parse_beast_output_files

'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.
'Tracer' (<https://github.com/beast-dev/tracer/>) is a GUI tool
to parse and analyze the files generated by 'BEAST2'.
This package provides a way to parse and analyze 'BEAST2' input
files without active user input, but using
R function calls instead.

Richel Bilderbeek

tracerer

Tracer from R

Richèl J.C. Bilderbeek

Joëlle Barido-Sottani

David Winter

parse_beast_output_files function

<dl><dt>log_filename</dt>
<dd>deprecated name
of the BEAST2 tracelog <code>.log</code> output file.
Use <code>tracelog_filename</code> instead</dd>
<dt>trees_filenames</dt>
<dd>the names of one or more a BEAST2
posterior <code>.trees</code> file.
Each <code>.trees</code> file can be read using parse_beast_trees</dd>
<dt>state_filename</dt>
<dd>name of the BEAST2 state <code>.xml.state</code> output file</dd></dl>

Arguments

Author

Parse all BEAST2 output files — parse_beast_output_files

<dl>

<dt>log_filename</dt>
<dd>deprecated name
of the BEAST2 tracelog <code>.log</code> output file.
Use <code>tracelog_filename</code> instead</dd>


<dt>trees_filenames</dt>
<dd>the names of one or more a BEAST2
posterior <code>.trees</code> file.
Each <code>.trees</code> file can be read using parse_beast_trees</dd>


<dt>state_filename</dt>
<dd>name of the BEAST2 state <code>.xml.state</code> output file</dd>

</dl>

Parse all BEAST2 output files

parse_beast_output_files: Parse all BEAST2 output files

Description

Usage

Value

Arguments

Author

See Also

Examples