MCMCglmm and phylogeny - huge variance problem
Hi, I tried compute.brlen but this works fine and computes branch lengths without any problem. I've used such trees before (without branch lengths, just topology) and they worked. Is it possible that this "duplicated levels" thing messes with everything? sz.
On 6 July 2011 17:11, Jarrod Hadfield <j.hadfield at ed.ac.uk> wrote:
Hi, There seems to be something amiss with the tree. Do you expect there to be branch lengths? Do you get warning messages outside of MCMCglmm if you use compute.brlen on the phylogeny? Jarrod On Wed, 2011-07-06 at 16:45 +0200, Szymek Drobniak wrote:
Dear mixed modellers, I'm trying to fit a comparative meta-analysis and everything's fine but I'm getting several warnings (some of which I don't quite understand and can't tell if they're causing the problem) and a weird result with huge animal (ergo phylogeny-related) variance. Below is the model and the prior, and of course the output with summary. Any idea if this huge variance might be due to these warnings ?(relating to the tree I guess) or due to the data (which has has high variance anyway). Could prior expansion fix these problems? Szymek #########(code) prior.fil <- list(R=list(V=1,n=0.002), G=list(G1=list(V=1,n=0.002),G2=list(V=1,n=0.002),G3=list(V=1,n=0.002))) meta.fil <- MCMCglmm(Zr~1, random=~ref+repeat+animal, prior=prior.fil, pedigree=tree, mev=data$mev, data=data, verbose=F, nitt=3000000, burnin=1000000, thin=800) ###########(summary of the model) ?Iterations = 100001:4999501 ?Thinning interval ?= 500 ?Sample size ?= 9800 ?DIC: 256.8579 ?G-structure: ?~ref ? ? post.mean ?l-95% CI u-95% CI eff.samp ref ? 0.03544 0.0002057 ? 0.1017 ? ? 9800 ? ? ? ? ? ? ? ?~repeat. ? ? ? ? post.mean ?l-95% CI u-95% CI eff.samp repeat. ? 0.01121 0.0001536 ?0.04053 ? ? 9800 ? ? ? ? ? ? ? ?~animal ? ? ? ?post.mean ?l-95% CI ?u-95% CI eff.samp animal 3.765e+15 1.450e+15 4.504e+15 ? ? 9507 ?R-structure: ?~units ? ? ? post.mean l-95% CI u-95% CI eff.samp units ? ?0.2345 ? 0.1703 ? 0.3107 ? ? 9502 ?Location effects: Zr ~ 1 ? ? ? ? ? ? post.mean ?l-95% CI ?u-95% CI eff.samp pMCMC (Intercept) ? ?-740.7 -453419.4 ?464404.3 ? ? 9800 0.988
############(warnings)
Warning messages:
1: In inverseA(pedigree, nodes = nodes, scale = scale) :
? no branch lengths: compute.brlen from ape has been used
2: In `levels<-`(`*tmp*`, value = c("JJJ", "DDD", "III", "GGG", "", ?:
? duplicated levels will not be allowed in factors anymore
3: In MCMCglmm(Zr ~ 1, random = ~ref + repeat. + animal, prior = prior.fil, ?:
? some combinations in animal do not exist and 50 missing records have
been generated
4: In `[<-.data.frame`(`*tmp*`, dim(data)[1] -
(dim(missing.combinations)[1] - ?:
? provided 50 variables to replace 2 variables
5: In `[<-.factor`(`*tmp*`, iseq, value = c("JJJ", "1", "JJJ", "1", ?:
? invalid factor level, NAs generated
6: In `levels<-`(`*tmp*`, value = c("JJJ", "DDD", "III", "GGG", "", ?:
? duplicated levels will not be allowed in factors anymore
-- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Szymon Drobniak || Population Ecology Group Institute of Environmental Sciences,?Jagiellonian University ul. Gronostajowa 7, 30-387 Krak?w, POLAND tel.: +48 12 664 52 19 fax: +48 12 664 69 12 www.eko.uj.edu.pl/drobniak