################################################################################
#
# RevBayes: Discrete morphology tutorials -- the plain Mk model, partitioned by
#           the number of states (no rate variation, no ascertainment-bias
#           correction), for comparison with the covariomorph model.
#
################################################################################

max_states = morpho.getStateDescriptions().size()
idx = 1

for (i in 1:(max_states-1)) {
    partition_state[i] = morpho
    partition_state[i].setNumStatesPartition(i+1)
    nc = partition_state[i].nchar()

    if (nc > 0) {
        Q_morpho[idx] := fnJC(i+1)
        phyMorpho[idx] ~ dnPhyloCTMC(tree=phylogeny, Q=Q_morpho[idx], nSites=nc, type="Standard")
        phyMorpho[idx].clamp(partition_state[i])
        idx = idx + 1
    }
}