Varying slope with phylogenetic structure

Interfaces brms
1

Greetings,

I just looked at the vignette “Estimating Phylogenetic Multilevel Models with brms”. Really cool stuff.

Towards the end it’s mentioned that it would be possible to estimate a varying intercept and a varying slope for these models. Does anybody has an example on how to write such models?

Thanks a lot in advance!

jm

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

  • Operating System: macOS high sierra
  • brms Version: 2.5
2

If x is your variable for which you want to model a varying slope, replace (1 | phylo) with (1 + x | phylo).

1 Like
3

Ah! thanks a lot!
It was indeed quite slow as you warned.

4

I was trying to understand how these models work and I am puzzled that the Cholesky factor obtained via make_standata is different from what I get using chol(as.matrix(A)).

That is, using the example from the vignette, if I do

d <- make_standata(
phen ~ cofactor + (1|phylo), data = data_simple,
family = gaussian(), cov_ranef = list(phylo = A))

then d$Lcov_1 has different values than chol(as.matrix(A))

Is there something I’m missing?

5

brms sorts the rows and columns according to the levels of the grouping factor and then transposes the cholesky factor as R and Stan have different definitions of cholesky factors. See brms:::data_gr for the code.

6

great, thank you!