tests/testthat/test-calc_fraction.R

In nodeSub: Simulate DNA Alignments Using Node Substitutions

context("calc_re_contr_node_time")

test_that("calc_fraction use", {
  if (requireNamespace("TreeSim")) {
    phy <- TreeSim::sim.bd.taxa(n = 30, numbsim = 1, lambda = 1, mu = 0)[[1]]
  } else {
    if (requireNamespace("ape")) {
      phy <- ape::rphylo(n = 30, birth = 1, death = 0)
    } else {
      stop("could not use TreeSim or ape to simulate tree")
    }
  }

  for (frac in seq(0, 0.9)) {
    req_node_time <- nodeSub::calc_required_node_time(phy, s = frac)

    estim_frac <- nodeSub::calc_fraction(phy, node_time = req_node_time)
    testthat::expect_equal(frac, estim_frac)

    req_node_time <- nodeSub::calc_required_node_time(phy, s = frac,
                                                      model = "linked")

    estim_frac <- nodeSub::calc_fraction(phy, node_time = req_node_time,
                                         model = "linked")
    testthat::expect_equal(frac, estim_frac)
  }
})