This function does nothing. It is intended to inherit is parameters' documentation.Source:
This function does nothing. It is intended to inherit is parameters' documentation.
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 )
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_filenameallows to store that file in a more permanently stored location.
'BEAST2' options, as can be created by create_beast2_options
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_filenameallows to store that file in a more permanently stored location.
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_filenameallows to store that file in a more permanently stored location.
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_filenamesallows to store these one or more files in a more permanently stored location.
name of either a 'BEAST2' binary file (usually simply
beast) or a 'BEAST2' jar file (usually has a
get_default_beast2_bin_pathto get the default BEAST binary file's path Use
get_default_beast2_jar_pathto get the default BEAST jar file's path
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
set to FALSE to keep all temporary files
one clock model, see create_clock_model
one or more clock models, see create_clock_models
a FASTA filename
one or more FASTA filename, each with one alignment
a Bayesian phylogenetic inference model, as returned by create_inference_model
the MCMC options, see create_mcmc
one Most Recent Common Ancestor prior, as returned by
a list of one or more Most Recent Common Ancestor priors, as returned by
will 'BEAST2' overwrite files? Like 'BEAST2', this is set to TRUE by default. If TRUE, 'BEAST2' will overwrite the
beast2_options$output_state_filenameif its present. If FALSE, 'BEAST2' will not overwrite the
beast2_options$output_state_filenameif its present and babette will give an error message. Note that if
overwriteis set to FALSE when a
screenlog(see create_screenlog) or
treelog(see create_treelog) file already exists, 'BEAST2' (and thus babette) will freeze.
the random number generator seed. Must be either
NAor a positive non-zero value. An RNG seed of
NAresults in 'BEAST2' picking a random seed.
one site model, see create_site_models
one or more site models, see create_site_models
name of the file containing tip dates
one tree priors, as created by create_tree_prior
one or more tree priors, see create_tree_priors
set to TRUE for more output
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