tests/testthat/test-vimp_ranger_S4.R

In familiar: End-to-End Automated Machine Learning and Model Evaluation

familiar:::test_all_vimp_methods_available(
  familiar:::.get_available_ranger_vimp_methods(show_general = TRUE))
familiar:::test_all_vimp_methods_available(
  familiar:::.get_available_ranger_default_vimp_methods(show_general = TRUE))

# Don't perform any further tests on CRAN due to time of running the complete test.
testthat::skip_on_cran()
testthat::skip_on_ci()

familiar:::test_all_vimp_methods(
  familiar:::.get_available_ranger_vimp_methods(show_general = FALSE),
  hyperparameter_list = list(
    "count" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "continuous" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "binomial" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "multinomial" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "survival" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    )
  )
)

familiar:::test_all_vimp_methods(
  familiar:::.get_available_ranger_default_vimp_methods(show_general = FALSE))

# Parallel test.
familiar:::test_all_vimp_methods_parallel(
  familiar:::.get_available_ranger_vimp_methods(show_general = FALSE),
  hyperparameter_list = list(
    "count" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "continuous" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "binomial" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "multinomial" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    ),
    "survival" = list(
      "n_tree" = 4,
      "sample_size" = 1.00,
      "m_try" = 0.3,
      "node_size" = 5,
      "tree_depth" = 5,
      "alpha" = 0.1
    )
  )
)

# Count outcome ----------------------------------------------------------------
data <- familiar:::test_create_good_data("count")

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_impurity",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "count",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest impurity method correctly ranks count data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c(
      "per_capita_crime", "lower_status_percentage",
      "residence_before_1940_proportion", "avg_rooms", "industry")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "count",
  cluster_method = "none",
  imputation_method = "simple"
)

testthat::test_that(
  paste0("The ranger random forest permutation method correctly ranks count data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "per_capita_crime", "lower_status_percentage",
      "residence_before_1940_proportion", "avg_rooms")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_holdout_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "count",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest hold-out permutation method correctly ranks count data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "per_capita_crime", "lower_status_percentage",
      "residence_before_1940_proportion", "avg_rooms")))
  }
)

# Continuous outcome -----------------------------------------------------------
data <- familiar:::test_create_good_data("continuous")

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_impurity",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "continuous",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest impurity method correctly ranks continuous data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "enrltot", "avginc", "calwpct")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "continuous",
  cluster_method = "none",
  imputation_method = "simple")


testthat::test_that(
  paste0("The ranger random forest permutation method correctly ranks continuous data."), 
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "enrltot", "avginc", "calwpct")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_holdout_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "continuous",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest hold-out permutation method correctly ranks continuous data."), 
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "enrltot", "avginc", "calwpct")))
  }
)

# Binomial outcome -------------------------------------------------------------
data <- familiar:::test_create_good_data("binomial")

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_impurity",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "binomial",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest impurity method correctly ranks binomial data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "cell_shape_uniformity", "clump_thickness",
      "epithelial_cell_size", "bare_nuclei")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "binomial",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest permutation method correctly ranks binomial data."), {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
      "cell_shape_uniformity", "clump_thickness",
      "epithelial_cell_size", "bare_nuclei")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_holdout_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "binomial",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest hold-out permutation method correctly ranks binomial data."),
  {
  vimp_table <- suppressWarnings(familiar:::get_vimp_table(
    familiar:::.vimp(vimp_object, data)))
  
  testthat::expect_true(any(vimp_table[rank <= 2]$name %in% c(
    "cell_shape_uniformity", "clump_thickness",
    "epithelial_cell_size", "bare_nuclei")))
  }
)

# Multinomial outcome ----------------------------------------------------------
data <- familiar:::test_create_good_data("multinomial")

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_impurity",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "multinomial",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest impurity method correctly ranks multinomial outcome data."), {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c(
      "Petal_Length", "Petal_Width")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "multinomial",
  cluster_method = "none",
  imputation_method = "simple")


testthat::test_that(
  paste0("The ranger random forest permutation method correctly ranks multinomial outcome data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c(
      "Petal_Length", "Petal_Width")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_holdout_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "multinomial",
  cluster_method = "none",
  imputation_method = "simple")


testthat::test_that(
  paste0(
    "The ranger random forest hold-out permutation method ",
    "correctly ranks multinomial outcome data."), 
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c(
      "Petal_Length", "Petal_Width")))
  }
)

# Survival outcome -------------------------------------------------------------
data <- familiar:::test_create_good_data("survival")

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_impurity",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "survival",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest impurity method correctly ranks survival outcome data."),
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c("nodes", "rx", "adhere")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "survival",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0("The ranger random forest permutation method correctly ranks survival outcome data."), 
  {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c("nodes", "rx", "adhere")))
  }
)

# Process dataset.
vimp_object <- familiar:::prepare_vimp_object(
  data = data,
  vimp_method = "random_forest_ranger_holdout_permutation",
  vimp_method_parameter_list = list(
    "n_tree" = 4,
    "sample_size" = 1.00,
    "m_try" = 0.3,
    "node_size" = 5,
    "tree_depth" = 5,
    "alpha" = 0.1),
  outcome_type = "survival",
  cluster_method = "none",
  imputation_method = "simple")

testthat::test_that(
  paste0(
    "The ranger random forest hold-out permutation method correctly ranks ",
    "survival outcome data."
  ), {
    vimp_table <- suppressWarnings(familiar:::get_vimp_table(
      familiar:::.vimp(vimp_object, data)))
    
    testthat::expect_true(all(vimp_table[rank <= 2]$name %in% c("nodes", "rx", "adhere")))
  }
)

testthat::skip("Skip hyperparameter optimisation, unless manual.")

familiar:::test_hyperparameter_optimisation(
  vimp_methods = familiar:::.get_available_ranger_vimp_methods(show_general = TRUE),
  debug = FALSE,
  parallel = FALSE)