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

[Nathanael Walker-Hale]

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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