[R-sig-phylo] very large sigma squared values

$regimes-as.factor(global) h3-hansen(tree=ot,data=otd[colnames(spdata)[1:4]],regimes=otd[regimes],sqrt.alpha=c(1,0,0,0,1,0,0,1,0,1),sigma=c(1,0,0,0,1,0,0,1,0,1),maxit=100) summary(h1) -Pascal Title -- Pascal Title Graduate Student Burns Lab http://kevinburnslab.com/ Department of Evolutionary

Re: [R-sig-phylo] very large sigma squared values

at 2:00 PM, Pascal Title pascalti...@gmail.comwrote: Hello I am trying to calculate sigma squared values under the Hansen OU model of evolution, so as to examine rate of evolution of certain characters. I have used PCA to reduce the dimensionality of my data and would like to get sigma

[R-sig-phylo] max iteration error in dismo maxent

. Thanks! -Pascal -- Pascal Title Graduate Student Burns Lab http://kevinburnslab.com/ Department of Evolutionary Biology San Diego State University 5500 Campanile Drive San Diego, CA 92182-4614 [[alternative HTML version deleted]] ___ R-sig-phylo

[R-sig-phylo] differing sigma2 results

! -- Pascal Title Graduate Student Burns Lab http://kevinburnslab.com/ Department of Evolutionary Biology San Diego State University 5500 Campanile Drive San Diego, CA 92182-4614 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig

[R-sig-phylo] Freckleton and Harvey randomization test

-- Pascal Title Graduate Student Burns Lab http://kevinburnslab.com/ Department of Evolutionary Biology San Diego State University 5500 Campanile Drive San Diego, CA 92182-4614 [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R

Re: [R-sig-phylo] convergence issues with hansen model

://phytools.blogspot.com On 3/12/2012 2:31 PM, Pascal Title wrote: Hi all I have a dataset of 5 PC axes for a phylogeny with 52 tips and I would like to get the variance-covariance matrix under a global OU model of evolution. I find that OU is strongly favored over BM, based

Re: [R-sig-phylo] convergence issues with hansen model

and sigma matrices are zero will the results be the same. hope that helps, -Carl On Mon, Mar 12, 2012 at 4:56 PM, Pascal Title pascalti...@gmail.com wrote: Thanks for the response, Liam. I just tried out OUwie and it works. However, it appears to only fit 1 variable at a time (I only get one

[R-sig-phylo] nonparametric PGLS

correlation, which is non-parametric. But with phylogenetic generalized least squares, is there any method that is nonparametric? Thanks! -Pascal Title [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https

Re: [R-sig-phylo] obtaining reasonable values from OUCH

wanted: Check NIMBioS' website Calendar: http://www.brianomeara.info/calendars/omeara On Sat, Jun 29, 2013 at 9:11 PM, Pascal Title pti...@umich.edu wrote: Thanks for the reply, Brian. Does OUwie implement the multivariate model? From the documentation, I don't see any mention of applying

[R-sig-phylo] overall p-value from multiple PGLS regression

/advice would be greatly appreciated. Thanks! -Pascal -- Pascal Title PhD candidate, Rabosky Lab http://www-personal.umich.edu/~drabosky/Home.html Dept of Ecology and Evolutionary Biology University of Michigan pti...@umich.edu pascaltitle.weebly.com [[alternative HTML version deleted