Testing the MCMC (task testMCMC)

To test MCMC parameters with levolution, specify task=testMCMC. Then one needs to specify the mandatory parameters: tree, traits, rootState, brownVar, alpha, lambda, numNVecs, thinning, and burnin. An example command line might look like this:

./levolution task=testMCMC tree=myTree.tree traits=myTraits.traits rootState=0 brownVar=1 alpha=10 lambda=0.3 numNVecs=10000 thinning=100 burnin=100

The output file will have the suffix "_MCMC.txt". In this file you will find the values of the parameters root state, brownian variance, and lambda sampled by the MCMC for each iteration.