Re: [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm)

2018-06-21 Thread Jarrod Hadfield
Hi Liam, In multi-level models DIC can be 'focused' at different levels. In MCMCglmm, DIC is focussed at the highest possible level because this is the only level at which it can be analytically computed for non-Gaussian models. The highest level is not the level at which most scientists want

[R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm)

2018-06-21 Thread jonnations
Hi Liam, I don't have the exact answer you are looking for, but I would highly recommend the brms package in R. It is incredibly flexible and has excellent diagnostic tools like LOO and WAIC that are easy to use and interpret for model selection. I think it would work well for the models you

[R-sig-phylo] ape-package: unknown states in ace analyses?

2018-06-21 Thread Théo Léger
Hello, I am working on the phylogeny of a subfamily of moths and I use ace from the ape-package to reconstruct the ancestral state of a bunch of morphological characters. I encountered a problem with the few unknown states I have on my matrix (coded "?", either because material for

Re: [R-sig-phylo] Comparing DIC of phylogenetic and non-phylogenetic GLMM run with MCMC (MCMCglmm)

2018-06-21 Thread Liam Kendall
Thank you all for your very informative responses. I will try the brms package as Jon suggested - I have read a bit about WAIC being more appropriate or favourable than the DIC but I was (until now) unfamiliar with the brms package. We are very much working within a predictive framework where