Dear all, I have a three-way response variable and a mixture of continuous & categorical explanatory variables that I model in MCMCglmm. These are linguistic data from related languages and I want to correct for genealogy. I have given up on the idea of doing this with a full phylogeny, which is possible in MCMCglmm but I cannot reach convergence. So I have decided to use different grouping variables (representing different hypotheses on how the languages are related). If I had a continuous response variable, I would use random effects, both intercepts & slopes if the model would converge, for the different explanatory variables. If the slopes all point in the same direction for the different groupings, I would feel confident that the effect of that variable is relevant. But with a categorical response variable, random effects seem to work differently. I have read about them on prof. Bolker's github (https://bbolker.github.io/mixedmodels-misc/ecostats_chap.html) where they are also called "conditional modes", but he does not verbally interpret the findings. Hence I have three questions: 1. Can I correct for genealogy using random effects? 2. How to interpret output like on Ben Bolker's page above? For instance, if the CI of a grouping/family does not overlap with 0, does that mean that grouping/family is divergent? If so, in what way is it divergent? (To me, it seems like random effects for multinomial models do not relate to the explanatory variables, which confuses me.) 3. Is my MCMCglmm code below correct for what I need to do (i.e. correct for shared descent of the individual datapoints)?: IJ <- (1/3) * (diag(2) + matrix(1, 2, 2)) prior = list(R = list(V = IJ, fix = 1), ???????????? G=list(G1 = list(V = diag(2), n = 2))) m_full <- MCMCglmm(factor(3way_response) ~ trait:(latitude + longitude + cont1 + cont2 + cat1), ?????????????????? random = ~us(trait):grouping1, ?????????????????? rcov = ~us(trait):units, ?????????????????? prior = prior, ?????????????????? data = x, ?????????????????? family = "categorical", ?????????????????? verbose = FALSE, ?????????????????? nitt=550000000, ?????????????????? thin=1000000, ?????????????????? burnin=50000000, ?????????????????? pl=FALSE, ?????????????????? pr=TRUE, ?????????????????? slice=TRUE) (I add "pr=TRUE" in the MCMCglmm call to get output on random effects in m_full$Sol.) Apologies for the long message, but I would be very, very thankful for any help you can offer. Also pointers to good sources on how to understand this aspect of multinomial regression are very welcome. With best wishes, Annemarie
Multinomial mixed model in MCMCglmm, correcting for genealogy with random effects?
1 message · Annemarie Verkerk