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prior
2012 May 02
0
MCMCglmm priors including phylogeny
...rate the phylogeny (almost fully resolved with only 2 polytomies, including branch lengths) in the error structure. There is only 1 explanatory variable, a 5-level factor. I'm using uninformative priors for fixed parameters (i.e. not specifying any priors).
Here's my code:
#prior model1
prior1<-list(R = list(V = diag(2)*x, n=2),
G = list(G1=list(V = diag(2)*x, n=2)))
#model1
m1<-MCMCglmm(cbind(y1.logit,y2.logit) ~ trait:Ecotype - 1,
random=~us(trait):animal, rcov=~us(trait):units, family=c("gaussian","gaussian"),
prior=pr...