tests/testthat/test-poly.R

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

library(testthat)
library(recipes)
skip_if_not_installed("modeldata")
data(biomass, package = "modeldata")


biomass_tr <- biomass[biomass$dataset == "Training", ]
biomass_te <- biomass[biomass$dataset == "Testing", ]

rec <- recipe(HHV ~ carbon + hydrogen + oxygen + nitrogen + sulfur,
  data = biomass_tr
)

test_that("correct basis functions", {
  with_poly <- rec %>%
    step_poly(carbon, hydrogen, id = "")

  exp_tidy_un <- tibble(
    terms = c("carbon", "hydrogen"),
    degree = rep(2L, 2),
    id = ""
  )
  expect_equal(exp_tidy_un, tidy(with_poly, number = 1))


  with_poly <- prep(with_poly, training = biomass_tr, verbose = FALSE)

  expect_equal(exp_tidy_un, tidy(with_poly, number = 1))

  with_poly_pred_tr <- bake(with_poly, new_data = biomass_tr)
  with_poly_pred_te <- bake(with_poly, new_data = biomass_te)

  carbon_poly_tr_exp <- poly(biomass_tr$carbon, degree = 2)
  hydrogen_poly_tr_exp <- poly(biomass_tr$hydrogen, degree = 2)
  carbon_poly_te_exp <- predict(carbon_poly_tr_exp, biomass_te$carbon)
  hydrogen_poly_te_exp <- predict(hydrogen_poly_tr_exp, biomass_te$hydrogen)

  carbon_poly_tr_res <- as.matrix(with_poly_pred_tr[, grep("carbon", names(with_poly_pred_tr))])
  colnames(carbon_poly_tr_res) <- NULL
  hydrogen_poly_tr_res <- as.matrix(with_poly_pred_tr[, grep("hydrogen", names(with_poly_pred_tr))])
  colnames(hydrogen_poly_tr_res) <- NULL

  carbon_poly_te_res <- as.matrix(with_poly_pred_te[, grep("carbon", names(with_poly_pred_te))])
  colnames(carbon_poly_te_res) <- 1:ncol(carbon_poly_te_res)
  hydrogen_poly_te_res <- as.matrix(with_poly_pred_te[, grep("hydrogen", names(with_poly_pred_te))])
  colnames(hydrogen_poly_te_res) <- 1:ncol(hydrogen_poly_te_res)

  ## remove attributes
  carbon_poly_tr_exp <- matrix(carbon_poly_tr_exp, ncol = 2)
  carbon_poly_te_exp <- matrix(carbon_poly_te_exp, ncol = 2)
  hydrogen_poly_tr_exp <- matrix(hydrogen_poly_tr_exp, ncol = 2)
  hydrogen_poly_te_exp <- matrix(hydrogen_poly_te_exp, ncol = 2)
  dimnames(carbon_poly_tr_res) <- NULL
  dimnames(carbon_poly_te_res) <- NULL
  dimnames(hydrogen_poly_tr_res) <- NULL
  dimnames(hydrogen_poly_te_res) <- NULL

  expect_equal(carbon_poly_tr_res, carbon_poly_tr_exp)
  expect_equal(carbon_poly_te_res, carbon_poly_te_exp)
  expect_equal(hydrogen_poly_tr_res, hydrogen_poly_tr_exp)
  expect_equal(hydrogen_poly_te_res, hydrogen_poly_te_exp)
})

test_that("check_name() is used", {
  dat <- mtcars
  dat$mpg_poly_1 <- dat$mpg

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

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

test_that("tunable", {
  rec <-
    recipe(~., data = iris) %>%
    step_poly(all_predictors())
  rec_param <- tunable.step_poly(rec$steps[[1]])
  expect_equal(rec_param$name, c("degree"))
  expect_true(all(rec_param$source == "recipe"))
  expect_true(is.list(rec_param$call_info))
  expect_equal(nrow(rec_param), 1)
  expect_equal(
    names(rec_param),
    c("name", "call_info", "source", "component", "component_id")
  )
})

test_that("old option argument", {
  expect_snapshot(
    res <-
      recipe(~., data = iris) %>%
      step_poly(Sepal.Width, options = list(degree = 3)) %>%
      prep() %>%
      bake(new_data = NULL)
  )
  exp_names <- c(
    "Sepal.Length", "Petal.Length", "Petal.Width", "Species",
    "Sepal.Width_poly_1", "Sepal.Width_poly_2", "Sepal.Width_poly_3"
  )
  expect_equal(
    names(res),
    exp_names
  )
})

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

test_that("bake method errors when needed non-standard role columns are missing", {
  with_poly <- rec %>%
    step_poly(carbon, hydrogen, id = "") %>%
    update_role(carbon, hydrogen, new_role = "potato") %>%
    update_role_requirements(role = "potato", bake = FALSE)

  exp_tidy_un <- tibble(
    terms = c("carbon", "hydrogen"),
    degree = rep(2L, 2),
    id = ""
  )

  with_poly <- prep(with_poly, training = biomass_tr, verbose = FALSE)

  expect_snapshot(error = TRUE, bake(with_poly, new_data = biomass_tr[, c(-3)]))
})

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

  expect <- tibble(terms = character(), degree = integer(), 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("mpg_poly_1", "mpg_poly_2")

  rec <- recipe(~ mpg, mtcars) %>%
    step_poly(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_poly(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_poly(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(HHV ~ carbon + hydrogen + oxygen + nitrogen + sulfur,
                data = biomass_tr) %>%
    step_poly(carbon, hydrogen)

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

test_that("tunable is setup to work with extract_parameter_set_dials", {
  skip_if_not_installed("dials")
  rec <- recipe(~., data = mtcars) %>%
    step_poly(
      all_predictors(),
      degree = hardhat::tune()
    )

  params <- extract_parameter_set_dials(rec)

  expect_s3_class(params, "parameters")
  expect_identical(nrow(params), 1L)
})

test_that("bad args", {

  expect_snapshot(
    recipe(mpg ~ ., data = mtcars) %>%
      step_poly(disp, degree = 0) %>%
      prep(),
    error = TRUE
  )

})