Runs that previously worked on the CRAN version of bayou are no longer working for me on the dev version. These runs use the probability of a shift proportional branch length prior outlined in some of the documentation. The runs work for a few generations, but ultimately crash. For instance,
prior2 <- make.prior(prunedMBC, dists=list(dalpha="dhalfcauchy", dsig2="dhalfcauchy",dsb="dsb", dk="cdpois", dtheta="dnorm"), param=list(dalpha=list(scale=1), dsig2=list(scale=1), dk=list(lambda=15, kmax=200), dsb=list(bmax=Inf,prob=prunedMBC$edge.length), dtheta=list(mean=mean(avMBC), sd=2)))
mcmc2 <- bayou.makeMCMC(prunedMBC, avMBC, SE=cvMBC, model="OU", prior=prior2, new.dir=TRUE, samp=10^2, chunk=10^3, ticker.freq=10^4, plot.freq=NULL)
system.time(mcmc2$run(ngen=10^7))
returns
Error in sample.int(x, size, replace, prob) : NA in probability vector
Calls: system.time ... .proposalFn -> .moveFn -> .sample -> sample -> sample.int
Timing stopped at: 2099.404 15.264 2117.245
Perhaps something needs to get fixed with this model on the dev version? Or, perhaps I've misspecified something in the code (entirely possible).