tests/testthat/test-sitesMinEntropy.R

In sitePath: Detection of site fixation in molecular evolution

test_that("The return value contains correct extra info", {
    data(h3n2_tree_reduced)
    data(h3n2_align_reduced)
    tr <- addMSA(tree = h3n2_tree_reduced,
                 alignment = h3n2_align_reduced)
    p <- lineagePath(tr)
    minEntropy <- sitesMinEntropy(p)
    # The result is grouped by path
    expect_true(length(p) == length(minEntropy))
    for (segs in minEntropy) {
        for (seg in segs) {
            for (node in names(seg)) {
                tips <- seg[[node]]
                # The major amino acid/nucleotide should be same as the fixed
                # and the node names should be the same
                dominantAA <-
                    names(which.max(attr(tips, "aaSummary")))
                if (is.null(attr(tips, "toMerge"))) {
                    expect_true(dominantAA == attr(tips, "AA"))
                }
                expect_true(node == attr(tips, "node"))
            }
        }
    }
})