tests/testthat/test-deprecation-utils.R

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

test_that("Deprecated functions", {
    balanced.cv.folds(1:10, nfolds = 10) |> lifecycle::expect_deprecated()
    my.colors() |> lifecycle::expect_deprecated()
    my.symbols() |> lifecycle::expect_deprecated()
    hallmarks() |> lifecycle::expect_defunct()
})

test_that("glmOrphan: deprecated parameters", {
    data <- prepareMAE(10)

    glmArgs <- list(
        data$xdata,
        data$ydata,
        "correlation",
        family = "cox",
        network.options = networkOptions(minDegree = .2),
        experiment.name = "RNASeq2GeneNorm"
    )

    list(glmOrphan, glmHub, glmDegree, glmSparseNet) |>
        lapply(function(funName) {
            do.call(funName, glmArgs) |>
                coef() |>
                nrow() |>
                expect_equal(nrow(data$xdata[["RNASeq2GeneNorm"]])) |>
                expect_warning("experiments.* dropped") |>
                expect_message("harmonizing input")
        })
})

test_that("networkCorParallel: deprecated parameters", {
    xdata <- matrix(rnorm(4), ncol = 2)
    networkCorParallel(xdata, build.output = "matrix") |>
        lifecycle::expect_deprecated("buildOutput")

    # write same expecations to n.cores force.recalc.network and show.message
    networkCorParallel(xdata, n.cores = 2) |>
        lifecycle::expect_deprecated("nCores")
    networkCorParallel(xdata, force.recalc.network = TRUE) |>
        lifecycle::expect_deprecated("forceRecalcNetwork")
    networkCorParallel(xdata, show.message = TRUE) |>
        lifecycle::expect_deprecated("showMessage")
})

test_that("networkCovParallel: deprecated parameters", {
    xdata <- matrix(rnorm(4), ncol = 2)
    networkCovParallel(xdata, build.output = "matrix") |>
        lifecycle::expect_deprecated("buildOutput")

    # write same expecations to n.cores force.recalc.network and show.message
    networkCovParallel(xdata, n.cores = 2) |>
        lifecycle::expect_deprecated("nCores")
    networkCovParallel(xdata, force.recalc.network = TRUE) |>
        lifecycle::expect_deprecated("forceRecalcNetwork")
    networkCovParallel(xdata, show.message = TRUE) |>
        lifecycle::expect_deprecated("showMessage")
})

test_that("cv.glmOrphan: deprecated parameters", {
    data <- prepareMAE(maxRows = 10)

    glmArgs <- list(
        data$xdata,
        data$ydata,
        "correlation",
        family = "cox",
        nfolds = 5,
        network.options = networkOptions(minDegree = .2),
        experiment.name = "RNASeq2GeneNorm"
    )

    list(cv.glmOrphan, cv.glmHub, cv.glmDegree, cv.glmSparseNet) |>
        lapply(function(funName) {
            do.call(funName, glmArgs) |>
                coef() |>
                nrow() |>
                expect_equal(nrow(data$xdata[["RNASeq2GeneNorm"]])) |>
                expect_warning("experiments.* dropped") |>
                expect_message("harmonizing input")
        })
})

test_that("buildLambda: deprecated parameters", {
    buildLambda(lambda.largest = NULL) |>
        lifecycle::expect_deprecated("lambdaLargest")

    buildLambda(lambda.per.order.magnitude = 100) |>
        lifecycle::expect_deprecated("lambdaPerOrderMagnitude")

    buildLambda(orders.of.magnitude.smaller = 3) |>
        lifecycle::expect_deprecated("ordersOfMagnitudeSmaller")
})

test_that("separate2GroupsCox: deprecated parameters", {
    data <- prepareOvarian()
    separate2GroupsCox(
        chosen.btas = c(1, 2), xdata = data$xdata, ydata = data$ydata
    ) |>
        lifecycle::expect_deprecated("chosenBetas")

    separate2GroupsCox(c(1, 2), data$xdata, data$ydata, no.plot = TRUE) |>
        lifecycle::expect_deprecated("noPlot")

    separate2GroupsCox(
        c(1, 2), data$xdata, data$ydata,
        noPlot = TRUE, expand.yzero = TRUE
    ) |>
        lifecycle::expect_deprecated("expandYZero")

    separate2GroupsCox(
        c(1, 2), data$xdata, data$ydata,
        noPlot = TRUE, plot.title = "Some title"
    ) |>
        lifecycle::expect_deprecated("plotTitle")

    separate2GroupsCox(
        c(1, 2), data$xdata, data$ydata,
        noPlot = TRUE, legend.outside = TRUE
    ) |>
        lifecycle::expect_deprecated("legendOutside")

    separate2GroupsCox(
        c(1, 2), data$xdata, data$ydata,
        noPlot = TRUE, stop.when.overlap = TRUE
    ) |>
        lifecycle::expect_deprecated("stopWhenOverlap")
})

test_that("netWorkOptions: deprecated parameters", {
    networkOptions(min.degree = 0.2) |>
        lifecycle::expect_deprecated("minDegree")

    networkOptions(n.cores = 1) |>
        lifecycle::expect_deprecated("nCores")

    networkOptions(trans.fun = \(x) x) |>
        lifecycle::expect_deprecated("transFun")
})

test_that("heuristicScale: deprecated parameters", {
    heuristicScale(1, sub.exp10 = -1) |>
        lifecycle::expect_deprecated("subExp10")

    heuristicScale(1, exp.mult = -1) |>
        lifecycle::expect_deprecated("expMult")

    heuristicScale(1, sub.exp = -1) |>
        lifecycle::expect_deprecated("subExp")
})