test_that("shrunken centroids", { library(dplyr) library(purrr) library(hardhat) # ---------------------------------------------------------------------------- set.seed(1) nsc_test <- tibble( x = rnorm(300), y = rnorm(300), class = rep(letters[1:3], each = 100) ) # make completely separable nsc_test$x[nsc_test$class == "a"] <- nsc_test$x[nsc_test$class == "a"] + 8 nsc_test$y[nsc_test$class == "b"] <- nsc_test$y[nsc_test$class == "b"] - 8 # ---------------------------------------------------------------------------- nsc_rec_zero <- recipe(class ~ x + y, data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", threshold = 0 ) %>% prep() exp_res <- dplyr::tibble( variable = character(0), class = character(0), global = numeric(0), by_class = numeric(0), shrunken = numeric(0), std_dev = numeric(0) ) cent_zero <- nsc_rec_zero$steps[[1]]$objects expect_equal(cent_zero[0,], exp_res) expect_equal(nrow(cent_zero), 6) expect_true(!any(cent_zero$shrunken == 0)) expect_equal( names(bake(nsc_rec_zero, new_data = NULL)), c("x", "y", "class", "classdist_a", "classdist_b", "classdist_c") ) # ---------------------------------------------------------------------------- nsc_rec_one <- recipe(class ~ x + y, data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", threshold = 1, log = FALSE, prefix = "potato_" ) %>% prep() cent_one <- nsc_rec_one$steps[[1]]$objects expect_equal(cent_one[0,], exp_res) expect_equal(nrow(cent_one), 6) expect_true(all(cent_one$shrunken == 0)) expect_equal( names(bake(nsc_rec_one, new_data = NULL)), c("x", "y", "class", "potato_a", "potato_b", "potato_c") ) # ---------------------------------------------------------------------------- nsc_rec_half <- recipe(class ~ x + y, data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", threshold = 1 / 2, keep_original_cols = FALSE ) nsc_rec_half_prep <- prep(nsc_rec_half) expect_snapshot(print(nsc_rec_half)) expect_snapshot(print(nsc_rec_half_prep)) tidy_spec <- tidy(nsc_rec_half, 1) tidy_prep <- tidy(nsc_rec_half_prep, 1) expect_snapshot(print(tidy_spec)) expect_snapshot(print(tidy_prep)) expect_equal( names(bake(nsc_rec_half_prep, new_data = NULL)), c("class", "classdist_a", "classdist_b", "classdist_c") ) # ---------------------------------------------------------------------------- expect_snapshot( recipe(class ~ x + y, data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", threshold = -1 ) %>% prep(), error = TRUE ) expect_snapshot( recipe(class ~ x + y, data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", sd_offset = -1 ) %>% prep(), error = TRUE ) # ------------------------------------------------------------------------------ nsc_test$weights <- importance_weights(1:nrow(nsc_test)) nsc_rec_weights <- recipe(class ~ ., data = nsc_test) %>% step_classdist_shrunken( all_numeric_predictors(), class = "class", threshold = 1 / 2, keep_original_cols = FALSE ) nsc_rec_weights_prep <- prep(nsc_rec_weights) tidy_weights_prep <- tidy(nsc_rec_weights_prep, 1) global_unwt <- tidy_prep %>% dplyr::filter(type == "global") %>% pluck("value") global_wt <- tidy_weights_prep %>% dplyr::filter(type == "global") %>% pluck("value") expect_true(all(global_unwt != global_wt)) expect_equal(unique(tidy_weights_prep$terms), c("x", "y")) # ------------------------------------------------------------------------------ expect_equal( required_pkgs(nsc_rec_weights), c("recipes", "dplyr", "tidyr") ) }) test_that("tunable", { rec <- recipe(~., data = iris) %>% step_classdist_shrunken(all_predictors()) rec_param <- tunable.step_classdist_shrunken(rec$steps[[1]]) expect_equal(rec_param$name, "threshold") 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") ) }) # Infrastructure --------------------------------------------------------------- test_that("bake method errors when needed non-standard role columns are missing", { rec <- recipe(Species ~ ., data = iris) %>% step_classdist_shrunken(Petal.Length, class = "Species", log = FALSE) %>% update_role(Petal.Length, new_role = "potato") %>% update_role_requirements(role = "potato", bake = FALSE) trained <- prep(rec, training = iris, verbose = FALSE) expect_error(bake(trained, new_data = iris[,c(-3)]), class = "new_data_missing_column") }) test_that("empty printing", { rec <- recipe(Species ~ ., iris) rec <- step_classdist_shrunken(rec, class = "Species") expect_snapshot(rec) rec <- prep(rec, iris) expect_snapshot(rec) }) test_that("empty selection prep/bake is a no-op", { rec1 <- recipe(Species ~ ., iris) rec2 <- step_classdist_shrunken(rec1, class = "Species") rec1 <- prep(rec1, iris) rec2 <- prep(rec2, iris) baked1 <- bake(rec1, iris) baked2 <- bake(rec2, iris) expect_identical(baked1, baked2) }) test_that("empty selection tidy method works", { rec <- recipe(Species ~ ., iris) rec <- step_classdist_shrunken(rec, class = "Species") expect <- tibble( terms = character(), value = double(), class = character(), type = character(), threshold = double(), id = character() ) expect_identical(tidy(rec, number = 1), expect) rec <- prep(rec, iris) expect_identical(tidy(rec, number = 1), expect) }) test_that("keep_original_cols works", { new_names <- c("Species", "classdist_setosa", "classdist_versicolor", "classdist_virginica") rec <- recipe(Species ~ Sepal.Length, data = iris) %>% step_classdist_shrunken(all_predictors(), class = "Species", keep_original_cols = FALSE) rec <- prep(rec) res <- bake(rec, new_data = NULL) expect_equal( colnames(res), new_names ) rec <- recipe(Species ~ Sepal.Length, data = iris) %>% step_classdist_shrunken(all_predictors(), class = "Species", keep_original_cols = TRUE) rec <- prep(rec) res <- bake(rec, new_data = NULL) expect_equal( colnames(res), c("Sepal.Length", new_names) ) }) test_that("keep_original_cols - can prep recipes with it missing", { # step_classdist_shrunken() was added after keep_original_cols # Making this test case unlikely expect_true(TRUE) }) test_that("printing", { rec <- recipe(Species ~ ., data = iris) %>% step_classdist_shrunken(all_predictors(), class = "Species") 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_classdist_shrunken( all_predictors(), threshold = hardhat::tune() ) params <- extract_parameter_set_dials(rec) expect_s3_class(params, "parameters") expect_identical(nrow(params), 1L) })