create_tracelog

Create a <code>tracelog</code> object

'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.

Richel Bilderbeek

beautier

'BEAUti' from R

Richèl J.C. Bilderbeek

Joëlle Barido-Sottani

David Winter

Paul Van Els

Raphael Scherrer

Yacine B. Chehida

Katharine S. Walter

Gary Napier

Jason Griffiths

Thijs Janzen

Pedro Taucce

Jana Riederer

create_tracelog function

<dl><dt>filename</dt>
<dd>name of the file to store the posterior traces.
Use <a href="/link/NA?package=beautier&version=2.6.9" data-mini-rdoc="beautier::NA">NA</a> to use the filename <code>[alignment_id].log</code>,
where <code>alignment_id</code> is obtained using get_alignment_id</dd>
<dt>log_every</dt>
<dd>number of MCMC states between writing to file</dd>
<dt>mode</dt>
<dd>mode how to log.
Valid values are the ones returned by get_log_modes</dd>
<dt>sanitise_headers</dt>
<dd>set to <a href="/link/TRUE?package=beautier&version=2.6.9" data-mini-rdoc="beautier::TRUE">TRUE</a> to sanitise the headers of the
log file</dd>
<dt>sort</dt>
<dd>how to sort the log.
Valid values are the ones returned by get_log_sorts</dd></dl>

Arguments

Create a tracelog object — create_tracelog

<dl>

<dt>filename</dt>
<dd>name of the file to store the posterior traces.
Use <a href='https://rdrr.io/r/base/NA.html'>NA</a> to use the filename <code>[alignment_id].log</code>,
where <code>alignment_id</code> is obtained using get_alignment_id</dd>


<dt>log_every</dt>
<dd>number of MCMC states between writing to file</dd>


<dt>mode</dt>
<dd>mode how to log.
Valid values are the ones returned by get_log_modes</dd>


<dt>sanitise_headers</dt>
<dd>set to <a href='https://rdrr.io/r/base/logical.html'>TRUE</a> to sanitise the headers of the
log file</dd>


<dt>sort</dt>
<dd>how to sort the log.
Valid values are the ones returned by get_log_sorts</dd>

</dl>

Create a <code>tracelog</code> object

create_tracelog: Create a `tracelog` object

Description

Usage

Arguments