default_params_doc: This function does nothing. It is intended to inherit is...
In richelbilderbeek/rbeast2: Control 'BEAST2'

default_params_doc

R Documentation

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

Description

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