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#
# RevBayes: Discrete morphology 
# the Mk model with ascertainment-bias correction ("Mkv")
#
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# Create the Q matrix. These data are binary, so we initialize the Jukes-Cantor
# matrix with two states.
Q_morpho <- fnJC(2)

# Combine the tree and the Q matrix into the phylogenetic CTMC. Because we have
# not observed any invariant sites, we specify the coding as 'variable' to
# correct for ascertainment bias.
phyMorpho ~ dnPhyloCTMC(tree=phylogeny, Q=Q_morpho, type="Standard", coding="variable")
phyMorpho.clamp(morpho)