BEAST v2.5.0 XML Reference
This documentation is used to help the user who wants to edit BEAST2 XML manually.
How to read:
There are three options for the validation rule of an input: "Required", "Optional", "Either this, or".
- 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.
If there is *** behind a type, it indicates this input type is actually a list (java.util.List) of this Java class.
- 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.
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 :