default_params_doc.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/default_params_doc.R
\name{default_params_doc}
\alias{default_params_doc}
\title{This function does nothing. It is intended to inherit is parameters'
documentation.}
\usage{
default_params_doc(beast2_bin_path, beast2_internal_filenames,
  beast2_jar_path, beast2_options, beast2_optionses, beast2_path,
  beast2_working_dir, 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, rng_seed,
  sequence_length, site_model, site_models, tree_prior, tree_priors,
  use_beagle, verbose)
}
\arguments{
\item{beast2_bin_path}{name of the BEAST2 binary file
(usually simply \code{beast}).
Use \link{get_default_beast2_bin_path} to get
the default BEAST binary file's path}

\item{beast2_internal_filenames}{a list of internally
used BEAST2 filenames,
as created by \link{create_beast2_internal_filenames}}

\item{beast2_jar_path}{name of the BEAST2 jar file
(usually has a \code{.jar} extension).
Use \link{get_default_beast2_jar_path} to get
the default BEAST jar file's path}

\item{beast2_options}{a set of BEAST2 options,
that are the R equivalent of the BEAST2 command-line options,
as can be created by \link{create_beast2_options}}

\item{beast2_optionses}{list of one or more \code{beast2_options}
structures,
as can be created by \link{create_beast2_options}.
Use of reduplicated plural to achieve difference with
\code{beast2_options}}

\item{beast2_path}{name of either a BEAST2 binary file
(usually simply \code{beast})
or a BEAST2 jar file
(usually has a \code{.jar} extension).
Use \link{get_default_beast2_bin_path} to get
the default BEAST binary file's path
Use \link{get_default_beast2_jar_path} to get
the default BEAST jar file's path}

\item{beast2_working_dir}{a (temporary) folder where BEAST2 can work in
isolation.  This is a new and empty temporary folder by default.
In this folder, BEAST2 is allowed to create all of its output files,
without the risk of overwriting existing ones.
Currently, it appears possible that one can set
\code{beast2_working_dir} to the same longer-storage folder
as where the BEAST2 output files are created, but this may change
in future version.
Using this working directory allows to call
BEAST2 in multiple parallel processes, as each process can have
its own separate environment}

\item{clock_model}{a \code{beautier} clock model}

\item{clock_models}{a list of one or more \code{beautier} clock models}

\item{crown_age}{the crown age of the phylogeny}

\item{crown_ages}{the crown ages of the phylogenies. Set to NA
if the crown age needs to be estimated}

\item{fasta_filename}{a FASTA filename.}

\item{fasta_filenames}{One or more FASTA filenames.}

\item{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.}

\item{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.}

\item{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 \code{ape::phylo}.}

\item{input_filename}{the name of a BEAST2 input XML file.
This file usually has an \code{.xml} extension.}

\item{mcmc}{one \code{beautier} MCMC}

\item{misc_options}{one \code{beautier} misc_options object}

\item{n_taxa}{The number of taxa}

\item{n_threads}{the number of computational threads to use.
Use \link{NA} to use the BEAST2 default of 1.}

\item{os}{name of the operating system,
must be \code{unix} (Linux, Mac) or \code{win} (Windows)}

\item{output_filename}{Name of the XML parameter file created by this
function. BEAST2 uses this file as input.}

\item{output_log_filename}{name of the .log file to create}

\item{output_state_filename}{name of the .xml.state file to create}

\item{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}

\item{overwrite}{if TRUE: overwrite the \code{.log}
 and \code{.trees} files if one of these exists.
 If FALSE, BEAST2 will not be started if
 \itemize{
   \item{the \code{.log} file exists}
   \item{the \code{.trees} files exist}
   \item{the \code{.log} file created by BEAST2 exists}
   \item{the \code{.trees} files created by BEAST2 exist}
}}

\item{rng_seed}{the random number generator seed of the BEAST2 run.
Must be a non-zero positive integer value or \link{NA}.
If \code{rng_seed} is \link{NA}, BEAST2 will pick a random seed}

\item{sequence_length}{a DNA sequence length, in base pairs}

\item{site_model}{a \code{beautier} site model}

\item{site_models}{one or more \code{beautier} site models}

\item{tree_prior}{a \code{beautier} tree prior}

\item{tree_priors}{one or more \code{beautier} tree priors}

\item{use_beagle}{use BEAGLE if present}

\item{verbose}{if TRUE, additional information is displayed, that
is potentially useful in debugging}
}
\value{
Nothing. This is an internal function that does nothing
}
\description{
This function does nothing. It is intended to inherit is parameters'
documentation.
}
\note{
This is an internal function, so it should be marked with
  \code{@noRd}. This is not done, as this will disallow all
  functions to find the documentation parameters
}
\author{
Richèl J.C. Bilderbeek
}