[R-sig-ME] Ordinal categorical variable as a random effect in MCMCglmm

[Jarrod Hadfield]

Dear Manabu,

Could you explain what Quality is? If it is ordered it is hard to see  
why you would be fitting it as random effect? Is this really your  
response variable?

Cheers,

Jarrod



Quoting Manabu Sakamoto <manabu.sakamoto at gmail.com> on Wed, 29 Oct  
2014 11:16:48 +0000:

> Dear list,
>
> I'm using MCMCglmm with some random effects, including a phylogeny and a
> categorical variable, scored along an ordinal scale, e.g., 1 < 2 < 3 <...
>
> If my phylogenetic tip names are stored as a character string Taxon (and
> there is an associated inverse A object), and my quality codes are stored
> as an ordered factor variable Quality, then my questions are:
>
> 1) Can I specify the random effect formula simply as: random= ~ Taxon +
> Quality --- i.e., without functions like us() or idh() around Quality?
> 2) What sort of prior should I assign for Quality? --- For the moment I am
> using:
>
> list(V=1, nu=1, alpha.mu = 0, alpha.V = 25^2)
>
>
> I'd appreciate any advise.
>
> Kind regards.
> Manabu
> --
> Manabu Sakamoto, PhD
> manabu.sakamoto at gmail.com
>
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>
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