Hi,
Thanks guys for the answers.
1) Yes, my tree isn't ultrametric, there are fossils in it. But I already
weigthed the tips (Liam, I saw your response to Dave Bapst long time ago). Do I
have to do something similar in CAPER ?2) I am comparing t tests, optimization
is ML, CAPER lambda bounds
Dear Jeremie.
I agree with Julien. If your tree is non-ultrametric or if you use
different fitting methods ("REML" vs. "ML") then you could obtain
different results. The other circumstance in which you might have a
different result is if your estimated value of lambda is outside the
default
Hello J�r�mie,
Hard to say without a working example, but here are some hints:
* Check if you�re using the same function to optimize (e.g. ML vs REML)
* Are you comparing the same tests? (t or F tests, type of sums of squares)
* Are you using non-ultrametric trees? In �nlme� for
