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] }
confint(m)
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,
Wouter
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