[R-sig-ME] MCMCglmm binary data

[Walid Mawass]

Hello everyone,

I am running an 'animal model' for a binary trait (0 or 1 value) using 
MCMCglmm. After reading Hadfield's course notes, i fixed the residual 
variance to 1 and used an inverse gamma distribution for the additive 
variance in my prior, and chose the family as "categorical" (link = 
logit)  since there is no order here. h2 would equal Va/Va+1+π²/3, right?

Also, a different study was suggesting to use a χ² distribution (V=1, 
nu=1000, alpha.mu=0, alpha.V=1) as the prior distribution for binary 
traits (and only binary traits) when the sample is big enough (in my 
case N = ~5000). I wanted to know your opinion on this and if I should 
opt for it.

Thank you

-- 
Walid Mawass

M.Sc. of Cellular and Molecular Biology

Population Genetics Laboratory

University of Québec at Trois-Rivières
3351, boul. des Forges, C.P. 500
Trois-Rivières (Québec) G9A 5H7
Telephone: 819-376-5011 poste 3384


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