MCMCglmm: tissue type as a random effect when not all species have been measured for all tissuess
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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