On 22 Jul 2024, at 17.15, Martina Carrete <mcarrete at upo.es> wrote:
Hi all,
We are doing a paper in which we are exploring the variables that can
explain the probability of occurrence of a particular behaviour
(binomial model) between plants and birds (the independent variables are
two continuous variables). Given that the literature gives an important
weight to the phylogeny of both plants and birds and that the
independent variables also have a phylogenetic signal, it was clear from
the beginning that we had to include the phylogenies of both groups.
This is only possible (to our knowledge) with MCMCglmm and we have done
so. Bayesian statistics, frankly, escapes us a lot. The priors and such
things are black boxes that we can't quite understand and, in addition,
we are missing things that we are used to when assessing the results of
a model: the explained variance (R2 or deviance), the posterior fit, the
possibility of seeing if the models are inflated to 0, etc. The glmmTMBs
are therefore a fantastic tool that we use all the time. However, in
this case, we tried to do them including two phylogenies and there was
no way. We don't know if it's something that hasn't been implemented or
if we didn't know how to do it. We've looked in forums and we haven't
been able to find anything either.
Below is the script we used, but considering only one phylogeny.
phyloZplant <- phylo.to.Z(pruned.tree.P)
q3_fylo_P <- datG %>% mutate(sp_plant = factor(sp_plant, levels =
phyloZplant at Dimnames[[1]]))
phyloZbird <- phylo.to.Z(pruned.treeB)
q3_fylo_B <- datG %>% mutate(sp_bird = factor(sp_bird, levels =
phyloZbird at Dimnames[[1]]))
glmmTMB_fit_gauss1 <- phylo_glmmTMB(binomial_variable~ continuous1 +
continuous2 + (1|sp_bird)
, data=q3_fylo_B
, phyloZ = phyloZbird
, phylonm = "sp_bird"
, doFit = TRUE
, REML = FALSE
, ziformula=~0,
, family = "binomial"
)
We are interested in a model where we can include the phylogeny of birds
but also the phylogeny of plants.
Any suggestions would be very welcome,
Thank you very much!
Un abrazo
Martina
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