Prob of shift proportional to branch length maybe broke on dev version?

[eliotmiller]

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).

[coyotree]

Hello,

I am running into the same error. I am using version 2.1. If I just keep re-running it, it will manage to run for a period of time and then throw an error again. Would really like to use branch lengths in the prior but the errors worrying me. See below for a very long example of the output. Thanks for your help!

`Checking inputs for errors:...........
seems fine...

fit.branches$run(100000)
gen lnL prior alpha sig2 rtheta k .alpha .sig2 .theta birth.k D0.slid D1.slid death.k U0.slid U1.slid U2.slid
1000 -119.15 -61.41 1.93 3.64 2.21 10 0.53 0.40 0.68 0.12 1.00 0.60 0.78 1.00
....
7000 -118.00 -43.52 1.26 2.21 2.04 6 0.47 0.45 0.62 0.10 1.00 0.36 0.59 0.94 0.34 0.24
Error in sample.int(x, size, replace, prob) : NA in probability vector
fit.branches$run(100000)
gen lnL prior alpha sig2 rtheta k .alpha .sig2 .theta birth.k D0.slid D1.slid death.k U0.slid U1.slid U2.slid
8000 -117.02 -52.69 1.44 2.40 2.12 8 0.42 0.43 0.60 0.07 1.00 0.08 0.45 1.00 0.00 0.18
....
10000 -120.05 -49.49 1.58 3.53 1.82 7 0.45 0.42 0.59 0.07 1.00 0.15 0.45 0.99 0.17 0.12
Error in sample.int(x, size, replace, prob) : NA in probability vector
fit.branches$run(100000)
gen lnL prior alpha sig2 rtheta k .alpha .sig2 .theta birth.k D0.slid D1.slid death.k U0.slid U1.slid U2.slid
11000 -126.16 -52.32 0.45 1.26 2.24 9 0.45 0.44 0.70 0.14 1.00 0.00 0.38 1.00
......
72000 -115.63 -54.08 0.14 0.22 2.31 8 0.48 0.48 0.68 0.10 0.95 0.30 0.60 0.00 0.94 0.31 0.25
Error in if (runif(1) < exp(nll - oll + pr2 - pr1 + hr)) { :
missing value where TRUE/FALSE needed
fit.branches$run(100000)
Error in sample.int(x, size, replace, prob) : NA in probability vector
fit.branches$run(100000)
Error in sample.int(x, size, replace, prob) : NA in probability vector
fit.branches$run(100000)
gen lnL prior alpha sig2 rtheta k .alpha .sig2 .theta birth.k D0.slid D1.slid death.k U0.slid U2.slid
73000 -125.83 -47.44 0.07 0.17 2.01 8 0.62 0.29 0.88 0.05 1.00 0.00 0.60 1.00 0.00
74000 -123.76 -45.19 0.34 0.61 2.23 8 0.46 0.54 0.75 0.10 1.00 0.38 0.62 0.92 0.40 0.04
75000 -117.79 -51.09 1.56 2.11 2.20 8 0.44 0.47 0.70 0.10 1.00 0.25 0.54 0.93 0.18 0.08
Error in if (runif(1) < exp(nll - oll + pr2 - pr1 + hr)) { :
missing value where TRUE/FALSE needed
fit.branches$run(100000)
gen lnL prior alpha sig2 rtheta k .alpha .sig2 .theta birth.k D0.slid D1.slid death.k U0.slid U1.slid U2.slid
76000 -117.55 -68.06 3.31 6.71 1.80 12 0.34 0.54 0.62 0.13 1.00 0.11 0.55 1.00 0.50 0.25
....
96000 -123.52 -57.11 0.06 0.09 2.20 10 0.48 0.48 0.65 0.09 0.98 0.31 0.58 0.95 0.33 0.19
Error in sample.int(x, size, replace, prob) : NA in probability vector`

[uyedaj]

Resolved this issue in version 2.1.3 (hopefully)