default_parameters_doc

Documentation of parameters (for example, <code>create_param</code>.
This function does nothing. It is intended to inherit documentation from.

'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.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.

Richèl J.C. Bilderbeek

beautier

'BEAUti' from R

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Olivier Roy

Jana Riederer

default_parameters_doc function

<dl><dt>dimension</dt>
<dd>the number of dimensions, for example, as used in
create_freq_param</dd>
<dt>estimate</dt>
<dd>TRUE if this parameter is to be estimated by BEAST2,
FALSE otherwise</dd>
<dt>id</dt>
<dd>the parameter's ID</dd>
<dt>lower</dt>
<dd>lowest possible value of the parameter. If the parameter
is estimated, <code>lower</code> must be less than <code>value</code></dd>
<dt>name</dt>
<dd>the parameters' name. Valid
names can be found in <code>get_param_names</code></dd>
<dt>upper</dt>
<dd>upper value of the parameter</dd>
<dt>value</dt>
<dd>value of the parameter</dd>
<dt>...</dt>
<dd>specific parameter parameters</dd></dl>

Arguments

Author

Documentation of parameters (for example, create_param.
This function does nothing. It is intended to inherit documentation from. — default_parameters_doc

<dl>

<dt>dimension</dt>
<dd>the number of dimensions, for example, as used in
create_freq_param</dd>


<dt>estimate</dt>
<dd>TRUE if this parameter is to be estimated by BEAST2,
FALSE otherwise</dd>


<dt>id</dt>
<dd>the parameter's ID</dd>


<dt>lower</dt>
<dd>lowest possible value of the parameter. If the parameter
is estimated, <code>lower</code> must be less than <code>value</code></dd>


<dt>name</dt>
<dd>the parameters' name. Valid
names can be found in <code>get_param_names</code></dd>


<dt>upper</dt>
<dd>upper value of the parameter</dd>


<dt>value</dt>
<dd>value of the parameter</dd>


<dt>...</dt>
<dd>specific parameter parameters</dd>

</dl>

Documentation of parameters (for example, <code>create_param</code>.
This function does nothing. It is intended to inherit documentation from.

default_parameters_doc: Documentation of parameters (for example, `create_param`. This function does nothing. It is intended to inherit documentation from.

Description

Usage

Arguments

Author