test_Predictor.R

VERBOSITY <- as.integer(
  Sys.getenv("LIGHTGBM_TEST_VERBOSITY", "-1")
)

library(Matrix)

test_that("Predictor$finalize() should not fail", {
    X <- as.matrix(as.integer(iris[, "Species"]), ncol = 1L)
    y <- iris[["Sepal.Length"]]
    dtrain <- lgb.Dataset(X, label = y)
    bst <- lgb.train(
        data = dtrain
        , params = list(
            objective = "regression"
        )
        , verbose = VERBOSITY
        , nrounds = 3L
    )
    model_file <- tempfile(fileext = ".model")
    bst$save_model(filename = model_file)
    predictor <- Predictor$new(modelfile = model_file)

    expect_true(lgb.is.Predictor(predictor))

    expect_false(lgb.is.null.handle(predictor$.__enclos_env__$private$handle))

    predictor$finalize()
    expect_true(lgb.is.null.handle(predictor$.__enclos_env__$private$handle))

    # calling finalize() a second time shouldn't cause any issues
    predictor$finalize()
    expect_true(lgb.is.null.handle(predictor$.__enclos_env__$private$handle))
})

test_that("predictions do not fail for integer input", {
    X <- as.matrix(as.integer(iris[, "Species"]), ncol = 1L)
    y <- iris[["Sepal.Length"]]
    dtrain <- lgb.Dataset(X, label = y)
    fit <- lgb.train(
        data = dtrain
        , params = list(
            objective = "regression"
        )
        , verbose = VERBOSITY
        , nrounds = 3L
    )
    X_double <- X[c(1L, 51L, 101L), , drop = FALSE]
    X_integer <- X_double
    storage.mode(X_double) <- "double"
    pred_integer <- predict(fit, X_integer)
    pred_double <- predict(fit, X_double)
    expect_equal(pred_integer, pred_double)
})

test_that("start_iteration works correctly", {
    set.seed(708L)
    data(agaricus.train, package = "lightgbm")
    data(agaricus.test, package = "lightgbm")
    train <- agaricus.train
    test <- agaricus.test
    dtrain <- lgb.Dataset(
        agaricus.train$data
        , label = agaricus.train$label
    )
    dtest <- lgb.Dataset.create.valid(
        dtrain
        , agaricus.test$data
        , label = agaricus.test$label
    )
    bst <- lightgbm(
        data = as.matrix(train$data)
        , label = train$label
        , params = list(
            num_leaves = 4L
            , learning_rate = 0.6
            , objective = "binary"
            , verbosity = VERBOSITY
        )
        , nrounds = 50L
        , valids = list("test" = dtest)
        , early_stopping_rounds = 2L
    )
    expect_true(lgb.is.Booster(bst))
    pred1 <- predict(bst, newdata = test$data, rawscore = TRUE)
    pred_contrib1 <- predict(bst, test$data, predcontrib = TRUE)
    pred2 <- rep(0.0, length(pred1))
    pred_contrib2 <- rep(0.0, length(pred2))
    step <- 11L
    end_iter <- 49L
    if (bst$best_iter != -1L) {
        end_iter <- bst$best_iter - 1L
    }
    start_iters <- seq(0L, end_iter, by = step)
    for (start_iter in start_iters) {
        n_iter <- min(c(end_iter - start_iter + 1L, step))
        inc_pred <- predict(bst, test$data
            , start_iteration = start_iter
            , num_iteration = n_iter
            , rawscore = TRUE
        )
        inc_pred_contrib <- bst$predict(test$data
            , start_iteration = start_iter
            , num_iteration = n_iter
            , predcontrib = TRUE
        )
        pred2 <- pred2 + inc_pred
        pred_contrib2 <- pred_contrib2 + inc_pred_contrib
    }
    expect_equal(pred2, pred1)
    expect_equal(pred_contrib2, pred_contrib1)

    pred_leaf1 <- predict(bst, test$data, predleaf = TRUE)
    pred_leaf2 <- predict(bst, test$data, start_iteration = 0L, num_iteration = end_iter + 1L, predleaf = TRUE)
    expect_equal(pred_leaf1, pred_leaf2)
})

.expect_has_row_names <- function(pred, X) {
    if (is.vector(pred)) {
        rnames <- names(pred)
    } else {
        rnames <- row.names(pred)
    }
    expect_false(is.null(rnames))
    expect_true(is.vector(rnames))
    expect_true(length(rnames) > 0L)
    expect_equal(row.names(X), rnames)
}

.expect_doesnt_have_row_names <- function(pred) {
    if (is.vector(pred)) {
        expect_null(names(pred))
    } else {
        expect_null(row.names(pred))
    }
}

.check_all_row_name_expectations <- function(bst, X) {

    # dense matrix with row names
    pred <- predict(bst, X)
    .expect_has_row_names(pred, X)
    pred <- predict(bst, X, rawscore = TRUE)
    .expect_has_row_names(pred, X)
    pred <- predict(bst, X, predleaf = TRUE)
    .expect_has_row_names(pred, X)
    pred <- predict(bst, X, predcontrib = TRUE)
    .expect_has_row_names(pred, X)

    # dense matrix without row names
    Xcopy <- X
    row.names(Xcopy) <- NULL
    pred <- predict(bst, Xcopy)
    .expect_doesnt_have_row_names(pred)

    # sparse matrix with row names
    Xcsc <- as(X, "CsparseMatrix")
    pred <- predict(bst, Xcsc)
    .expect_has_row_names(pred, Xcsc)
    pred <- predict(bst, Xcsc, rawscore = TRUE)
    .expect_has_row_names(pred, Xcsc)
    pred <- predict(bst, Xcsc, predleaf = TRUE)
    .expect_has_row_names(pred, Xcsc)
    pred <- predict(bst, Xcsc, predcontrib = TRUE)
    .expect_has_row_names(pred, Xcsc)

    # sparse matrix without row names
    Xcopy <- Xcsc
    row.names(Xcopy) <- NULL
    pred <- predict(bst, Xcopy)
    .expect_doesnt_have_row_names(pred)
}

test_that("predict() keeps row names from data (regression)", {
    data("mtcars")
    X <- as.matrix(mtcars[, -1L])
    y <- as.numeric(mtcars[, 1L])
    dtrain <- lgb.Dataset(
      X
      , label = y
      , params = list(
        max_bins = 5L
        , min_data_in_bin = 1L
      )
    )
    bst <- lgb.train(
        data = dtrain
        , obj = "regression"
        , nrounds = 5L
        , verbose = VERBOSITY
        , params = list(min_data_in_leaf = 1L)
    )
    .check_all_row_name_expectations(bst, X)
})

test_that("predict() keeps row names from data (binary classification)", {
    data(agaricus.train, package = "lightgbm")
    X <- as.matrix(agaricus.train$data)
    y <- agaricus.train$label
    row.names(X) <- paste("rname", seq(1L, nrow(X)), sep = "")
    dtrain <- lgb.Dataset(X, label = y, params = list(max_bins = 5L))
    bst <- lgb.train(
        data = dtrain
        , obj = "binary"
        , nrounds = 5L
        , verbose = VERBOSITY
    )
    .check_all_row_name_expectations(bst, X)
})

test_that("predict() keeps row names from data (multi-class classification)", {
    data(iris)
    y <- as.numeric(iris$Species) - 1.0
    X <- as.matrix(iris[, names(iris) != "Species"])
    row.names(X) <- paste("rname", seq(1L, nrow(X)), sep = "")
    dtrain <- lgb.Dataset(X, label = y, params = list(max_bins = 5L))
    bst <- lgb.train(
        data = dtrain
        , obj = "multiclass"
        , params = list(num_class = 3L)
        , nrounds = 5L
        , verbose = VERBOSITY
    )
    .check_all_row_name_expectations(bst, X)
})

test_that("predictions for regression and binary classification are returned as vectors", {
    data(mtcars)
    X <- as.matrix(mtcars[, -1L])
    y <- as.numeric(mtcars[, 1L])
    dtrain <- lgb.Dataset(
      X
      , label = y
      , params = list(
        max_bins = 5L
        , min_data_in_bin = 1L
      )
    )
    model <- lgb.train(
      data = dtrain
      , obj = "regression"
      , nrounds = 5L
      , verbose = VERBOSITY
      , params = list(min_data_in_leaf = 1L)
    )
    pred <- predict(model, X)
    expect_true(is.vector(pred))
    expect_equal(length(pred), nrow(X))
    pred <- predict(model, X, rawscore = TRUE)
    expect_true(is.vector(pred))
    expect_equal(length(pred), nrow(X))

    data(agaricus.train, package = "lightgbm")
    X <- agaricus.train$data
    y <- agaricus.train$label
    dtrain <- lgb.Dataset(X, label = y)
    model <- lgb.train(
      data = dtrain
      , obj = "binary"
      , nrounds = 5L
      , verbose = VERBOSITY
    )
    pred <- predict(model, X)
    expect_true(is.vector(pred))
    expect_equal(length(pred), nrow(X))
    pred <- predict(model, X, rawscore = TRUE)
    expect_true(is.vector(pred))
    expect_equal(length(pred), nrow(X))
})

test_that("predictions for multiclass classification are returned as matrix", {
    data(iris)
    X <- as.matrix(iris[, -5L])
    y <- as.numeric(iris$Species) - 1.0
    dtrain <- lgb.Dataset(X, label = y)
    model <- lgb.train(
      data = dtrain
      , obj = "multiclass"
      , nrounds = 5L
      , verbose = VERBOSITY
      , params = list(num_class = 3L)
    )
    pred <- predict(model, X)
    expect_true(is.matrix(pred))
    expect_equal(nrow(pred), nrow(X))
    expect_equal(ncol(pred), 3L)
    pred <- predict(model, X, rawscore = TRUE)
    expect_true(is.matrix(pred))
    expect_equal(nrow(pred), nrow(X))
    expect_equal(ncol(pred), 3L)
})