BEAST v2.5.0 XML Reference

This documentation is used to help the user who wants to edit BEAST2 XML manually.

How to read:

Example of beast.core.MCMC:

A common example for beast.core.MCMC is :

<run chainLength="100000000" id="mcmc" spec="MCMC">

But through its XML reference, we know there is a "Optional" input preBurnin available to define the burn-in, and it has to be an integer.

So we can modify the XML to :

<run chainLength="1000000" id="mcmc" spec="MCMC" preBurnin="1000">

Example of beast.evolution.operators.ScaleOperator:

ScaleOperator has a "Either this or" rule for inputs tree and parameter, so that it has to either scale a tree :

<operator id='treeScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" tree="@tree"/>

or a RealParameter, such as kappa of HKY :

<parameter id="hky.kappa" value="1.0" lower="0.0"/> <operator id='kappaScaler' spec='ScaleOperator' scaleFactor="0.5" weight="1" parameter="@hky.kappa"/>