[R-sig-phylo] How to incorporate intraspecific variation in MCMCglmm

2017-07-14 Thread Diogo B. Provete
Dear list, I'm trying to fit a mixed-effects model to a problem that includes: a continuous response variable (mean jumped distance by 17 species of frogs) in 3 different arenas and under 2 types of stimuli. So, it's a kind of two-way ANOVA design. I have the species phylogeny and prepared its

Re: [R-sig-phylo] How to incorporate intraspecific variation in MCMCglmm

2017-07-14 Thread Jarrod Hadfield
Hi Diogo, First, your model1 is unlikely to be valid unless the residual variance happens to be 1. You should not fix it at one, and use a prior like: prior = list(R = list(V = 1, nu = 0.02), G=list(G1=list(V=1, nu=0.02))) Note that the residual variance (Ve) is the intra-specific variance,