Dear Liam, dear Alejandro
Thank you so much for your answers, that was very helpful!
Just (hopefully) one last question: As branch lengths are not known for the
tree I am using, I calculated them as suggested by Grafen (branch lengths being
the number of descending taxa minus 1). So, I would
Hi Yanthe,
Just to second what Graham says - it sounds like a crunch problem. The crunch()
and brunch() functions in caper do both take the raw data and then calculate
contrasts in all the variables in the model simultaneously. The pic() function
in the ape package does the same for one
Hi Karin,
I would suggest setting all branch lengths to a unit value and then using
corPagel() in ape as the model of trait evolution. Using corPagel the value of
lambda is estimated simultaneously with model fit, lambda is an estimate of the
phylogenetic signal in your residuals and basically
