Description
Call 'BEAST2'.
Description
'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 a command-line tool. This package provides a way to call 'BEAST2' from an 'R' function call.
README.md
extdata
beast beast2_error.xml
File to create a BEAST2 error.
:warning: the BEAST2 NS package must not be installed :warning:
Upon running this file in BEAST2, the output will end with:
Error 1017 parsing the xml input file
Class could not be found. Did you mean beast.core.util.ESS?
Perhaps a package required for this class is not installed?
Error detected about here:
<beast>
<run id='mcmc' spec='beast.gss.NS'>
The error message says it all: one needs to install the BEAST2 NS package. beastier cannot do this (note that mauricer can).
beast2_warning.xml
File to create a BEAST2 warning.
Upon running this file in BEAST2, the output will end with:
WARNING: StateNode (freqParameter.s:anthus_aco) found that has no effect on posterior!
[...]
Fatal exception: Could not find a proper state to initialise. Perhaps try another seed.
See http://www.beast2.org/2018/07/04/fatal-errors.html for other possible solutions.
[...]
The word WARNING is used to detect a warning. Regardless of the fatal exceptions, BEAST2 exits without an error code (i.e. exit code zero).