Nothing
# test species tree output is a list of trees with correct length
sim_test_spt_loct <- function(gbr, gdr, lgtr, numLoci, species_tree_len = 5.0){
tr <- sim_stBD_t(0.1, 0.05, 1, species_tree_len)
sim_ltBD(tr[[1]],
gbr = gbr,
gdr = gdr,
lgtr = lgtr,
num_loci = numLoci)
}
sim_test_spt_loct <- function(gbr, gdr, lgtr, numLoci, species_tree_len = 5.0){
tr <- sim_stBD_t(0.1, 0.05, 1, species_tree_len)
sim_ltBD(tr[[1]],
gbr = gbr,
gdr = gdr,
lgtr = lgtr,
num_loci = numLoci)
}
sim_test_spt_loct_equality <- function(gene_birth = 0.0, gene_death = 0.0, transfers = 0.0, numLoci){
tr <- sim_stBD_t(0.1, 0.05, 1, 5.0)
loctr <- sim_ltBD(tr[[1]],
gbr = gene_birth,
gdr = gene_death,
lgtr = transfers,
num_loci = numLoci)
all(sapply(loctr, ape::all.equal.phylo, current = tr[[1]], use.tip.label = FALSE))
}
test_that("sim_ltBD produces the right number of trees", {
expect_equal(length(sim_test_spt_loct(0.1, 0.05, 0.05, 10)), 10)
expect_equal(length(sim_test_spt_loct(0.1, 0.05, 0.05, 5)), 5)
expect_equal(length(sim_test_spt_loct(0.1, 0.05, 0.05, 50)), 50)
})
# test that input species tree is the same as locus tree if every param is set
# 0.0
test_that("sim_ltBD returns tree concordant with species tree when locus tree parameters are 0.0",{
expect_true(sim_test_spt_loct_equality(numLoci = 20))
})
get_length_tree <- function(tr){
max(ape::node.depth.edgelength(tr)) + tr$root.edge
}
get_all_tree_lengths <- function(multiTree){
min(sapply(multiTree, get_length_tree))
}
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