[R-sig-ME] Heritability of ordinal data in MCMCglmm and estimatingfixed effects

[David Duffy]

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 ;)

-- 
| David Duffy (MBBS PhD)                                         ,-_|\
| email: davidD at qimr.edu.au  ph: INT+61+7+3362-0217 fax: -0101  /     *
| Epidemiology Unit, Queensland Institute of Medical Research   \_,-._/
| 300 Herston Rd, Brisbane, Queensland 4029, Australia  GPG 4D0B994A v