Skip to content
Prev 12818 / 20628 Next

MCMCglmm priors and random effects for phylogenetic mixed model

Hi Alberto,

1/ You can fit it at both levels if you like:

us(1+I2.M1.within.species):phylo + us(1+I2.M1.within.species):species

where the first term models between-species phylogentically correlated  
variation in intercepts and slopes  and the second term models  
between-species variation in intercepts and slopes that is not  
phylogenetically correlated. However, you have to be quite careful  
with the van der Pol & Wright method because measurement error in the  
species means (which will be high when n=3) can appear as random  
variation in slopes. The section "Within-Population Slope  
Heterogeneity" in this paper:

http://www.pnas.org/content/107/18/8292.full

discusses the problem, but unfortunately without a good resolution.

2/ I generally use parameter expanded priors of the form:

G2 = list(V = diag(2), nu = 2, alpha.mu = rep(0, 2), alpha.V= diag(500, 2, 2))

note V is an identity matrix rather than I*0.5. However, you should  
check to make sure you don't get big changes when you use other types  
of prior.

Cheers,

Jarrod







Quoting Alberto Gallano <alberto.gc8 at gmail.com> on Sun, 21 Dec 2014  
17:59:09 -0500: