pps-revscripts/MCMC_Simulation.Rev at master · PhyleauxLab/pps-revscripts · GitHub

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################################################################################
#
# RevBayes Example: Bayesian model testing using posterior predictive simulation
#
# authors: Lyndon M. Coghill, Sebastian Hoehna and Jeremy M. Brown
#
################################################################################

source( model_file_name )

mni = 0


monitors[++mni] = mnModel(filename="output_" + model_name + "/" + analysis_name + "_posterior.log",printgen=50, separator = TAB)
monitors[++mni] = mnFile(filename="output_" + model_name + "/" + analysis_name + "_posterior.trees",printgen=50, separator = TAB, phylogeny)
monitors[++mni] = mnScreen(printgen=1000, TL)
monitors[++mni] = mnStochasticVariable(filename="output_" + model_name + "/" + analysis_name + "_posterior.var",printgen=50)


mymcmc = mcmc(mymodel, monitors, moves, nruns=2)
#mymcmc.burnin(generations=10000,tuningInterval=10)
mymcmc.run(generations=50000)