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

[Nathanael Walker-Hale]

Thank you! I will.

On Wed, Jun 6, 2018 at 1:09 PM, Ben Bolker <bbolker using gmail.com> wrote:

>
>   My guess is that it would be no problem to treat tissue as fixed and
> species as random (and phylogenetically correlated) (and the
> species:tissue interaction as random, so that you can model variation
> within species -- **or** simply pool the multiple measurements from each
> species/tissue combination, see Murtaugh "Simplicity and complexity in
> ecological data analysis").
>   Why not try it (maybe with a subset of your data) and see what happens?
>
> On 2018-06-06 01:07 PM, Nathanael Walker-Hale wrote:
> > 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,
> >
> > Nathanael
> >
> > On Wed, Jun 6, 2018 at 11:46 AM, Ben Bolker <bbolker using gmail.com
> > <mailto: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
> >     >
> >     >       [[alternative HTML version deleted]]
> >     >
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