The main issue is that the MCMC element in the Standard (and other) templates has id mcmc and there are many connector rules that use this id for connecting operators. Switching to say CoupledMCMC means that these connector rules are ignored, and operators that should be present do not end up in the XML.
The CoupleMCMC object cannot share the mcmc id, since it is the main-id in a subtemplate, and these must be unique in order for BEAUti to be able to identify which template to use.
A hackier solution is to have connector rules check for the target being mcmc and replace the target with the Runnable in BeautiDoc.mcmc. This will work for CoupledMCMC and nested sampling.
The main issue is that the MCMC element in the Standard (and other) templates has id
mcmc
and there are many connector rules that use this id for connecting operators. Switching to say CoupledMCMC means that these connector rules are ignored, and operators that should be present do not end up in the XML.The CoupleMCMC object cannot share the
mcmc
id, since it is the main-id in a subtemplate, and these must be unique in order for BEAUti to be able to identify which template to use.A hackier solution is to have connector rules check for the target being
mcmc
and replace the target with theRunnable
inBeautiDoc.mcmc
. This will work for CoupledMCMC and nested sampling.