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 instance, it�s a
correlation rather than a covariance structure that is optimized while other
approaches are dealing with the covariances. This may produce discrepancies on
non-ultrametric trees.
Cheers,
Julien
________________________________
De : R-sig-phylo <r-sig-phylo-boun...@r-project.org> de la part de J�r�mie
Bardin <jeremiebar...@yahoo.fr>
Envoy� : vendredi 17 janvier 2020 11:22
� : r-sig-phylo@r-project.org <r-sig-phylo@r-project.org>
Objet : [R-sig-phylo] pgls_different_pacakges_different_results
Hello everyone,
I did pgls on real data and I tried the 3 common solutions : ape+nlme, caper
and phytools. I used BM as model and optimized lambda. I was surprized to get
different results especially on intercepts. Lambdas were different but close ,
and results were still not the same by fixing the same lambda value.
Then, I tried few simulations by varying the correlation strength between the
two variables and the source of the correlation (independent but both simulated
on the tree, linearly dependent, these two cases with varying proportion...).
The fewer the signal, the bigger the differences of the optimized coefficients.
However, sometimes pvalues of coefficients are very small with one package and
greater than .5 with another one.
Have you ever seen such results ? I precise that I am using both three
solutions in their most simple form as can be founded on Liam's blog or
classical tutos.
Cheers, J�r�mie.
----
J�r�mie Bardin, Dr.
CR2P - Centre de Recherche en Pal�ontologie - ParisSorbonne Universit� - MNHN
- CNRS
Site Jussieu, Tour 46-56, 5�et.
4 place Jussieu, 75252 Paris Cedex 05
tel. +331.44.27.51.77.
jeremie.bar...@upmc.fr / jbar...@mnhn.fr / jeremiebar...@yahoo.fr
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