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Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Source: R/default_params_doc.R
default_params_doc.Rd

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Usage

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
)

Arguments

beast2_bin_path

path to the the BEAST2 binary file

beast2_folder

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.

beast2_working_dir

folder in which BEAST2 will run and produce intermediate files. By default, this is a temporary folder

beast2_options

a beast2_options structure, as can be created by create_mcbette_beast2_options.

beast2_optionses

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

clock_model

a clock model, as can be created by create_clock_model

clock_models

a list of one or more clock models, as can be created by create_clock_models

epsilon

measure of relative accuracy. Smaller values result in longer, more precise estimations

fasta_filename

name of the FASTA file

inference_model

an inference model, as can be created by create_inference_model

inference_models

a list of one or more inference models, as can be created by create_inference_model

marg_liks

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.

mcbette_state

the mcbette state, which is a list with the following elements:

  • beast2_installed TRUE if BEAST2 is installed, FALSE otherwise

  • ns_installed NA if BEAST2 is not installed. TRUE if the BEAST2 NS package is installed FALSE if the BEAST2 NS package is not installed

mcmc

an MCMC for the Nested Sampling run, as can be created by create_mcmc_nested_sampling

os

name of the operating system, must be unix (Linux, Mac) or win (Windows)

rng_seed

a random number generator seed used for the BEAST2 inference

site_model

a site model, as can be created by create_site_model

site_models

a list of one or more site models, as can be created by create_site_models

tree_prior

a tree prior, as can be created by create_tree_prior

tree_priors

a list of one or more tree priors, as can be created by create_tree_priors

verbose

if TRUE show debug output

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author

Richèl J.C. Bilderbeek