CompEvol/beast2 — pull request #184 by armanbilge (2014-08-12 01:03:46+00:00)
Title: Condition on origin for birth-death process

An implementation of conditioning on the origin for birth-death processes as described in "The conditioned reconstructed process" (Gernhard 2008). Feature suggested by @alexeid. Validated against against Tanja's R package [TreeSim](http://cran.r-project.org/web/packages/TreeSim/).

I have XML parsing currently implemented such that adding a parameter representing the origin height in the XML implicitly activates conditioning on the origin. A warning is raised if conditioning on both the root and the origin is specified.

Most of my code is simply a rearrangement of the code for conditioning on the root. However I was surprised to find that, when conditioned, the birth-death prior ignores any specified sampling probability although Tanja has derived densities for these cases. Is there a particular reason why this is not implemented?