[R-sig-ME] MCMCglmm: tissue type as a random effect when not all species have been measured for all tissuess

[Ben Bolker]

  In principle this kind of missing data is no problem, but it seems odd
to treat tissue type as random if (as I understand it) you only have two
types of tissue (root, leaf) ... Perhaps you have more? Even so (say you
had a few more), this would present both technical issues [you'd
probably need a moderately strongly informative prior on the
among-tissue variance], and it seems odd to me to treat tissues as
exchangeable.

On 2018-06-06 11:29 AM, Nathanael Walker-Hale wrote:
> Hi all,
> 
> I am planning to use MCMCglmm to do a phylogenetic comparative analysis. I
> have multiple metabolite measurements on multiple tissue types per species
> (e.g. leaf, three measurements, root, three measurements, per species). I
> am interested in analyzing how levels of metabolite are predicted by the
> presence or absence of a gene. Ideally, I would like to model both
> between-species relationships (from a phylogeny) and tissue type as random
> effects. However, not all species have measurements on all tissue types.
> 
> Will this be a problem for the analysis? Is it possible to run the model in
> the presence of missing data like this? There is not a particularly heavy
> bias to the pattern of missing tissue across the phylogeny, but some tissue
> types have been measured much less than others (e.g. far fewer species have
> floral measurements).
> 
> Best wishes,
> 
> Nathanael
> 
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