tests/testthat/test-varfreq_obs_freq.R

In HopkinsIDD/phylosamp: Sample Size Calculations for Molecular and Phylogenetic Studies

test_that("varfreq_obs_freq input arguments are valid", {

    expect_error(varfreq_obs_freq(p_v1 = 0, c_ratio = 1))

    expect_error(varfreq_obs_freq(p_v1 = 1.1, c_ratio = 1))

    expect_error(varfreq_obs_freq(p_v1 = "invalid", c_ratio = 1))

    expect_error(varfreq_obs_freq(p_v1 = 0.1, c_ratio = -2))

    expect_error(varfreq_obs_freq(p_v1 = 0.1, c_ratio = FALSE))
})

test_that("varfreq_obs_freq return object is valid double", {

    expect_type(varfreq_obs_freq(p_v1 = 0.2, c_ratio = 1.5), "double")

})

test_that("varfreq_obs_freq observed variant prevalence is equal to actual variant prevalence if c_ratio is 1",
    {

        expect_equal(varfreq_obs_freq(p_v1 = 0.8, c_ratio = 1), 0.8)
    })

test_that("varfreq_obs_freq observed_variant prevalence is greater than actual variant prevalence if c_ratio is above 1",
    {

        expect_gt(varfreq_obs_freq(p_v1 = 0.4, c_ratio = 2), 0.4)

    })

test_that("varfreq_obs_freq observed variant prevalence is less than actual variant prevalence if c_ratio is below 1",
    {

        expect_lt(varfreq_obs_freq(p_v1 = 0.75, c_ratio = 0.3), 0.75)

    })

test_that("varfreq_obs_freq manuscript results remain valid", {

    expect_equal(round(varfreq_obs_freq(p_v1 = 0.02, c_ratio = (0.975 * 0.8)/(0.6 *
        0.95)), 3), 0.027)
})