Node-dating with fully constrained topology

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Zachary Griebenow

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Mar 26, 2024, 6:07:02 PM3/26/24
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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.
constraints_monophyly = v(clade_extant_Apidae,...etc.,topology)

# prior probability distributions for each calibrated node
### taken from https://revbayes.github.io/tutorials/dating/nodedate
source("node_dates_exponential.rev")

# Define a stochastic node for the constrained tree topology #
timetree ~ dnConstrainedTopology(tree_dist, constraints=constraints)

Hopefully, this provides sufficient detail.

Regards, Zach
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