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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_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
)

Arguments

beast2_bin_path

name of the BEAST2 binary file (usually simply beast). Use get_default_beast2_bin_path to get the default BEAST binary file's path

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.

beast2_jar_path

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

beast2_options

a set of BEAST2 options, that are the R equivalent of the BEAST2 command-line options, as can be created by create_beast2_options

beast2_optionses

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

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_version

the version of BEAST2. By default, this is the version as returned by get_default_beast2_version

beast2_working_dir

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.

beastier_folder

the path to the beastier temporary files folder

beautier_folder

temporary folder used by beautier

clock_model

a beautier clock model

clock_models

a list of one or more beautier clock models

crown_age

the crown age of the phylogeny

crown_ages

the crown ages of the phylogenies. Set to NA if the crown age needs to be estimated

fasta_filename

a FASTA filename.

fasta_filenames

One or more FASTA filenames.

fixed_crown_age

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.

fixed_crown_ages

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.

initial_phylogenies

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.

input_filename

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.

mcmc

one beautier MCMC

misc_options

one beautier misc_options object

n_taxa

The number of taxa

n_threads

the number of computational threads to use. Use NA to use the BEAST2 default of 1.

os

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

output_filename

Name of the XML parameter file created by this function. BEAST2 uses this file as input.

output_log_filename

name of the .log file to create

output_state_filename

name of the .xml.state file to create. Use create_temp_state_filename to create a temporary filename with that extension.

output_trees_filenames

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

overwrite

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

rename_fun

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

rng_seed

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

sequence_length

a DNA sequence length, in base pairs

site_model

a beautier site model

site_models

one or more beautier site models

tree_prior

a beautier tree prior

tree_priors

one or more beautier tree priors

use_beagle

use BEAGLE if present

verbose

if TRUE, additional information is displayed, that is potentially useful in debugging

Value

Nothing. This is an internal function that does nothing

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