tests/testthat/test-utils.R

In BPRMeth: Model higher-order methylation profiles

context("Checking utils functions work")

test_that("data centering works", {
    region <- c(2, 4, 5)
    tss <- 3
    expect_identical(.do_centre_loc(region, tss, "+"), c(-1, 1, 2))
    expect_identical(.do_centre_loc(region, tss, "-"), c(1, -1, -2))
    expect_error(.do_centre_loc(region, tss, 9))
    expect_error(.do_centre_loc(region, "tss", 9))
    expect_identical(.do_centre_loc(21, 2, "+"), 19)
})

test_that("minmax scaling works", {
    data <- c(-20, 0, 15, 20)
    xmin <- -20
    xmax <- 20
    expect_identical(.minmax_scaling(data, xmin, xmax, fmin = 0, fmax = 1),
                     c(0, 0.5, 0.875, 1))
    data <- c(-20, 20)
    expect_identical(.minmax_scaling(data, fmin = -2, fmax = 2), c(-2, 2))
    expect_identical(.minmax_scaling(data, -xmin, xmax, fmin = 0, fmax = 1),
                     c(-20, 20))
    expect_identical(.minmax_scaling(4, 0, 8, fmin = 0, fmax = 1), 0.5)
})

test_that("partition data works", {
    set.seed(123)
    x <- matrix(c(-20, 0, 15, 20, 20, 10, 4, 5), ncol = 2)
    y <- c(2, 5, 0, 8)
    expect_identical(.partition_data(x, y, c(4, 1, 3))$train$y, c(8, 2, 0))
    expect_identical(.partition_data(x, y, c(4, 1, 3))$test$y, c(5))
    expect_identical(.partition_data(x, y, c(4, 1, 3))$test$x.2, c(10))
})

test_that("calculate errors works", {
    x <- c(4, 6, 9, 10, 4, 6, 4, 7, 8, 7)
    y <- c(5, 6, 8, 10, 4, 8, 4, 9, 8, 9)
    expect_identical(.calculate_errors(x, y)$mae, 0.8)
    expect_identical(.calculate_errors(x, y)$mse, 1.4)
    expect_gt(.calculate_errors(x, y)$pcc, 0.87)
    expect_lt(.calculate_errors(x, y)$pcc, 0.88)
})


test_that("log sum exp function works", {
    x <- c(0.001, 0.5, 2, 1.4, 1.5)
    expect_gt(.log_sum_exp(x), 2.92)
    expect_lt(.log_sum_exp(x), 2.93)
})