tests/testthat/test_example_functions.R

In cvms: Cross-Validation for Model Selection

library(cvms)
context("example functions")

## preprocess_functions()

test_that("the expected function definitions are returned in preprocess_functions()", {
  testthat::skip("Fails in check - IMPROVE THESE TESTS")
  expect_equal(
    head(capture.output(preprocess_functions("standardize")), 22),
    c(
      "function(train_data, test_data, formula, hyperparameters){",
      "",
      "      # Get centering and scaling parameters from the train_data",
      "      preprocess_params <- caret::preProcess(train_data,",
      "                                             method = c(\"scale\", \"center\"))",
      "",
      "      # Apply standardization to all numeric variables in",
      "      # train_data and test_data",
      "      train_data <- stats::predict(preprocess_params, train_data)",
      "      test_data <- stats::predict(preprocess_params, test_data)",
      "",
      "      # Extract parameters and add to tibble",
      "      tidy_parameters <- tibble::tibble(\"Measure\" = c(\"Mean\", \"SD\")) %>%",
      "        dplyr::bind_cols(",
      "          dplyr::bind_rows(preprocess_params$mean,",
      "                           preprocess_params$std)",
      "          )",
      "",
      "      list(\"train\" = train_data,",
      "           \"test\" = test_data,",
      "           \"parameters\" = tidy_parameters)",
      "    }"
    )
  )

  expect_equal(
    head(capture.output(preprocess_functions("normalize")), 22),
    c(
      "function(train_data, test_data, formula, hyperparameters){",
      "",
      "        # Get normalization parameters from the train_data",
      "        preprocess_params <- caret::preProcess(train_data,",
      "                                               method = c(\"range\"),",
      "                                               rangeBounds = c(0,1))",
      "",
      "        # Apply normalization to all numeric variables in",
      "        # train_data and test_data",
      "        train_data <- stats::predict(preprocess_params, train_data)",
      "        test_data <- stats::predict(preprocess_params, test_data)",
      "",
      "        # Extract parameters and add to tibble",
      "        tidy_parameters <- tibble::tibble(\"Measure\" = c(\"Min\", \"Max\")) %>%",
      "          dplyr::bind_cols(",
      "            dplyr::as_tibble(preprocess_params$ranges)",
      "          )",
      "",
      "        list(\"train\" = train_data,",
      "             \"test\" = test_data,",
      "             \"parameters\" = tidy_parameters)", "      }"
    )
  )
})

test_that("the expected output is returned from preprocess_functions() functions", {

  # Standardize

  # Load data and fold it
  xpectr::set_test_seed(1)
  partitions <- groupdata2::partition(participant.scores,
    p = 0.75,
    cat_col = "diagnosis",
    id_col = "participant",
    list_out = FALSE
  ) %>%
    dplyr::mutate(
      diagnosis = as.numeric(diagnosis),
      notAVar = 1
    ) %>%
    dplyr::ungroup()
  train_set <- partitions[partitions[[".partitions"]] == 1, ]
  test_set <- partitions[partitions[[".partitions"]] == 2, ]

  # Standardize with preprocess_fn
  standardize_fn <- preprocess_functions("standardize")
  standardized_by_fn <- standardize_fn(
    train_data = train_set, test_data = test_set,
    # notAVar is just to avoid changing the unit tests below
    # when diagnosis wouldn't be standardized
    formula = as.formula("notAVar ~ ."),
    hyperparameters = NULL
  )

  # Standardize manually
  train_mean_age <- mean(train_set$age)
  train_sd_age <- sd(train_set$age)
  train_mean_score <- mean(train_set$score)
  train_sd_score <- sd(train_set$score)
  train_mean_session <- mean(train_set$session)
  train_sd_session <- sd(train_set$session)
  train_mean_diagnosis <- mean(train_set$diagnosis)
  train_sd_diagnosis <- sd(train_set$diagnosis)

  standardized_train <- train_set
  standardized_test <- test_set
  standardized_train[["age"]] <- (standardized_train[["age"]] - train_mean_age) / train_sd_age
  standardized_test[["age"]] <- (standardized_test[["age"]] - train_mean_age) / train_sd_age
  standardized_train[["score"]] <- (standardized_train[["score"]] - train_mean_score) / train_sd_score
  standardized_test[["score"]] <- (standardized_test[["score"]] - train_mean_score) / train_sd_score
  standardized_train[["session"]] <- (standardized_train[["session"]] - train_mean_session) / train_sd_session
  standardized_test[["session"]] <- (standardized_test[["session"]] - train_mean_session) / train_sd_session
  standardized_train[["diagnosis"]] <- (standardized_train[["diagnosis"]] - train_mean_diagnosis) / train_sd_diagnosis
  standardized_test[["diagnosis"]] <- (standardized_test[["diagnosis"]] - train_mean_diagnosis) / train_sd_diagnosis

  # Test
  expect_equal(standardized_by_fn[["train"]], standardized_train)
  expect_equal(standardized_by_fn[["test"]], standardized_test)
  expect_equal(
    standardized_by_fn[["parameters"]]$Measure,
    c("Mean", "SD")
  )

  expect_equal(standardized_by_fn[["parameters"]]$age,
    c(train_mean_age, train_sd_age),
    tolerance = 1e-4
  )
  expect_equal(standardized_by_fn[["parameters"]]$age,
    c(29.2857142857143, 7.93185260290972),
    tolerance = 1e-4
  )

  expect_equal(standardized_by_fn[["parameters"]]$diagnosis,
    c(0.571428571428571, 0.50709255283711),
    tolerance = 1e-4
  )
  expect_equal(standardized_by_fn[["parameters"]]$diagnosis,
    c(train_mean_diagnosis, train_sd_diagnosis),
    tolerance = 1e-4
  )

  expect_equal(standardized_by_fn[["parameters"]]$score,
    c(40.2857142857143, 19.4220051929322),
    tolerance = 1e-4
  )
  expect_equal(standardized_by_fn[["parameters"]]$score,
    c(train_mean_score, train_sd_score),
    tolerance = 1e-4
  )

  expect_equal(standardized_by_fn[["parameters"]]$session,
    c(2, 0.836660026534076),
    tolerance = 1e-4
  )
  expect_equal(standardized_by_fn[["parameters"]]$session,
    c(train_mean_session, train_sd_session),
    tolerance = 1e-4
  )

  # Normalize

  # Normalize with preprocess_fn
  normalize_fn <- preprocess_functions("range")
  normalized_by_fn <- normalize_fn(
    train_data = train_set, test_data = test_set,
    formula = as.formula("notAVar ~ ."),
    hyperparameters = NULL
  )

  # Normalize manually
  train_min_age <- min(train_set[["age"]])
  train_max_age <- max(train_set[["age"]])
  train_min_diagnosis <- min(train_set[["diagnosis"]])
  train_max_diagnosis <- max(train_set[["diagnosis"]])
  train_min_score <- min(train_set[["score"]])
  train_max_score <- max(train_set[["score"]])
  train_min_session <- min(train_set[["session"]])
  train_max_session <- max(train_set[["session"]])

  minMaxScaler <- function(x, min__, max__) {
    (x - min__) / (max__ - min__)
  }

  normalized_train_set <- train_set
  normalized_test_set <- test_set
  normalized_train_set[["age"]] <- minMaxScaler(
    normalized_train_set[["age"]],
    train_min_age, train_max_age
  )
  normalized_train_set[["diagnosis"]] <- minMaxScaler(
    normalized_train_set[["diagnosis"]],
    train_min_diagnosis, train_max_diagnosis
  )
  normalized_train_set[["score"]] <- minMaxScaler(
    normalized_train_set[["score"]],
    train_min_score, train_max_score
  )
  normalized_train_set[["session"]] <- minMaxScaler(
    normalized_train_set[["session"]],
    train_min_session, train_max_session
  )
  normalized_test_set[["age"]] <- minMaxScaler(
    normalized_test_set[["age"]],
    train_min_age, train_max_age
  )
  normalized_test_set[["diagnosis"]] <- minMaxScaler(
    normalized_test_set[["diagnosis"]],
    train_min_diagnosis, train_max_diagnosis
  )
  normalized_test_set[["score"]] <- minMaxScaler(
    normalized_test_set[["score"]],
    train_min_score, train_max_score
  )
  normalized_test_set[["session"]] <- minMaxScaler(
    normalized_test_set[["session"]],
    train_min_session, train_max_session
  )

  # Test
  expect_identical(normalized_by_fn[["train"]], normalized_train_set)
  expect_identical(normalized_by_fn[["test"]], normalized_test_set)
  expect_equal(
    normalized_by_fn[["parameters"]]$Measure,
    c("Min", "Max")
  )
  expect_equal(normalized_by_fn[["parameters"]]$age,
    c(20, 43),
    tolerance = 1e-4
  )
  expect_equal(normalized_by_fn[["parameters"]]$diagnosis,
    c(0, 1),
    tolerance = 1e-4
  )
  expect_equal(normalized_by_fn[["parameters"]]$score,
    c(10, 81),
    tolerance = 1e-4
  )
  expect_equal(normalized_by_fn[["parameters"]]$session,
    c(1, 3),
    tolerance = 1e-4
  )
})

# TODO test the other example function functions