----- Forwarded message from Dean Adams <[email protected]> ----- Date: Wed, 17 Apr 2013 10:05:56 -0400 From: Dean Adams <[email protected]> Reply-To: Dean Adams <[email protected]> Subject: Re: calculating phylogenetic signal in EFA data To: [email protected]
Ryan, Conceptually, the K&G method should be applicable to EFA coefficients, or any multi-dimensional dataset for that matter. The procedure can be slow because to implement it one must first estimate the ancestral states, which can take some time in R. This must be done for the observed data, and for each iteration of the permutation test, where species data are shuffled on the tips of the phylogeny, and the process is repeated. Dean -- Dr. Dean C. Adams Professor Department of Ecology, Evolution, and Organismal Biology Department of Statistics Iowa State University Ames, Iowa 50011 www.public.iastate.edu/~dcadams/ phone: 515-294-3834 On 4/16/2013 9:11 PM, [email protected] wrote: > ----- Forwarded message from Ryan Felice <[email protected]> ----- > > Date: Mon, 15 Apr 2013 10:04:53 -0400 > From: Ryan Felice <[email protected]> > Reply-To: Ryan Felice <[email protected]> > Subject: calculating phylogenetic signal in EFA data > To: [email protected] > > Hello- > > I am using EFA to quantify shape, and I want to measure phylogenetic > signal in this data. I think the best way to do this is using the > permutation test described by Klingenberg, and Gidaszewski (2010) and > implemented as the "physignal" function in the {geomorph} package in > R. By tweaking the code for "physignal" a little bit, I have managed > to get the function to run with my EFA data and return a result, > although it goes quite slowly. Is there any reason that this method, > which was developed for landmark data, should not be used with other > types of multidimensional data? > > Cheers, > > Ryan Felice > PhD Candidate > Ohio University Department of Biological Sciences > 107 Irvine Hall > Athens, OH 45701 > www.rnfelice.com > [email protected] > (201)981-8642 > > ----- End forwarded message ----- > ----- End forwarded message -----
