def add_constrainedrandomtree_init(self, beastxml):
attribs = {"estimate":"false", "id":"startingTree", "initial":"@Tree.t:beastlingTree", "taxonset":"@taxa", "spec":"beast.evolution.tree.ConstrainedRandomTree", "constraints":"@constraints"}
if self.birthrate_estimate is not None:
attribs["rootHeight"] = str(self.treeheight_estimate)
beastxml.init = xml.init(beastxml.run, attrib=attribs)
popmod = xml.populationModel(beastxml.init, spec="ConstantPopulation")
xml.popSize(popmod, spec="parameter.RealParameter", value="1")
def add_prior(self, beastxml):
"""Add a Yule tree prior."""
coalescent = xml.distribution(beastxml.prior,
id="Coalescent.t:beastlingTree",
spec="Coalescent")
popmod = xml.populationModel(coalescent,
id="ConstantPopulation:beastlingTree",
spec="ConstantPopulation")
xml.parameter(popmod, idref="popSize.t:beastlingTree", name="popSize")
xml.treeIntervals(coalescent,
id="TreeIntervals",
spec="TreeIntervals",
tree="@Tree.t:beastlingTree")