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

Ben Bolker bbolker @ending from gm@il@com
Wed Jun 6 17:46:42 CEST 2018

  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

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]]
> _______________________________________________
> R-sig-mixed-models using r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-sig-mixed-models

More information about the R-sig-mixed-models mailing list