Re: [R-sig-phylo] Using OU model in PGLS

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 11-01-05 12:50 PM, Alanna Maltby wrote: Hi all I'm trying to run a PGLS using the function 'gls' in 'nlme', which works when I use corBrownian as the correlation structure, but not when I use corMartins. Typing: oumodel-corMartins(1, tree)

Re: [R-sig-phylo] GLM, GLMM, CAIC, mcmcGLMM - AIC model selection for phylogentic data

-- perhaps I'm missing something. Given that you have reasonably strong effects of your predictors, reasonably minor differences in the way that you account for correlation won't change the qualitative conclusions. Ben Bolker I was wondering why this maybe? Does anybody know of similar studies

Re: [R-sig-phylo] GLM, GLMM, CAIC, mcmcGLMM - AIC model selection for phylogentic data

not in this case) have a big effect on the conclusions Ben Bolker Chris I think your comparison is really worthwhile, but I don't see why this is surprising at all -- perhaps I'm missing something. Given that you have reasonably strong effects of your predictors, reasonably minor

Re: [R-sig-phylo] GLM, GLMM, CAIC, mcmcGLMM - AIC model selection for phylogentic data

or heuristic arguments of when they will differ. Simulations guided by this analysis will then show the magnitude of the difference across a range of situations. cheers Ben Bolker The fact that *for this analysis* all the methods used give the same answer doesn't invalidate the general

Re: [R-sig-phylo] NEVERMIND -read.tree and read.nexus error

On the other hand, if anyone has any ideas about a paranoid and verbose Newick file-checker that gives verbose output about what precisely might be wrong/non-conforming in a Newick file (lint for Newick for the old-fashioned programmers) to help track this sort of thing down, that would be

Re: [R-sig-phylo] ape processing time

On 11-06-13 12:02 PM, alfredo tello wrote: Hi Folks, Can anyone tell me how to roughly calculate the processing time required to compute a phylogenetic matrix (K80) with ape given a certain hardware? I just want to have a rough idea before pressing Go Try running a few tiny- to

Re: [R-sig-phylo] 2 root edges in phylocom tree, but suggested fix in ape FAQ doesn't help

that phylocom is using. Someone else will probably respond more helpfully ... Ben Bolker ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo

Re: [R-sig-phylo] LL ratio test

On 12-06-17 07:35 AM, Joe Felsenstein wrote: Ben Bolker wrote: I'd like to chime in here ... again ready to be corrected by others. The description above doesn't match my understanding of AIC at all (although again I will be perfectly happy, and in fact really interested, if you can

Re: [R-sig-phylo] problem installing phylobase package

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13-02-07 08:42 AM, Marc Octavo wrote: Hi François, I have upgraded R from 2.15.0 to 2.15.2 and the problem is solved. Thanks Good to know. My best guess is that there is an Rcpp version mismatch; the current version of Rcpp depends on

Re: [R-sig-phylo] Question about model selection using compar.gee

to ... Let's see if anyone else on the list has suggestions. good luck, Ben Bolker ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r

Re: [R-sig-phylo] read.nexus.data parser

On 13-04-05 01:29 PM, Jessica Sabo wrote: Hi All, I am wondering if there is anyway to increase the speed of the read.nexus.data parser. Or if there is an alternative that is a faster nexus file data parser. THanks, Jess I don't know if it's faster or not, but there is ?readNexus in

Re: [R-sig-phylo] phylobase::descendants issue

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 Thanks for the heads-up. I or one of the other phylobase developers will try to take a look ... cheers Ben Bolker On 13-04-26 06:50 PM, Nick Matzke wrote: Hi all, Not sure if this is a bug, but I noticed weird behavior when loading

Re: [R-sig-phylo] Extracting all interaction estimates from compar.gee output

On 13-12-02 07:00 AM, Nina Hobbhahn wrote: Dear fellow list users, how do I extract estimates for all possible combinations of effects in significant interactions from compar.gee? To illustrate: I'm interested in flower-head size in males and females of wind- or insect-pollinated

Re: [R-sig-phylo] fitting cuadratic model using gnls

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 13-12-10 12:57 PM, Theodore Garland Jr wrote: I don't know, but one thing to watch out for is a high correlation between X and Xsquared. That gives multicollinearity and can lead to numerical problems. One thing that is commonly done is: 1.

[R-sig-phylo] dangerous tree

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 I came across this in one of my example files. Just thought I'd report it: library(ape) sessionInfo() ## R Under development (unstable) (2015-02-11 r67792) ## Platform: i686-pc-linux-gnu (32-bit) ## Running under: Ubuntu precise (12.04.5 LTS) ##

Re: [R-sig-phylo] dangerous tree

9:02 PM, Ben Bolker wrote: I came across this in one of my example files. Just thought I'd report it: library(ape) sessionInfo() ## R Under development (unstable) (2015-02-11 r67792) ## Platform: i686-pc-linux-gnu (32-bit) ## Running under: Ubuntu precise (12.04.5 LTS) ## ... ## other

Re: [R-sig-phylo] phytools - evaluating significance of pgls.Ives

-BEGIN PGP SIGNED MESSAGE- Hash: SHA1 On 15-03-01 11:40 PM, Simon Blomberg wrote: Am I missing something? The OP only has 8 species in the data set. I wouldn't put much store in fancy PCM modelling based on such a small data set. And 3 individuals per species is not enough for a good