I have a question conserning the pgls regression in package caper. The function allows to estimate or fix three branch length transformations. I wanna figure out which transformation gives me the best model fit by comparing for example a model with lambda estimated (lambda="ML") to a model where I fix lambda at 0.5 (lambda=0.5). However, if I use anova(model1, model2) to compare the two models I get the error message that the two models are run with different branch length transformations, which makes sense. But is there any other possbility to compare models with different branch length transformations? How do I know which model is better?
For any help I am very grateful.
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