beter

Create BEAST2 XML files from individual XML chunks using {{ moustache }} templating system and TOML configuration files.

beter allows you to:

• write XML templates with {{ mustache }} tags
• {{ mustache }} tags are replaced by values in TOML config
• structure your TOML config with additional subconfigs

See https://biods.github.io/beter/ for more information.

Installation

devtools::install_github("biods/beter")

Usage

Lets have a (simplistic) BEAST2 XML with all the required parts. What we often need to do is run the same file for different number of generations because it often turns out that our first run didn't have enough ESS. This can be easily done by replacing specific number for chainLength with a {{ mustache }} tag:

<!--template.xml-->
<xml>
...
<run id="mcmc" spec="MCMC" chainLength="{{chain_length}}">
...
</xml>

and writing a TOML config for this:

# config.toml
[defaults]
chain_length = 5000

Now by running:

library(beter)
process_template("template.xml", "result.xml", "config.toml")

the {{chain_length}} will get replaced by 5000. Instead of replacing a number, you can insert whole XML chunks. This way you can programatically create templates with values and models you require.