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This function does nothing. It is intended to inherit is parameters' documentation.

Source: R/default_params_doc.R
default_params_doc.Rd

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  beast2_input_filename,
  beast2_options,
  beast2_output_log_filename,
  beast2_output_state_filename,
  beast2_output_trees_filenames,
  beast2_path,
  beast2_working_dir,
  cleanup,
  clock_model,
  clock_models,
  fasta_filename,
  fasta_filenames,
  inference_model,
  mcmc,
  mrca_prior,
  mrca_priors,
  overwrite,
  rng_seed,
  site_model,
  site_models,
  tipdates_filename,
  tree_prior,
  tree_priors,
  verbose
)

Arguments

beast2_input_filename

path of the 'BEAST2' configuration file. By default, this file is put in a temporary folder with a random filename, as the user needs not read it: it is used as input of 'BEAST2'. Specifying a beast2_input_filename allows to store that file in a more permanently stored location.

beast2_options

'BEAST2' options, as can be created by create_beast2_options

beast2_output_log_filename

name of the log file created by 'BEAST2', containing the parameter estimates in time. By default, this file is put a temporary folder with a random filename, as the user needs not read it: its content is parsed and returned by this function. Specifying a beast2_output_log_filename allows to store that file in a more permanently stored location.

beast2_output_state_filename

name of the final state file created by 'BEAST2', containing the operator acceptances. By default, this file is put a temporary folder with a random filename, as the user needs not read it: its content is parsed and returned by this function. Specifying a beast2_output_state_filename allows to store that file in a more permanently stored location.

beast2_output_trees_filenames

name of the one or more trees files created by 'BEAST2', one per alignment. By default, these files are put a temporary folder with a random filename, as the user needs not read it: their content is parsed and returned by this function. Specifying beast2_output_trees_filenames allows to store these one or more files in a more permanently stored location.

beast2_path

name of either a 'BEAST2' binary file (usually simply beast) or a 'BEAST2' jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path

beast2_working_dir

the folder 'BEAST2' will work in. This is an (empty) temporary folder by default. This allows to call 'BEAST2' in multiple parallel processes, as each process can have its own working directory

cleanup

set to FALSE to keep all temporary files

clock_model

one clock model, see create_clock_model

clock_models

one or more clock models, see create_clock_models

fasta_filename

a FASTA filename

fasta_filenames

one or more FASTA filename, each with one alignment

inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model

mcmc

the MCMC options, see create_mcmc

mrca_prior

one Most Recent Common Ancestor prior, as returned by create_mrca_prior

mrca_priors

a list of one or more Most Recent Common Ancestor priors, as returned by create_mrca_prior

overwrite

will 'BEAST2' overwrite files? Like 'BEAST2', this is set to TRUE by default. If TRUE, 'BEAST2' will overwrite the beast2_options$output_state_filename if its present. If FALSE, 'BEAST2' will not overwrite the beast2_options$output_state_filename if its present and babette will give an error message. Note that if overwrite is set to FALSE when a tracelog (see create_tracelog), screenlog (see create_screenlog) or treelog (see create_treelog) file already exists, 'BEAST2' (and thus babette) will freeze.

rng_seed

the random number generator seed. Must be either NA or a positive non-zero value. An RNG seed of NA results in 'BEAST2' picking a random seed.

site_model

one site model, see create_site_models

site_models

one or more site models, see create_site_models

tipdates_filename

name of the file containing tip dates

tree_prior

one tree priors, as created by create_tree_prior

tree_priors

one or more tree priors, see create_tree_priors

verbose

set to TRUE for more 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