Hi everyone,
I am very new to the multivariate analysis with phylogenetic restraints and have searched the internet for a couple of days now, but I have not been able to find a way to include multiple phylogenies into functions in e.g. ape or caper.
Does anyone know if this is possible or if maybe there are other R packages with this capability?
My data:
Phenotypic traits of different bacterial isolates from different subspecies (both continous (e.g. growth rate), binary (e.g. presence/absence of a phenotype), and categorial (e.g. presence of one of four different gene clusters) data).
Phylogenetic trees of the different subspecies.
The subspecies have been subjected to the same treatment, and I am only interested in what happens after this treatment, which is why I want to include only the mutations that arose after this point. - So as to avoid too much noise from the mutations which separate the subspecies. Which is why I want to include multiple phylogenies to the analysis, instead of one big tree.
I'm not sure I follow, can you elaborate a bit more?
Check if a Random effects model makes sense, but this is more of a general direction irrespective of phylogenetic comparative methods...
https://en.wikipedia.org/wiki/Random_effects_model
Of cause.
The thing is I have bacterial isolates with different phenotypes, that I wish to correlate with mutations. But because I don't want to overestimate the mutations if they happen early on I need to take the phylogeny into account.
That is, if the mutation(s) causing the phenotypic change happens early they will be present in most of the isolates, and I want to take this into account, so that this mutation is not overrepresented compared to another mutation which might happen later and thus not be present in a lot of the isolates.
I don't know if this makes sense. But I think I will look closer at the reference (Garamszegi and Mundry 2014) recomended by Alejandro Gonzalez-Voyer, and hopefulley get a better understanding of what I need to do, and maybe return with at better formulated question.
Thank you
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