Phylogenetic model with repeated measurements without using species mean


#1

I am working on a phylogenetic regression model in brms with multiple measurements per species. I have read over the excellent brms_phylogenetics vignette several times, but still have a question about repeated measurements. I will use the sample data variables and scripts from the vignette to ask my question.

Here is the head of the dataset:

       phen  cofactor species phylo spec_mean_cf
1 107.41919 11.223724    sp_1  sp_1    10.309588
2 109.16403  9.805934    sp_1  sp_1    10.309588
3  91.88672 10.308423    sp_1  sp_1    10.309588
4 121.54341  8.355349    sp_1  sp_1    10.309588
5 105.31638 11.854510    sp_1  sp_1    10.309588
6  64.99859  4.314015    sp_2  sp_2     3.673914

spec_mean_cf is the mean value of the cofactor for the species.
There are several examples in the vignette of modeling phen ~ spec_mean_cf, including a way to incorporate the variability of the cofactor for each species by using the distance from the mean of each individual (a separate variable called within_spec_cf in the vignette).

phen ~ spec_mean_cf + (1 | phylo) + (1 | species) + within_spec_cf 

However, the mean of the species is always used as a predictor variable.

In brms, is there a way to use the individual values, and not the mean, as the predictor while still accounting for species measurement variability? In MCMCglmm it would be written as:

MCMCglmm( fixed = phen ~ cofactor,  random = ~ species + phylo)

I have tried a few variations with my own data, such as:

phen ~ cofactor + (1 | phylo) +  within_spec_cf 

and

phen ~ cofactor + (1 | phylo) +  (1 | within_spec_cf )

but I don’t think this is correct, as I get an estimate of zero for cofactor for each model (not possible in this case)

I apologize if this is very naive. I am trying to learn-by-doing.

Thanks!

Please also provide the following information in addition to your question:

  • Operating System: OSX 10.11.6
  • brms Version: 2.3.0

#2

Go for phen ~ cofactor + (1 | phylo) + (1 | species)

In the vignette I just split up cofactor into spec_mean_cf and within_spec_cf following the book from which I have the data.


#3

Thanks Paul!

I am still getting strange results, but that is an issue for another post.