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

Nathanael Walker-Hale n@th@n@el@w@lker@h@le @ending from gm@il@com
Wed Jun 6 19:07:19 CEST 2018

Hi Ben,

Thanks very much for your response. There are more tissues (six in all), I
just chose those as an example of the data format. I was under the
impression that the missing data would be a problem if attempting to treat
tissue type as fixed, but is this not the case? I have seen in other
threads the ways in which missing responses are imputed in MCMCglmm, and I
could perhaps merge tissue types into two or three classes (say root, shoot
and flower) and model them as fixed, if the missing data does not create
problems for the analysis.

Thanks again for your help,


On Wed, Jun 6, 2018 at 11:46 AM, Ben Bolker <bbolker using gmail.com> wrote:

>   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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> >
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