Heritability of ordinal data in MCMCglmm and estimatingfixed effects
On Tue, 30 Oct 2012, Samantha Patrick wrote:
Hi I am estimating the heritability of an ordinal trait using MCMCglmm and have come across two problems: one regarding heritability and one specific to ordinal data sets. _My data_ Trait1 = ordinal score from 0 - 4 Colony = factor with 2 options ID = repeated measures per individual (818 individuals) So the heritability: /posterior.heritability1.1 <- model2.1$VCV[, "animal"]/(model2.1$VCV[, "animal"]+ model2.1$VCV[, "ID"] + model2.1$VCV[, "units"]+1)/ /posterior.mode(posterior.heritability1.1)/ /h^2 = 0.21 (0.05- 0.45)/
Why are there repeated measures? Is the between-occasion variation of interest, or a nuisance? That is, is animal/(animal+units) a better measure of h2?
/model2.2<-MCMCglmm(Trait1~ Colony , random =~animal + BYEAR + MOTHER + ID, pedigree = Ped3, data = Data, prior = prior2.1, family='ordinal',burnin = 20000, nitt = 500000, thin = 200, pr=TRUE)/
doesn't work. How many levels of BYEAR, how many obs per year, do you want a random regression on BYEAR (ie do you expect a linear relationship?)
My second question is specific to ordinal analyses I need to extract one score per individual and I wondered if anyone knows if there is any methods for doing this? I can fit ID as a random effect but I am not sure this changes anything, and is associated with the curse of BLUPS.
BLUPs are what you want, curse them ;)
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