tests/testthat/test-separate_2_groups_cox.R

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

context("separate2GroupsCox")

test_that("Calculates kaplan-meier data", {
    ovarian <- survival::ovarian
    result <- separate2GroupsCox(
        c(age = 1),
        ovarian$age,
        data.frame(time = ovarian$futime, status = ovarian$fustat)
    )

    expect_lt(result$pvalue - 0.0518148, 1e-2)
})

test_that("Only one group in kaplan.meier gives error", {
    ovarian <- survival::ovarian
    expect_warning(expect_error(separate2GroupsCox(
        c(age = 0),
        ovarian$age,
        data.frame(time = ovarian$futime, status = ovarian$fustat)
    )))
})

test_that("All combinations of parameters possible for draw.kapan", {
    ovarian <- survival::ovarian
    xdata <- ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    # list, data.frame, data.frame
    separate2GroupsCox(list(c(1, 0)), xdata, ydata) |>
        expect_silent()
    # list, matrix, data.frame
    separate2GroupsCox(list(c(1, 0)), Matrix::as.matrix(xdata), ydata) |>
        expect_silent()

    # list, numeric, data.frame
    separate2GroupsCox(list(c(1)), xdata$age, ydata) |>
        expect_silent()
    # list, numeric, data.frame
    separate2GroupsCox(1, xdata$age, ydata) |>
        expect_silent()

    # numeric, data.frame, data.frame
    separate2GroupsCox(c(1, 0), xdata, ydata) |>
        expect_silent()
    # numeric, matrix, data.frame
    separate2GroupsCox(c(1, 0), Matrix::as.matrix(xdata), ydata) |>
        expect_silent()
})

test_that("Some bad arguments for separate2GroupsCox", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    # list, data.frame, data.frame
    separate2GroupsCox(list(c(1, 0), c(0, 1, 2)), xdata, ydata) |>
        expect_error("All or some of the.*have different number")
    # list, matrix, data.frame
    separate2GroupsCox(
        list(c(1, 0)), Matrix::as.matrix(xdata), ydata[1:10, ]
    ) |>
        expect_error("Rows in xdata .* and ydata .* must be the same")

    # list, numeric, data.frame
    separate2GroupsCox(list(c(1, 0)), xdata$age, ydata) |>
        expect_error()
    # list, numeric, data.frame
    separate2GroupsCox(c(1, 2), xdata$age, ydata) |>
        expect_error()

    # numeric, data.frame, data.frame
    separate2GroupsCox(c(1, 0, 1), xdata, ydata) |>
        expect_error()
    # numeric, matrix, data.frame
    separate2GroupsCox(c(1, 0), t(Matrix::as.matrix(xdata)), ydata) |>
        expect_error()
})

test_that("separate2GroupsCox: throws cuttof error when overlapping prob.", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    separate2GroupsCox(c(1, 0), xdata, ydata, probs = c(.55, .45)) |>
        expect_error("The cutoff values")
})

test_that("separate2GroupsCox: throws warning when overlapping prob.", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    separate2GroupsCox(
        c(1, 0), xdata, ydata,
        probs = c(.55, .45), stop.when.overlap = FALSE
    ) |>
        expect_warning("The cutoff values")
})

test_that("separate2GroupsCox: no plot is returned when argument is given", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    separate2GroupsCox(
        c(1, 0), xdata, ydata,
        noPlot = TRUE
    ) |>
        magrittr::extract2("plot") |>
        expect_null()
})

test_that("separate2GroupsCox: kaplan-meier should have 4 groups", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    separate2GroupsCox(list(yada = c(1, 0), bla = c(0, 1)), xdata, ydata) |>
        magrittr::extract2("km") |>
        magrittr::extract2("strata") |>
        expect_length(4)
})

test_that("separate2GroupsCox: kaplan-meier should have 4 groups", {
    ovarian <- survival::ovarian
    xdata <- survival::ovarian[, c("age", "resid.ds")]
    ydata <- data.frame(time = ovarian$futime, status = ovarian$fustat)

    separate2GroupsCox(list(c(1, 0), c(0, 1)), xdata, ydata) |>
        magrittr::extract2("km") |>
        magrittr::extract2("strata") |>
        expect_length(4)
})