tests/testthat/test-isomap.R

In recipes: Preprocessing and Feature Engineering Steps for Modeling

library(testthat)
library(recipes)

## expected results form the `dimRed` package

exp_res <- structure(list(
  Isomap1 = c(
    0.312570873898531, 0.371885353599467, 2.23124009833741,
    0.248271457498181, -0.420128801874122
  ),
  Isomap2 = c(
    -0.443724171391742, -0.407721529759647, 0.245721022395862,
    3.112001672258, 0.0292770508011519
  ),
  Isomap3 = c(
    0.761529345514676, 0.595015565588918, 1.59943072269788,
    0.566884409484389, 1.53770327701819
  )
),
.Names = c("Isomap1", "Isomap2", "Isomap3"),
class = c("tbl_df", "tbl", "data.frame"),
row.names = c(NA, -5L)
)

set.seed(1)
dat1 <- matrix(rnorm(15), ncol = 3)
dat2 <- matrix(rnorm(15), ncol = 3)
colnames(dat1) <- paste0("x", 1:3)
colnames(dat2) <- paste0("x", 1:3)

rec <- recipe(~., data = dat1)

scrub_timestamp <- function(x) {
  if (grepl("\\d{4}-\\d{2}-\\d{2} \\d{2}:\\d{2}:\\d{2}", x[1])) {
    return(NULL)
  }
  x
}

test_that("correct Isomap values", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  im_rec <- rec %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3, id = "")

  im_trained <- prep(im_rec, training = dat1, verbose = FALSE)

  im_pred <- bake(im_trained, new_data = dat2)

  # unique up to sign
  all.equal(abs(as.matrix(im_pred)), abs(as.matrix(exp_res)))

  im_tibble <-
    tibble(terms = c("x1", "x2", "x3"), id = "")

  expect_equal(tidy(im_rec, 1), im_tibble)
  expect_equal(tidy(im_trained, 1), im_tibble)
})

test_that("No ISOmap", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  im_rec <- rec %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 0, id = "") %>%
    prep()

  expect_equal(
    names(bake(im_rec, new_data = NULL)),
    colnames(dat1)
  )
  expect_null(im_rec$steps[[1]]$res)
  expect_snapshot(print(im_rec))
  expect_equal(
    tidy(im_rec, 1),
    tibble::tibble(terms = unname(im_rec$steps[[1]]$columns), id = "")
  )
})


test_that("ISOmap fails gracefully", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  expect_snapshot(error = TRUE,
    recipe(Sepal.Length ~ ., data = iris) %>%
      step_bs(Sepal.Width, deg_free = 1, degree = 1) %>%
      step_bs(Sepal.Length, deg_free = 1, degree = 1) %>%
      step_other(Species, threshold = .000000001) %>%
      step_isomap(all_numeric_predictors(), num_terms = 1, neighbors = 1) %>%
      prep(),
    transform = scrub_timestamp
  )
})

test_that("check_name() is used", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")
  dat <- dplyr::as_tibble(dat1)
  dat$Isomap1 <- dat$x1

  rec <- recipe(~ ., data = dat) %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3)

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

test_that("tunable", {
  rec <-
    recipe(~., data = iris) %>%
    step_isomap(all_predictors())
  rec_param <- tunable.step_isomap(rec$steps[[1]])
  expect_equal(rec_param$name, c("num_terms", "neighbors"))
  expect_true(all(rec_param$source == "recipe"))
  expect_true(is.list(rec_param$call_info))
  expect_equal(nrow(rec_param), 2)
  expect_equal(
    names(rec_param),
    c("name", "call_info", "source", "component", "component_id")
  )
})

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

test_that("bake method errors when needed non-standard role columns are missing", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  im_rec <- rec %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3) %>%
    update_role(x1, x2, x3, new_role = "potato") %>%
    update_role_requirements(role = "potato", bake = FALSE)

  im_trained <- prep(im_rec, training = dat1, verbose = FALSE)

  expect_error(bake(im_trained, new_data = dat2[, 1:2]),
               class = "new_data_missing_column")
})

test_that("empty printing", {
  rec <- recipe(mpg ~ ., mtcars)
  rec <- step_isomap(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_isomap(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_isomap(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", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  new_names <- c("Isomap1", "Isomap2", "Isomap3")

  rec <- recipe(~., data = dat1) %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3,
                keep_original_cols = FALSE)

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

  expect_equal(
    colnames(res),
    new_names
  )

  rec <- recipe(~., data = dat1) %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3,
                keep_original_cols = TRUE)

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

  expect_equal(
    colnames(res),
    c("x1", "x2", "x3", new_names)
  )
})

test_that("keep_original_cols - can prep recipes with it missing", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  rec <- recipe(~., data = dat1) %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3)

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

  expect_snapshot(
    rec <- prep(rec),
    transform = scrub_timestamp
  )

  expect_error(
    bake(rec, new_data = dat1),
    NA
  )
})

test_that("printing", {
  skip_on_cran()
  skip_if_not_installed("RSpectra")
  skip_if_not_installed("igraph")
  skip_if_not_installed("RANN")
  skip_if_not_installed("dimRed")
  skip_if(getRversion() <= "3.4.4")

  rec <- recipe(~., data = dat1) %>%
    step_isomap(x1, x2, x3, neighbors = 3, num_terms = 3)

  expect_snapshot(print(rec))
  expect_snapshot(prep(rec), transform = scrub_timestamp)
})

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

  params <- extract_parameter_set_dials(rec)

  expect_s3_class(params, "parameters")
  expect_identical(nrow(params), 2L)
})