context("testing gpb.Dataset functionality") # Avoid that long tests get executed on CRAN if(Sys.getenv("GPBOOST_ALL_TESTS") == "GPBOOST_ALL_TESTS"){ data(agaricus.test, package = "gpboost") test_data <- agaricus.test$data[1L:100L, ] test_label <- agaricus.test$label[1L:100L] test_that("gpb.Dataset: basic construction, saving, loading", { # from sparse matrix dtest1 <- gpb.Dataset(test_data, label = test_label) # from dense matrix dtest2 <- gpb.Dataset(as.matrix(test_data), label = test_label) expect_equal(getinfo(dtest1, "label"), getinfo(dtest2, "label")) # save to a local file tmp_file <- tempfile("gpb.Dataset_") capture.output( gpb.Dataset.save(dtest1, tmp_file) , file='NUL') # read from a local file dtest3 <- gpb.Dataset(tmp_file) capture.output( gpb.Dataset.construct(dtest3) , file='NUL') unlink(tmp_file) expect_equal(getinfo(dtest1, "label"), getinfo(dtest3, "label")) }) test_that("gpb.Dataset: getinfo & setinfo", { dtest <- gpb.Dataset(test_data) dtest$construct() setinfo(dtest, "label", test_label) labels <- getinfo(dtest, "label") expect_equal(test_label, getinfo(dtest, "label")) expect_true(length(getinfo(dtest, "weight")) == 0L) expect_true(length(getinfo(dtest, "init_score")) == 0L) # any other label should error expect_error(setinfo(dtest, "asdf", test_label)) }) test_that("gpb.Dataset: slice, dim", { dtest <- gpb.Dataset(test_data, label = test_label) gpb.Dataset.construct(dtest) expect_equal(dim(dtest), dim(test_data)) dsub1 <- gpboost::slice(dtest, seq_len(42L)) gpb.Dataset.construct(dsub1) expect_equal(nrow(dsub1), 42L) expect_equal(ncol(dsub1), ncol(test_data)) }) test_that("gpb.Dataset: colnames", { dtest <- gpb.Dataset(test_data, label = test_label) expect_equal(colnames(dtest), colnames(test_data)) gpb.Dataset.construct(dtest) expect_equal(colnames(dtest), colnames(test_data)) expect_error({ colnames(dtest) <- "asdf" }) new_names <- make.names(seq_len(ncol(test_data))) expect_silent(colnames(dtest) <- new_names) expect_equal(colnames(dtest), new_names) }) test_that("gpb.Dataset: nrow is correct for a very sparse matrix", { nr <- 1000L x <- Matrix::rsparsematrix(nr, 100L, density = 0.0005) # we want it very sparse, so that last rows are empty expect_lt(max(x@i), nr) dtest <- gpb.Dataset(x) expect_equal(dim(dtest), dim(x)) }) test_that("gpb.Dataset: Dataset should be able to construct from matrix and return non-null handle", { rawData <- matrix(runif(1000L), ncol = 10L) ref_handle <- NULL handle <- .Call( gpboost:::LGBM_DatasetCreateFromMat_R , rawData , nrow(rawData) , ncol(rawData) , gpboost:::gpb.params2str(params = list()) , ref_handle ) expect_is(handle, "externalptr") expect_false(is.null(handle)) .Call(gpboost:::LGBM_DatasetFree_R, handle) handle <- NULL }) test_that("cpp errors should be raised as proper R errors", { data(agaricus.train, package = "gpboost") train <- agaricus.train dtrain <- gpb.Dataset( train$data , label = train$label , init_score = seq_len(10L) ) expect_error({ dtrain$construct() }, regexp = "Initial score size doesn't match data size") }) test_that("gpb.Dataset$setinfo() should convert 'group' to integer", { ds <- gpb.Dataset( data = matrix(rnorm(100L), nrow = 50L, ncol = 2L) , label = sample(c(0L, 1L), size = 50L, replace = TRUE) ) ds$construct() current_group <- ds$getinfo("group") expect_null(current_group) group_as_numeric <- rep(25.0, 2L) ds$setinfo("group", group_as_numeric) expect_identical(ds$getinfo("group"), as.integer(group_as_numeric)) }) test_that("gpb.Dataset should throw an error if 'reference' is provided but of the wrong format", { data(agaricus.test, package = "gpboost") test_data <- agaricus.test$data[1L:100L, ] test_label <- agaricus.test$label[1L:100L] # Try to trick gpb.Dataset() into accepting bad input expect_error({ dtest <- gpb.Dataset( data = test_data , label = test_label , reference = data.frame(x = seq_len(10L), y = seq_len(10L)) ) }, regexp = "reference must be a") }) test_that("Dataset$get_params() successfully returns parameters if you passed them", { # note that this list uses one "main" parameter (feature_pre_filter) and one that # is an alias (is_sparse), to check that aliases are handled correctly params <- list( "feature_pre_filter" = TRUE , "is_sparse" = FALSE ) ds <- gpb.Dataset( test_data , label = test_label , params = params ) returned_params <- ds$get_params() expect_identical(class(returned_params), "list") expect_identical(length(params), length(returned_params)) expect_identical(sort(names(params)), sort(names(returned_params))) for (param_name in names(params)) { expect_identical(params[[param_name]], returned_params[[param_name]]) } }) test_that("Dataset$get_params() ignores irrelevant parameters", { params <- list( "feature_pre_filter" = TRUE , "is_sparse" = FALSE , "nonsense_parameter" = c(1.0, 2.0, 5.0) ) ds <- gpb.Dataset( test_data , label = test_label , params = params ) returned_params <- ds$get_params() expect_false("nonsense_parameter" %in% names(returned_params)) }) test_that("Dataset$update_parameters() does nothing for empty inputs", { ds <- gpb.Dataset( test_data , label = test_label ) initial_params <- ds$get_params() expect_identical(initial_params, list()) # update_params() should return "self" so it can be chained res <- ds$update_params( params = list() ) expect_true(gpboost:::gpb.is.Dataset(res)) new_params <- ds$get_params() expect_identical(new_params, initial_params) }) test_that("Dataset$update_params() works correctly for recognized Dataset parameters", { ds <- gpb.Dataset( test_data , label = test_label ) initial_params <- ds$get_params() expect_identical(initial_params, list()) new_params <- list( "data_random_seed" = 708L , "enable_bundle" = FALSE ) res <- ds$update_params( params = new_params ) expect_true(gpboost:::gpb.is.Dataset(res)) updated_params <- ds$get_params() for (param_name in names(new_params)) { expect_identical(new_params[[param_name]], updated_params[[param_name]]) } }) test_that("Dataset$finalize() should not fail on an already-finalized Dataset", { dtest <- gpb.Dataset( data = test_data , label = test_label ) expect_true(gpboost:::gpb.is.null.handle(dtest$.__enclos_env__$private$handle)) dtest$construct() expect_false(gpboost:::gpb.is.null.handle(dtest$.__enclos_env__$private$handle)) dtest$finalize() expect_true(gpboost:::gpb.is.null.handle(dtest$.__enclos_env__$private$handle)) # calling finalize() a second time shouldn't cause any issues dtest$finalize() expect_true(gpboost:::gpb.is.null.handle(dtest$.__enclos_env__$private$handle)) }) test_that("gpb.Dataset: should be able to run gpb.train() immediately after using gpb.Dataset() on a file", { dtest <- gpb.Dataset( data = test_data , label = test_label ) tmp_file <- tempfile(pattern = "gpb.Dataset_") capture.output( gpb.Dataset.save( dataset = dtest , fname = tmp_file ) , file='NUL') # read from a local file dtest_read_in <- gpb.Dataset(data = tmp_file) param <- list( objective = "binary" , metric = "binary_logloss" , num_leaves = 5L , learning_rate = 1.0 ) # should be able to train right away bst <- gpb.train( params = param , data = dtest_read_in , verbose = 0 ) expect_true(gpboost:::gpb.is.Booster(x = bst)) }) test_that("gpb.Dataset: should be able to run gpb.cv() immediately after using gpb.Dataset() on a file", { dtest <- gpb.Dataset( data = test_data , label = test_label ) tmp_file <- tempfile(pattern = "gpb.Dataset_") capture.output( gpb.Dataset.save( dataset = dtest , fname = tmp_file ) , file='NUL') # read from a local file dtest_read_in <- gpb.Dataset(data = tmp_file) param <- list( objective = "binary" , metric = "binary_logloss" , num_leaves = 5L , learning_rate = 1.0 ) # should be able to train right away bst <- gpb.cv( params = param , data = dtest_read_in , verbose = 0 ) expect_is(bst, "gpb.CVBooster") }) }