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beastier

Call 'BEAST2'

'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

# 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:

```text
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:

<!-- markdownlint-disable MD013 -->

```text
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.
[...]
```

<!-- markdownlint-enable MD013 -->

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).

Versions across snapshots

VersionRepositoryFileSize
2.5.2 2026-04-09 windows/windows R-4.5 beastier_2.5.2.zip 571.0 KiB

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