# R script to test if pirouette runs on peregrine
# Added an extra check
remotes::install_github("ropensci/beastier", ref = "develop")
# Copied from peregrine
get_pff_tempdir <- function() {
dirname <- file.path(
rappdirs::user_cache_dir(),
basename(tempfile())
)
dirname
}
# Copied from peregrine
get_pff_tempfile <- function(
pattern = "pff_",
pff_tmpdir = get_pff_tempdir(),
fileext = ""
) {
filename <- tempfile(
pattern = pattern,
tmpdir = pff_tmpdir,
fileext = fileext
)
testit::assert(!file.exists(filename))
filename
}
fasta_filename <- system.file("extdata", "simple.fas", package = "mcbette")
# Inaccurate MCMC
mcmc <- beautier::create_ns_mcmc(epsilon = 1e2)
inference_model_1 <- beautier::create_inference_model(
site_model = beautier::create_jc69_site_model(),
clock_model = beautier::create_strict_clock_model(),
tree_prior = beautier::create_yule_tree_prior(),
mcmc = mcmc
)
inference_model_2 <- beautier::create_inference_model(
site_model = beautier::create_jc69_site_model(),
clock_model = beautier::create_strict_clock_model(),
tree_prior = beautier::create_bd_tree_prior(),
mcmc = mcmc
)
inference_models <- list(
inference_model_1,
inference_model_2
)
beast2_options <- beastier::create_beast2_options(
input_filename = get_pff_tempfile(pattern = "in_", fileext = ".xml"),
output_state_filename = get_pff_tempfile(pattern = "out_", fileext = ".state.xml"),
beast2_working_dir = get_pff_tempfile(),
beast2_path = beastier::get_default_beast2_bin_path()
)
beast2_optionses <- list(
beast2_options,
beast2_options
)
mcbette::est_marg_liks(
fasta_filename,
inference_models = inference_models,
beast2_optionses = beast2_optionses,
verbose = TRUE
)
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