context("test-create_beast2_input_file_1_12")
test_that("create data set of two alignments, with/out fixed crown ages", {
output_filename <- tempfile()
testit::assert(!file.exists(output_filename))
fasta_filename_1 <- get_beautier_path("anthus_aco.fas")
fasta_filename_2 <- get_beautier_path("anthus_nd2.fas")
fasta_filenames <- c(fasta_filename_1, fasta_filename_2)
phylo_1_15 <- fasta_to_phylo(fasta_filename_1, crown_age = 15)
phylo_2_15 <- fasta_to_phylo(fasta_filename_2, crown_age = 15)
phylo_2_26 <- fasta_to_phylo(fasta_filename_2, crown_age = 26)
testthat::expect_silent(
create_beast2_input_file_1_12(
fasta_filenames,
"anthus_na_na.xml",
mcmc = create_mcmc(chain_length = 10000, store_every = 1000)
)
)
testthat::expect_silent(
create_beast2_input_file_1_12(
fasta_filenames,
"anthus_15_15.xml",
mcmc = create_mcmc(chain_length = 10000, store_every = 1000),
fixed_crown_ages = c(TRUE, TRUE),
initial_phylogenies = list(phylo_1_15, phylo_2_15)
)
)
testthat::expect_silent(
create_beast2_input_file_1_12(
fasta_filenames,
"anthus_na_15.xml",
mcmc = create_mcmc(chain_length = 10000, store_every = 1000),
fixed_crown_ages = c(FALSE, TRUE),
initial_phylogenies = list(NA, phylo_2_15)
)
)
testthat::expect_silent(
create_beast2_input_file_1_12(
fasta_filenames,
"anthus_15_na.xml",
mcmc = create_mcmc(chain_length = 10000, store_every = 1000),
fixed_crown_ages = c(TRUE, FALSE),
initial_phylogenies = list(phylo_1_15, NA)
)
)
testthat::expect_silent(
create_beast2_input_file_1_12(
fasta_filenames,
"anthus_15_26.xml",
mcmc = create_mcmc(chain_length = 10000, store_every = 1000),
fixed_crown_ages = c(TRUE, TRUE),
initial_phylogenies = list(phylo_1_15, phylo_2_26)
)
)
})
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