################################################################################
#
# RevBayes Example: Inferring a Phylogeny of Fossil Bears Using the Mk Model
#                   with a discretized Beta distribution for the stationary
#                   frequencies.
#
# This file: Runs the full MCMC.
#
# authors:  April M. Wright, Michael J. Landis, Sebastian Höhna
#
################################################################################

#######################
# Reading in the Data #
#######################
morpho <- readDiscreteCharacterData("data/bears.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")

###########################################
# Binary morphological substitution model #
###########################################

source("scripts/model_freqs_beta.Rev")

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

mymodel = model(phylogeny)

monitors.append( mnModel(filename="output/mkv_beta.log", printgen=10) )
monitors.append( mnFile(filename="output/mkv_beta.trees", printgen=10, phylogeny) )
monitors.append( mnScreen(printgen=100) )

mymcmc = mcmc(mymodel, monitors, moves, nruns=2, combine="mixed")
mymcmc.run(generations=30000, tuningInterval=200)
mymcmc.operatorSummary()

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

q()