BEAST v2.6.7 XML Reference

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

How to read:

• Each page is documenting a BEAST object, which is used for a value of the spec attribute in the XML. It may contain one or more inputs.
• An input connects this BEAST object with the output from another BEAST object that is also the type of this input. Each input is documented in a table of the HTML page.
  • The table title is the input name.
  • The first row is its type defined by either a Java primitive wrapper class or Java implementation of a BEAST object.
  • The second row describes what the input do.
  The last row shows its validation rule, and the default value.
• There are three options for the validation rule of an input: "Required", "Optional", "Either this, or".
• Required means this input is compulsory in the XML.
• Optional means this input can be absent in the XML, in this case, the default value is used.
• Either this or represents the situation that you have to choose this input or the alternative input in the XML, and it will be invalid if both are missing.
• If there is *** behind a type, it indicates this input type is actually a list (java.util.List) of this Java class.

Example of beast.core.MCMC:

A common example for beast.core.MCMC is :

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 :

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 :

or a RealParameter, such as kappa of HKY :