[R-sig-phylo] number of fitted parameters in lm and pgls in R

Hi everybody, I was comparing a simple lm model and a pgls model in R and realised that the AICs are not identical. I found out thatfor the pgls there is one fitted parameter (k) less than in the lm. Can anybody explain me the difference and why in a simple lm there is one more fitted parameter

[R-sig-phylo] comp.gee not converging

Hi everyone, I have a problem with the compar.gee function when ruuning a phylogenetic logistic regression with the following error message: Error in gee(binary.y ~ X2.1 + binary.X3, c(1, 1, 1, 1, 1, 1, 1, 1, 1, : Cgee: error: logistic model for probability has fitted value very close to 1.

Re: [R-sig-phylo] WG: Re: Re: MCMCglmm for categorical data with more than 2 levels - prior specification?

distribution of the predictors and the outcomes results in extreme categorical problems. You then might want to follow Gelmans advice on priors for fixed effects. See the function gelman.prior. Cheers, Jarrod Quoting Sereina Graber sereina.gra...@gmx.ch on Fri, 2 Aug 2013 14:48:44 +0200 (CEST

[R-sig-phylo] compar.gee crashing R

Dear r-sig-phylo users, I am running a phylogenetic logistic regression using the function compar.gee() in the package ape. Sometimes, when running such a phylogenetic logistic regression, RStudio crashes. However, it never happened to me when using compar.gee for modelling a normal continuous

[R-sig-phylo] PLogReg.m: error in phylogenetic logistic regression in MATLAB

Dear r-sig-phylo users, Dear Mr. Garland, I am running a phylogenetic logistic regression in MATLAB using the programm PLogReg.m. Now the data set provided in the folder of Ives and Garland works perfectly. However, now I simulated my own data and corresponding tree, this does not work anymore

[R-sig-phylo] Interaction effects in PGLS

Dear all, I have question concerning the interaction effects in PGLS. Using several different data sets and questions, I have tried to inlcude interaction effects in pgls regression models for several times now, however, I have never had a significant interaction effect, even though it is

[R-sig-phylo] convergence in compar.gee (ape)

Dear list members, I have a question concerning the compar.gee function in ape. Often, the models dont converge, and now I would like to safe whether a model converged or not. Is there a way to somehow get the number of iterations reached the max number, or is there something like a convergence

[R-sig-phylo] caper model comparison with different branch length transformations

Dear all, 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

Re: [R-sig-phylo] caper model comparison with different branch length transformations

All the best, Liam Liam J. Revell, Assistant Professor of Biology University of Massachusetts Boston web: http://faculty.umb.edu/liam.revell/ email: liam.rev...@umb.edu blog: http://blog.phytools.org On 8/20/2014 9:32 AM, Sereina Graber wrote: Dear all, I have a question conserning the pgls r

[R-sig-phylo] phylogenetic PCA including categorical variables

Dear all,   I have a mixture of continuous and categorical variables and would like to perform a PCA on those. Does anybody know a way of performing sort of a phylogenetically corrected PCA analysis for continuous and categorical variables? something analogue to the dudi.mix() function in the