Nothing
## ----setup, include = FALSE---------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----check_empty_cache_at_start, include = FALSE------------------------------
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
## ----load_babette-------------------------------------------------------------
library(babette)
## -----------------------------------------------------------------------------
fasta_filename <- get_babette_path("anthus_aco_sub.fas")
library(testthat)
expect_true(file.exists(fasta_filename))
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model()
names(inference_model)
## -----------------------------------------------------------------------------
print(inference_model$mcmc$chain_length)
## ----cache=TRUE---------------------------------------------------------------
if (is_beast2_installed()) {
beast2_options <- create_beast2_options()
out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model(
site_model = create_jc69_site_model()
)
## ----cache=TRUE---------------------------------------------------------------
if (is_beast2_installed()) {
beast2_options <- create_beast2_options()
out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model(
clock_model = create_strict_clock_model()
)
## ----cache=TRUE---------------------------------------------------------------
if (is_beast2_installed()) {
beast2_options <- create_beast2_options()
out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model(
tree_prior = create_yule_tree_prior()
)
## ----cache=TRUE---------------------------------------------------------------
if (is_beast2_installed()) {
beast2_options <- create_beast2_options()
out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## -----------------------------------------------------------------------------
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename)[1:2],
is_monophyletic = TRUE
)
## -----------------------------------------------------------------------------
mrca_distr <- create_normal_distr(
mean = 15.0,
sigma = 1.0
)
## -----------------------------------------------------------------------------
mrca_prior <- create_mrca_prior(
alignment_id = get_alignment_id(fasta_filename = fasta_filename),
taxa_names = get_taxa_names(filename = fasta_filename),
mrca_distr = mrca_distr
)
## -----------------------------------------------------------------------------
inference_model <- create_test_inference_model(
mrca_prior = mrca_prior
)
## ----cache=TRUE---------------------------------------------------------------
if (is_beast2_installed()) {
beast2_options <- create_beast2_options()
out <- bbt_run_from_model(
fasta_filename = fasta_filename,
inference_model = inference_model,
beast2_options = beast2_options
)
bbt_delete_temp_files(
inference_model = inference_model,
beast2_options = beast2_options
)
}
## ----check_empty_cache_at_end, include = FALSE--------------------------------
beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()
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