Greetings
all, I am attempting node-dating with a fully constrained, bifurcating a priori topology. This presents a syntactic challenge in that I know how to calibrate nodes with the clade() function, and a given prior distribution on the age of that node, but these constrained nodes cannot be jointly included with the topology in the vector constraints that is fed to dnConstrainedTopology.
Can Newick-formatted trees (topology below) be included as constraints at all in RevBayes? Has anyone solved similar challenges in their divergence-dating analyses?
Here are the relevant lines of code for reference (modified for brevity):
source("./clade_constraints/clade_extant_Apidae.rev")...etc.
# Define a stochastic node for the constrained tree topology #
timetree ~ dnConstrainedTopology(tree_dist, constraints=constraints)
Hopefully, this provides sufficient detail.
Regards, Zach