default_params_doc

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

'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is commonly accompanied by 'BEAUti 2' (<https://www.beast2.org>),
which, among others, allows one to install 'BEAST2' package.
This package allows to work with 'BEAST2' packages from 'R'.

Richel Bilderbeek

mauricer

Work with 'BEAST2' Packages

default_params_doc function

<dl><dt>beast2_folder</dt>
<dd>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.
Use get_default_beast2_jar_path
 to get the full path to the default BEAST2 jar file.</dd>
<dt>has_internet</dt>
<dd>boolean to indicate if the user has access to the
internet. By default, this value equals the result
of <code><a href="/link/curl%3A%3Ahas_internet?package=mauricer&version=2.5.2" data-mini-rdoc="mauricer::curl::has_internet">curl::has_internet</a></code></dd>
<dt>name</dt>
<dd>the package's name</dd>
<dt>show_warnings</dt>
<dd>set to TRUE to show warnings</dd>
<dt>verbose</dt>
<dd>set to TRUE for extra output, as can be used in debugging</dd></dl>

Arguments

Author

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

<dl>

<dt>beast2_folder</dt>
<dd>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.
Use get_default_beast2_jar_path
 to get the full path to the default BEAST2 jar file.</dd>


<dt>has_internet</dt>
<dd>boolean to indicate if the user has access to the
internet. By default, this value equals the result
of <code><a href='https://rdrr.io/pkg/curl/man/nslookup.html'>curl::has_internet</a></code></dd>


<dt>name</dt>
<dd>the package's name</dd>


<dt>show_warnings</dt>
<dd>set to TRUE to show warnings</dd>


<dt>verbose</dt>
<dd>set to TRUE for extra output, as can be used in debugging</dd>

</dl>

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

Description

Usage

Arguments

Author