tests/testthat/test-degree_cov.R

In sysbiomed/glmSparseNet: Network Centrality Metrics for Elastic-Net Regularized Models

set.seed(1985)
xdata <- matrix(rnorm(7000), nrow = 175)

covPearson <- abs(cov(xdata, method = "pearson"))
diag(covPearson) <- 0
covSpearman <- abs(cov(xdata, method = "spearman"))
diag(covSpearman) <- 0

context("Degree - Covariance - Pearson")

# use a temporary directory that can be written
withr::local_tempdir(pattern = "base.dir") |>
    .baseDir()

test_that("Degree with cutoff", {
    covPearsonLocal <- covPearson
    covPearsonLocal[covPearsonLocal < 0.05] <- 0
    diffDegree <- degreeCov(
        xdata,
        method = "pearson",
        cutoff = 0.05,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covPearsonLocal)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree forcing recalculation", {
    diffDegree <- degreeCov(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covPearson)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree forcing recalculation of degree only", {
    diffDegree <- degreeCov(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE
    ) - Matrix::colSums(covPearson)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree using cache", {
    degreeCov(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(covPearson)
    diffDegree <- degreeCov(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(covPearson)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

context("Degree - Covariance - Spearman")

test_that("Degree with cutoff", {
    covSpearmanLocal <- covSpearman
    covSpearmanLocal[covSpearmanLocal < 0.05] <- 0
    diffDegree <- degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0.05,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covSpearmanLocal)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree forcing recalculation of all", {
    diffDegree <- degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covSpearman)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree forcing recalculation of degree", {
    degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covSpearman)
    diffDegree <- degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE
    ) - Matrix::colSums(covSpearman)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})

test_that("Degree using cache", {
    # forcing recalculation
    degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(covSpearman)
    # actual call to get from cache
    diffDegree <- degreeCov(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(covSpearman)
    expect_lt(sum(abs(diffDegree)), 1e-09)
})