[R-sig-ME] Inflated heritability estimate for animal model with binary response using MCMCglmm

Kanix Wang kanixwang at uchicago.edu
Wed Aug 26 22:11:17 CEST 2015

Dear list,

I'm using MCMglmm to estimate heritability for binary traits with the model
below. I have seen a inflated heritbility estimate when I use sex and age
as fixed effects vs only using intercept. Both estimates passed the
convergence test and half-width test.
Can anyone help me identify the likely causes of this inflation? Is the
model mis-specified? Also, I'm wondering if using age as a random effect
make any sense.

priorA <- list(R = list(V = 1, fix = 1), G = list(G1 =list(V = 1, nu =
1000, alpha.mu = 0, alpha.V = 1), G2 =list(V = 1, n = 1)))

modelbin <- MCMCglmm(pheno ~ sex + age, random = ~animal +fam , family =
"ordinal", pedigree = pedigree, prior = priorA, data = databin, nitt =
nitt, burnin = burnin, thin = 500, slice=TRUE, pl=TRUE)

Sex and age are factor variables. The fam variable is for the common
environment effects in the descendants. All parents have NA for fam.

Any help would be greatly appreciated.

Kanix Wang

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