Hello,
I have characterized a few hundred bacteria from two environments and want to
know if the bacteria from one environment is more likely to show a trait than
the bacteria isolated from the other environment. So my data is binary in both
the independent and in the dependent variable: "environment 1?" yes/no, and
"degrades carbon source?" yes/no. If I wasn’t accounting for phylogeny, I think
I would use a Chi-Squared test. But I would like to account for phylogeny in my
analysis, since some of the bacteria form clusters on my phylogenetic tree with
members only from one environment.
I thought maybe I could use MCMCglmm to test this, and have been following the
examples previously posted on r-sig-phylo and in the MCMCglmm course notes.
However, my model either fails to converge even after millions of iterations,
or the autocorrelation plot shows strong positive correlations at a range of
lags. So I think either I cannot use MCMCglmm for this, or I am specifying my
model wrong. Any pointers in the right direction would be greatly appreciated.
Here is my model:
prior.m2c.5 = list(B = list(mu = c(0, 0), V = diag(2) *(1 + pi^2/3)), R =
list(V = 1, fix = 1), G = list(G1 = list(V = 1, nu = 1, alpha.mu = 0, alpha.V =
1000)))
simplemcmcCMCv2_5<-MCMCglmm(carbon01~environment01, random=~animal,
pedigree=ctree, data=wcboth, family="categorical”, nitt=10000000,
burnin=100000,thin=2000, prior=prior.m2c.5)
Thank you in advance for any help,
Grace Pold
Graduate Program in Organismic and Evolutionary Biology
University of Massachusetts, Amherst
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