Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
default_params_doc(
beast2_bin_path,
beast2_folder,
beast2_working_dir,
beast2_options,
beast2_optionses,
clock_model,
clock_models,
epsilon,
fasta_filename,
inference_model,
inference_models,
marg_liks,
mcbette_state,
mcmc,
os,
rng_seed,
site_model,
site_models,
tree_prior,
tree_priors,
verbose
)path to the the BEAST2 binary file
the folder where the BEAST2 is installed. Note that this is not the folder where the BEAST2 executable is installed: the BEAST2 executable is in a subfolder. Use get_default_beast2_folder to get the default BEAST2 folder. Use get_default_beast2_bin_path to get the full path to the default BEAST2 executable. Use get_default_beast2_jar_path to get the full path to the default BEAST2 jar file.
folder in which BEAST2 will run and produce intermediate files. By default, this is a temporary folder
a beast2_options structure,
as can be created by create_mcbette_beast2_options.
list of one or more beast2_options
structures,
as can be created by create_mcbette_beast2_options.
Use of reduplicated plural to achieve difference with
beast2_options
a clock model, as can be created by create_clock_model
a list of one or more clock models, as can be created by create_clock_models
measure of relative accuracy. Smaller values result in longer, more precise estimations
name of the FASTA file
an inference model, as can be created by create_inference_model
a list of one or more inference models, as can be created by create_inference_model
a table of (estimated) marginal likelihoods, as, for example, created by est_marg_liks. This data.frame has the following columns:
site_model_name: name of the site model,
must be an element of get_site_model_names
clock_model_name: name of the clock model,
must be an element of get_clock_model_names
tree_prior_name: name of the tree prior,
must be an element of get_tree_prior_names
marg_log_lik: estimated marginal (natural) log likelihood
marg_log_lik_sd: estimated error of marg_log_lik
weight: relative model weight, a value from 1.0 (all
evidence is in favor of this model combination) to 0.0 (no
evidence in favor of this model combination)
ess: effective sample size of the marginal likelihood
estimation
Use get_test_marg_liks to get a test marg_liks.
Use is_marg_liks to determine if a marg_liks is valid.
Use check_marg_liks to check that a marg_liks is valid.
the mcbette state, which is a list with the following elements:
an MCMC for the Nested Sampling run, as can be created by create_mcmc_nested_sampling
name of the operating system,
must be unix (Linux, Mac) or win (Windows)
a random number generator seed used for the BEAST2 inference
a site model, as can be created by create_site_model
a list of one or more site models, as can be created by create_site_models
a tree prior, as can be created by create_tree_prior
a list of one or more tree priors, as can be created by create_tree_priors
if TRUE show debug output
Richèl J.C. Bilderbeek