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| @@ -1,96 +1,100 @@ | ||
| # # TODO: check differences variable names with / without '' | ||
| # | ||
| # test_that("option 1: fully pre-specified settings file works", { | ||
| # ### Tests for EXPLORE using iris dataset | ||
| # data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| # settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| # output_path <- system.file("examples", "output", package = "Explore") | ||
| # data <- farff::readARFF(data_path) | ||
| # # Required dependencies | ||
| # withr::local_package("farff") | ||
| # model <- Explore::trainExplore(output_path = output_path, | ||
| # file_name = "iris", | ||
| # train_data = data, | ||
| # ClassFeature = "'class'", | ||
| # PositiveClass = '"Iris-versicolor"') | ||
| # expect_equal(class(model), "character") | ||
| # # expect_true(is.na(model), info = "Test failed because model is NA") | ||
| # expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") | ||
| # }) | ||
| # | ||
| # test_that("option 2: pre-specified settings file with input data works", { | ||
| # | ||
| # ### Tests for EXPLORE using iris dataset | ||
| # data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| # settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| # output_path <- system.file("examples", "output", package = "Explore") | ||
| # data <- farff::readARFF(data_path) | ||
| # # Required dependencies | ||
| # withr::local_package("farff") | ||
| # model <- Explore::trainExplore(output_path = output_path, | ||
| # train_data = data, | ||
| # settings_path = settings_path, | ||
| # ClassFeature = "'class'", | ||
| # PositiveClass = '"Iris-versicolor"') | ||
| # expect_equal(class(model), "character") | ||
| # expect_false(model == "NA", info = "Test failed because model is NA") | ||
| # expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") # OR "'sepallength'>4.85" ? | ||
| # }) | ||
| # | ||
| # test_that("option 3: only input parameters (no settings file) works", { | ||
| # ### Tests for EXPLORE using iris dataset | ||
| # data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| # settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| # output_path <- system.file("examples", "output", package = "Explore") | ||
| # data <- farff::readARFF(data_path) | ||
| # # Required dependencies | ||
| # withr::local_package("farff") | ||
| # model <- Explore::trainExplore(output_path = output_path, | ||
| # file_name = "iris", | ||
| # train_data = data, | ||
| # ClassFeature = "'class'", | ||
| # PositiveClass = '"Iris-versicolor"') | ||
| # expect_equal(class(model), "character") | ||
| # expect_false(model == "NA", info = "Test failed because model is NA") | ||
| # expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") | ||
| # }) | ||
| # | ||
| # test_that("prediction", { | ||
| # ### Tests for EXPLORE using iris dataset | ||
| # data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| # settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| # output_path <- system.file("examples", "output", package = "Explore") | ||
| # data <- farff::readARFF(data_path) | ||
| # # Required dependencies | ||
| # withr::local_package("farff") | ||
| # model <- Explore::trainExplore(output_path = output_path, | ||
| # train_data = data, | ||
| # settings_path = settings_path, | ||
| # ClassFeature = "'class'", | ||
| # PositiveClass = '"Iris-versicolor"') | ||
| # prediction <- Explore::predictExplore(model, test_data = data) | ||
| # expect_equal(class(prediction), "integer") | ||
| # expect_equal(length(prediction), nrow(data)) | ||
| # expect_equal(sum(prediction %in% c(0,1) == FALSE),0) | ||
| # }) | ||
| # | ||
| # test_that("compute AUC", { | ||
| # ### Tests for EXPLORE using iris dataset | ||
| # data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| # settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| # output_path <- system.file("examples", "output", package = "Explore") | ||
| # # output_path <- system.file("examples", "output//", package = "Explore") | ||
| # # output_path <- paste0(output_path, "//") | ||
| # data <- farff::readARFF(data_path) | ||
| # | ||
| # # Required dependencies | ||
| # withr::local_package("farff") | ||
| # auroc <- Explore::aurocEXPLORE(output_path = output_path, | ||
| # train_data = data, | ||
| # settings_path = settings_path, | ||
| # ClassFeature = "'class'", | ||
| # PositiveClass = '"Iris-versicolor"') | ||
| # expect_equal(class(auroc), "numeric") | ||
| # expect_true(auroc < 100) | ||
| # expect_true(auroc > 0) | ||
| # }) | ||
| # TODO: check differences variable names with / without '' | ||
|
|
||
| test_that("option 1: fully pre-specified settings file works", { | ||
| ### Tests for EXPLORE using iris dataset | ||
| data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| output_path <- system.file("examples", "output", package = "Explore") | ||
| output_path <- paste0(output_path, "/") | ||
| data <- farff::readARFF(data_path) | ||
| # Required dependencies | ||
| withr::local_package("farff") | ||
| model <- Explore::trainExplore(output_path = output_path, | ||
| file_name = "iris", | ||
| train_data = data, | ||
| ClassFeature = "'class'", | ||
| PositiveClass = '"Iris-versicolor"') | ||
| expect_equal(class(model), "character") | ||
| # expect_true(is.na(model), info = "Test failed because model is NA") | ||
| expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") | ||
| }) | ||
|
|
||
| test_that("option 2: pre-specified settings file with input data works", { | ||
|
|
||
| ### Tests for EXPLORE using iris dataset | ||
| data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| output_path <- system.file("examples", "output", package = "Explore") | ||
| output_path <- paste0(output_path, "/") | ||
| data <- farff::readARFF(data_path) | ||
| # Required dependencies | ||
| withr::local_package("farff") | ||
| model <- Explore::trainExplore(output_path = output_path, | ||
| train_data = data, | ||
| settings_path = settings_path, | ||
| ClassFeature = "'class'", | ||
| PositiveClass = '"Iris-versicolor"') | ||
| expect_equal(class(model), "character") | ||
| expect_false(model == "NA", info = "Test failed because model is NA") | ||
| expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") # OR "'sepallength'>4.85" ? | ||
| }) | ||
|
|
||
| test_that("option 3: only input parameters (no settings file) works", { | ||
| ### Tests for EXPLORE using iris dataset | ||
| data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| output_path <- system.file("examples", "output", package = "Explore") | ||
| output_path <- paste0(output_path, "/") | ||
| data <- farff::readARFF(data_path) | ||
| # Required dependencies | ||
| withr::local_package("farff") | ||
| model <- Explore::trainExplore(output_path = output_path, | ||
| file_name = "iris", | ||
| train_data = data, | ||
| ClassFeature = "'class'", | ||
| PositiveClass = '"Iris-versicolor"') | ||
| expect_equal(class(model), "character") | ||
| expect_false(model == "NA", info = "Test failed because model is NA") | ||
| expect_equal(model, "'petallength'>2.45AND'petallength'<=4.95AND'petalwidth'<=1.65") | ||
| }) | ||
|
|
||
| test_that("prediction", { | ||
| ### Tests for EXPLORE using iris dataset | ||
| data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| output_path <- system.file("examples", "output", package = "Explore") | ||
| output_path <- paste0(output_path, "/") | ||
| data <- farff::readARFF(data_path) | ||
| # Required dependencies | ||
| withr::local_package("farff") | ||
| model <- Explore::trainExplore(output_path = output_path, | ||
| train_data = data, | ||
| settings_path = settings_path, | ||
| ClassFeature = "'class'", | ||
| PositiveClass = '"Iris-versicolor"') | ||
| prediction <- Explore::predictExplore(model, test_data = data) | ||
| expect_equal(class(prediction), "integer") | ||
| expect_equal(length(prediction), nrow(data)) | ||
| expect_equal(sum(prediction %in% c(0,1) == FALSE),0) | ||
| }) | ||
|
|
||
| test_that("compute AUC", { | ||
| ### Tests for EXPLORE using iris dataset | ||
| data_path <- system.file("examples", "iris.arff", package = "Explore") | ||
| settings_path <- system.file("examples", "iris.project", package = "Explore") | ||
| output_path <- system.file("examples", "output", package = "Explore") | ||
| # output_path <- system.file("examples", "output//", package = "Explore") | ||
| output_path <- paste0(output_path, "/") | ||
| data <- farff::readARFF(data_path) | ||
|
|
||
| # Required dependencies | ||
| withr::local_package("farff") | ||
| auroc <- Explore::aurocEXPLORE(output_path = output_path, | ||
| train_data = data, | ||
| settings_path = settings_path, | ||
| ClassFeature = "'class'", | ||
| PositiveClass = '"Iris-versicolor"') | ||
| expect_equal(class(auroc), "numeric") | ||
| expect_true(auroc < 100) | ||
| expect_true(auroc > 0) | ||
| }) |