Nothing
context("Sumstat Tajima's D")
test_that("calulation works", {
# example from http://ocw.mit.edu/courses/health-sciences-and-technology/hst-508-quantitative-genomics-fall-2005/study-materials/tajimad1.pdf #nolint
ss <- create_segsites(matrix(c(1, 1, 0, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 1, 0, 0,
0, 0, 0, 1, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 1, 1, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 1, 0, 1, 1, 0, 0, 1, 1, 0, 0, 0,
0, 1, 0, 0, 0, 0, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 1, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 1, 0, 0, 1, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 1,
0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 1, 0, 0, 0, 0, 0), #nolint
10, 16, byrow = TRUE), 1:16 / 16)
tajd <- sumstat_tajimas_d(population = 1)
model <- coal_model(10, 1)
expect_true(abs(tajd$calculate(list(ss), NULL, NULL, model) + 1.446172)
< 1e-6)
tajd <- sumstat_tajimas_d(population = "all")
expect_true(abs(tajd$calculate(list(ss), NULL, NULL, model) + 1.446172)
< 1e-6)
expect_error(tajd$calculate(list(ss), NULL, coal_model(1, 1)))
expect_equal(tajd$calculate(list(create_empty_segsites(10)),
NULL, NULL, model),
NaN)
})
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