This function does nothing. It is intended to inherit is parameters' documentation.
default_params_doc(
beast2_bin_path,
beast2_folder,
beast2_jar_path,
beast2_options,
beast2_optionses,
beast2_path,
beast2_version,
beast2_working_dir,
beastier_folder,
beautier_folder,
clock_model,
clock_models,
crown_age,
crown_ages,
fasta_filename,
fasta_filenames,
fixed_crown_age,
fixed_crown_ages,
initial_phylogenies,
input_filename,
mcmc,
misc_options,
n_taxa,
n_threads,
os,
output_filename,
output_log_filename,
output_state_filename,
output_trees_filenames,
overwrite,
rename_fun,
rng_seed,
sequence_length,
site_model,
site_models,
tree_prior,
tree_priors,
use_beagle,
verbose
)Nothing. This is an internal function that does nothing
name of the BEAST2 binary file
(usually simply beast).
Use get_default_beast2_bin_path to get
the default BEAST binary file's path
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.
name of the BEAST2 jar file
(usually has a .jar extension).
Use get_default_beast2_jar_path to get
the default BEAST jar file's path
a set of BEAST2 options, that are the R equivalent of the BEAST2 command-line options, as can be created by create_beast2_options
list of one or more beast2_options
structures,
as can be created by create_beast2_options.
Use of reduplicated plural to achieve difference with
beast2_options
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
the version of BEAST2. By default, this is the version as returned by get_default_beast2_version
a folder where BEAST2 can work in isolation. For each BEAST2 run, a new subfolder is created in that folder. Within this folder, BEAST2 is allowed to create all of its output files, without the risk of overwriting existing ones, allowing BEAST2 to run in multiple parallel processes.
the path to the beastier temporary files folder
temporary folder used by beautier
a beautier clock model
a list of one or more beautier clock models
the crown age of the phylogeny
the crown ages of the phylogenies. Set to NA if the crown age needs to be estimated
a FASTA filename.
One or more FASTA filenames.
determines if the phylogeny's crown age is fixed. If FALSE, crown age is estimated by BEAST2. If TRUE, the crown age is fixed to the crown age of the initial phylogeny.
one or more booleans to determine if the phylogenies' crown ages are fixed. If FALSE, crown age is estimated by BEAST2. If TRUE, the crown age is fixed to the crown age of the initial phylogeny.
one or more MCMC chain's initial phylogenies.
Each one set to NA will result in BEAST2 using a random phylogeny. Else
the phylogeny is assumed to be of class ape::phylo.
the name of a BEAST2 input XML file.
This file usually has an .xml extension.
Use create_temp_input_filename to create a temporary
filename with that extension.
one beautier MCMC
one beautier misc_options object
The number of taxa
the number of computational threads to use. Use NA to use the BEAST2 default of 1.
name of the operating system,
must be unix (Linux, Mac) or win (Windows)
Name of the XML parameter file created by this function. BEAST2 uses this file as input.
name of the .log file to create
name of the .xml.state file to create.
Use create_temp_state_filename to create a temporary
filename with that extension.
one or more names for .trees file to create. There will be one .trees file created per alignment in the input file. The number of alignments must equal the number of .trees filenames, else an error is thrown. Alignments are sorted alphabetically by their IDs
if TRUE: overwrite the .log
and .trees files if one of these exists.
If FALSE, BEAST2 will not be started if
the .log file exists
the .trees files exist
the .log file created by BEAST2 exists
the .trees files created by BEAST2 exist
a function to rename a filename, as can be checked by check_rename_fun. This function should have one argument, which will be a filename or NA. The function should return one filename (when passed one filename) or one NA (when passed one NA). Example rename functions are:
get_remove_dir_fun get a function that removes the directory paths from the filenames, in effect turning these into local files
get_replace_dir_fun get a function that replaces the directory paths from the filenames
get_remove_hex_fun get a function that
removes the hex string from filenames.
For example, tracelog_82c1a522040.log becomes tracelog.log
the random number generator seed of the BEAST2 run.
Must be a non-zero positive integer value or NA.
If rng_seed is NA, BEAST2 will pick a random seed
a DNA sequence length, in base pairs
a beautier site model
one or more beautier site models
a beautier tree prior
one or more beautier tree priors
use BEAGLE if present
if TRUE, additional information is displayed, that is potentially useful in debugging
Richèl J.C. Bilderbeek