Hi all,

I'm successfully using ape::binaryPGLMM to fit logistic regression models while taking phylogeny into account. I can obtain the estimates, standard errors and p-values, as they are directly returned in the model object.

However, can I calculate confidence intervals for the regression coefficients?

One way to get some numbers is to define the vcov and coef functions for binaryPGLMM objects and use the standard confint function:

m <- binaryPGLMM(Y ~ X1, phy=phy, data=sim.dat) # from ?binaryPGLMM
vcov.binaryPGLMM <- function(object, ...) { object$B.cov }
coef.binaryPGLMM <- function(object, ...) { object$B[, 1] }

This gives us CI's, but given the fact that confint.glm uses profiling it seems unlikely to me that these numbers are correct.

If I can't figure it out, I think I will change the phylopath package to use phylolm::phyloglm instead.

Thanks for your help in advance,


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