View source: R/create_all_coal_experiments.R
create_all_coal_experiments | R Documentation |
These tree priors are both the pure-birth (or Yule) model (as created by create_yule_tree_prior) and the constant-rate birth-death model (as created by create_bd_tree_prior).
create_all_coal_experiments(
site_models = beautier::create_site_models(),
clock_models = beautier::create_clock_models(),
tree_priors = list(beautier::create_cbs_tree_prior(),
beautier::create_ccp_tree_prior(), beautier::create_cep_tree_prior()),
mcmc = beautier::create_mcmc(store_every = 1000),
exclude_model = NA
)
site_models |
a list of one or more site models, as created by create_site_model |
clock_models |
a list of one or more clock models, as created by create_clock_model |
tree_priors |
a list of one or more tree priors, as created by create_tree_prior |
mcmc |
MCMC options, as created by create_mcmc |
exclude_model |
an inference model that has to be excluded, as can be created by create_inference_model |
These experiments are used in the create_pir_params function
all pirouette experiments.
Richèl J.C. Bilderbeek
Use create_all_experiments to create experiments with all combinations of tree model, clock model and tree priors
Use create_all_bd_experiments to create experiments with all combinations of tree model, clock model and tree priors, except for only using birth-death tree priors
Use create_all_coal_experiments to create all experiments with all combinations of tree model, clock model and tree priors, except for only coalescent tree priors
if (rappdirs::app_dir()$os != "win" && beautier::is_on_github_actions()) {
# it does not work on Windows
experiments <- create_all_coal_experiments()
check_experiments(experiments)
pir_params <- create_pir_params(
alignment_params = create_test_alignment_params(),
experiments = experiments,
evidence_filename = get_temp_evidence_filename()
)
}
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