tests/testthat/test-degree_cor.R

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

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

corPearson <- abs(cor(xdata, method = "pearson")) - diag(ncol(xdata))
corSpearman <- abs(cor(xdata, method = "spearman")) - diag(ncol(xdata))

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

context("Degree - Correlation - Pearson")

test_that("Degree with cutoff", {
    corPearsonLocal <- corPearson
    corPearsonLocal[corPearsonLocal < 0.5] <- 0
    diffDegree <- degreeCor(
        xdata,
        method = "pearson",
        cutoff = 0.5,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corPearsonLocal)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree forcing recalculation", {
    diffDegree <- degreeCor(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corPearson)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree forcing recalculation of degree only", {
    diffDegree <- degreeCor(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE
    ) - Matrix::colSums(corPearson)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree using cache", {
    degreeCor(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(corPearson)
    diffDegree <- degreeCor(
        xdata,
        method = "pearson",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(corPearson)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

context("Degree - Correlation - Spearman")

test_that("Degree with cutoff", {
    corSpearmanLocal <- corSpearman
    corSpearmanLocal[corSpearmanLocal < 0.5] <- 0
    diffDegree <- degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0.5,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corSpearmanLocal)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree forcing recalculation of all", {
    diffDegree <- degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corSpearman)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree forcing recalculation of degree", {
    degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0.05,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corSpearman)
    diffDegree <- degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE
    ) - Matrix::colSums(corSpearman)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})

test_that("Degree using cache", {
    # forcing recalculation
    degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = TRUE,
        forceRecalcNetwork = TRUE
    ) - Matrix::colSums(corSpearman)
    # actual call to get from cache
    diffDegree <- degreeCor(
        xdata,
        method = "spearman",
        cutoff = 0,
        chunks = 10,
        nCores = 2,
        forceRecalcDegree = FALSE
    ) - Matrix::colSums(corSpearman)
    expect_lt(sum(abs(diffDegree)), 5e-14)
})