[R-sig-ME] Priors for MCMCglmm with haplodiploid relatedness matrix

Michael Sheehan msheehan at cornell.edu
Tue Oct 4 18:00:44 CEST 2016

Dear all,

I am attempting to examine the heritability of a number of traits in a haplodiplod species using MCMCglmm. This has presented a number of challenges since the standard relatedness matrix calculated from a pedigree as part of the program assumes diploid relatedness, which underestimates relatedness among sisters. I have been able to make a haplodiploid appropriate relatedness matrix but when I run the following:

model1=MCMCglmm(trait~1, random=~animal, ginverse=list(animal=haplo.mat.inverse), data=data, family="ordinal", prior=prior1, nitt=105000, thin=100, burnin=5000, verbose=T)

I immediately get the following error:

"G-structure 1 is ill-conditioned (possibly because of ginverse): use proper priors if you haven't, or rescale data if you have"

If I run the same code with a diploid relatedness matrix (calling it through pedigree or ginverse) the program runs without error. I have tried a wide range of priors and even run without priors and get the same error for the haplodiploid matrix while the diploid matrix runs.

I am curious if others have received a similar message and how it was dealt with.

Thanks in advance for any help!

Mike Sheehan

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