe(mpg ~ ., mtcars)
  rec <- step_indicate_na(rec)

  expect <- tibble(terms = character(), id = character())

  expect_identical(tidy(rec, number = 1), expect)

  rec <- prep(rec, mtcars)

  expect_identical(tidy(rec, number = 1), expect)
})

test_that("keep_original_cols works", {
  new_names <- c("na_ind_mpg")

  rec <- recipe(~mpg, mtcars) %>%
    step_indicate_na(all_predictors(), keep_original_cols = FALSE)

  rec <- prep(rec)
  res <- bake(rec, new_data = NULL)

  expect_equal(
    colnames(res),
    new_names
  )

  rec <- recipe(~mpg, mtcars) %>%
    step_indicate_na(all_predictors(), keep_original_cols = TRUE)

  rec <- prep(rec)
  res <- bake(rec, new_data = NULL)

  expect_equal(
    colnames(res),
    c("mpg", new_names)
  )
})

test_that("keep_original_cols - can prep recipes with it missing", {
  rec <- recipe(~mpg, mtcars) %>%
    step_indicate_na(all_predictors())

  rec$steps[[1]]$keep_original_cols <- NULL

  expect_snapshot(
    rec <- prep(rec)
  )

  expect_no_error(
    bake(rec, new_data = mtcars)
  )
})

test_that("printing", {
  rec <- recipe(Ozone ~ ., data = airquality) %>%
    step_indicate_na(all_predictors())

  expect_snapshot(print(rec))
  expect_snapshot(prep(rec))
})

test_that("0 and 1 rows data work in bake method", {
  data <- mtcars
  rec <- recipe(~., data) %>%
    step_indicate_na(disp, mpg) %>%
    prep()

  expect_identical(
    nrow(bake(rec, slice(data, 1))),
    1L
  )
  expect_identical(
    nrow(bake(rec, slice(data, 0))),
    0L
  )
})