tests/testthat/test-5evenness.R

In microbiome/mia: Microbiome analysis

context("estimateEvenness")

test_that("estimateEvenness", {

    test_internal_estimateEvenness <- function(tse){

        # Check that every index is calculated by checking the column names from
        # colData.
        # Check that the order of indices is right / the same as the order
        # in the input vector.
	tse_idx <- estimateEvenness(tse)

        # Check that the type of output is the same as the type of input.
        expect_true(typeof(tse_idx) == typeof(tse))

        expect_named(colData(tse_idx), c("camargo", "pielou", "simpson_evenness", "evar",
                              "bulla"))

        mat <- assay(tse_idx,"counts")

        expect_equal(round(as.vector(mia:::.get_evenness_values(mat, index = "camargo")), 7),
                     round(c(0.6942294, 0.6230541, 0.8010094)), 7)

        expect_equal(round(as.vector(mia:::.get_evenness_values(mat, index="pielou")),7),
                     round(c(0.6750387, 0.7900423, 0.5587478),7))

        expect_equal(round(as.vector(mia:::.get_evenness_values(mat, index="simpson_evenness")), 7),
                     round(c(0.21179306, 0.31351703, 0.07873068), 7))

        expect_equal(round(as.vector(mia:::.get_evenness_values(mat, index="evar")), 7),
                     round(c(0.3723086, 0.4073989, 0.4820153), 7))

        expect_equal(round(as.vector(mia:::.get_evenness_values(mat, index="bulla")), 7),
                     round(c(0.3627075, 0.4897059, 0.3519684), 7))
    }

    # TSE object
    data(esophagus, package="mia")
    tse <- esophagus 
    test_internal_estimateEvenness(tse)
    
    assay(tse,"counts") <- DelayedArray(assay(tse,"counts"))
    test_internal_estimateEvenness(tse)
})