16 June 2015 by Remco Bouckaert

When developing a BEAUti template, you have to keep in mind that a BEAST model is directed acyclic graph of BEAST objects such as for example shown here. A BEAUti template describes a sub-graph that can be slotted into the overall model. This means the template has to define two things:

1. A set of BEAST objects
2. A set of rules on how to put the sub-network into the full graph

Up to now, the rules on how to connect networks to the graph was through BeautiConnector rules specifying the srcID of one of the BEAST objects in the sub-network, and a targetID and inputName specifying which object in the larger network to connect to. Furthermore, connections are not always necessary; if a parameter is kept fixed instead of estimated, there is no need to log it, so there is no need to connect that parameter to any logger. A BeautiConnector only connects conditional on whatever is specified in the if attribute.

Below is a simple template that specifies the HKY substitution model. The BEAST objects are specified in the CDATA section: the HKY substitution model and its kappa parameter and frequencies object, two operators and a prior on kappa. If kappa is estimated (the default) kappa should be connected to the state (see first connector rule). Likewise for frequencies (second rule).

    
    
    
	
    



    
	
	
    





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Scale HKY transition-transversion
parameter of partition s:$(n)


Exchange values of frequencies of partition s:$(n)





HKY transition-transversion
parameter of partition s:$(n)

From BEAST v2.3.0, the connector rules can be integrated in the XML fragment that specify the BEAST objects. At the top level, the target objects are specified through their IDs, and anything that need to be connected can be inserted through nesting these objects. The conditions are encoded in the if attribute in the beauti namespace, so they look like beauti:if followed by the condition. Let’s walk through the example above.

First, we specify the subtemplate header, and the HKY object:

So far nothing different from above. However, next we will connect the kappa and frequency parameter to the state; just define a state element and specify an idref to the state object. The kappa and frequency parameters will be connected to the stateNode input, for which we specify two stateNode elements, and idrefs to the kappa and frequency parameters specified in the HKY block above.

This replaces the first two connector rules in the original template.

Next, we define the prior on kappa. Since it will be connected to the prior, we wrap it in a distribution element with idref to prior. The condition on which to connect (that kappa is in the likelihood and is estimated) is specified in the prior element. We added name="distribution" in order to ensure the prior is connected to the distribution input.

There is another way to specify conditions which is especially handy when there are several items to be connected that are to be connected under the same condition. The if element specified just inside a top-level element in the CDATA block is interpreted as a condition that applies to all of the elements inside. The condition itself is specified in the cond attribute. For example, the operators can be defined like so;

That leaves the connections to the loggers to be defined;

    
                

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And that completes the HKY template.

The hope is that this new way for specifying sub-templates is a bit more intuitive once you are used to writing plain BEAST 2 XML. The idea is that going from an example XML to a sub-template just means

• remove all XML elements outside sub-graph that is not connected to
• replace all BEAST objects outside the sub-graph with idrefs
• add conditions (in beauti:if attributes or if elements)

Then the only thing left is to rename IDs so they math partition information and wrap the BEAUti subtemplate bits around the CDATA section.