################################################################################
#
# RevBayes Example: Inferring a phylogeny of herons (Ardeidae) with ordered
#                   and unordered characters
#
# This file: Runs the full MCMC.
#
# authors -- Basanta Khakurel and April Wright
#
################################################################################

#######################
# Reading in the Data #
#######################
morpho = readDiscreteCharacterData("data/Ardeidae.nex")

## helpers
taxa <- morpho.names()
num_taxa <- taxa.size()
num_branches <- 2 * num_taxa - 2

moves    = VectorMoves()
monitors = VectorMonitors()

##############
# Tree model #
##############

source("scripts/model_tree.Rev")

####################################################
# Substitution model with ordered and unordered    #
# characters, partitioned by the number of states  #
####################################################

source("scripts/model_ordered_partition.Rev")

########
# MCMC #
########

mymodel = model(phylogeny)

monitors.append( mnModel(filename="output/ordered.log", printgen=10) )
monitors.append( mnFile(filename="output/ordered.trees", printgen=10, phylogeny) )
monitors.append( mnScreen(printgen=1000, tree_length) )

mymcmc = mcmc(mymodel, monitors, moves, nruns=2, combine="mixed")
mymcmc.run(generations=20000, tuningInterval=200)

trace = readTreeTrace("output/ordered.trees", treetype="non-clock")
trace.setBurnin(0.25)
mapTree(trace, file="output/ordered.map.tre")
consensusTree(trace, file="output/ordered.majrule.tre")

q()