Structured Tree Likelihood

The Structured Tree Likelihood component

The STreeLikelihoodODE class computes the log-likelihood of a genealogy given a population model. The STreeLikelihoodODE component takes as input a structured tree set of intervals and an instantiation of a PopModelODE. A typical STreeLikelihoodODE entry looks like this:

<distribution spec='STreeLikelihoodODE' id = 'stlikelihood'
      useStateName='true' popmodel='@sirmodel'             	 
      solvePL='true' stepSize='0.01'>                
      <treeIntervals spec="STreeIntervals" tree='@tree'> </treeIntervals>                
</distribution>

where @popmodel is reference to a PopModelODE element and '@tree' is a reference to a Tree element.

It is important to take into consideration the following:

How do we introduce population structure?
How do we time the tree?

Population Structure

Population structure is introduced by mapping tip nodes to deme names.

<sequence id="EBOV|G4973.1|KR105286|SLE|x|2014-08-12_I"  
          taxon="EBOV|G4973.1|KR105286|SLE|x|2014-08-12_I"  
          totalcount="4" value="??"/>