Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors
There is also an implementation of this method in two functions in ape, see: ?pic.ortho ?varCompPhylip There are examples with simulated data in both help pages. The second function requires PHYLIP (similarly to Rphylip) . Best, Emmanuel Le 04/08/2017 à 14:36, Joe Felsenstein a écrit : There is also my C program Contrast, which implements a method from a 2008 paper I wrote: Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725. This estimates the within-species covariances and the between-species evolutionary variances.It is not an R program but can be accessed through Liam Revell's package Rphylip, if you also have my (non-R) package PHYLIP installed. A pretty good (but not ML) estimate of the within-species phenotypic variance can be gotten by pooling the within-species sampling error. The harder part is using that to correct one's estimate of the covariances of the between-species change, which using ordinary methods will have some within-species variation mixed in. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ 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-project.org/ ___ 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-project.org/
Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors
There is also my C program Contrast, which implements a method from a 2008 paper I wrote: Felsenstein, J. 2008. Comparative methods with sampling error and within-species variation: contrasts revisited and revised. American Naturalist 171: 713-725. This estimates the within-species covariances and the between-species evolutionary variances.It is not an R program but can be accessed through Liam Revell's package Rphylip, if you also have my (non-R) package PHYLIP installed. A pretty good (but not ML) estimate of the within-species phenotypic variance can be gotten by pooling the within-species sampling error. The harder part is using that to correct one's estimate of the covariances of the between-species change, which using ordinary methods will have some within-species variation mixed in. Joe Joe Felsenstein j...@gs.washington.edu Department of Genome Sciences and Department of Biology, University of Washington, Box 355065, Seattle, WA 98195-5065 USA ___ 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-project.org/
Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors
The original paper is here, with Matlab code. Others can tell you where this is in R. Ives, A. R., P. E. Midford, and T. Garland, Jr. 2007. Within-species variation and measurement error in phylogenetic comparative methods. Systematic Biology 56:252–270. Cheers, Ted On Wed, Aug 2, 2017 at 7:50 AM, Vincenzo Ellis wrote: > Dear list users, > > I'm interested in testing for phylogenetic signal in a trait of parasites: > the number of host species a parasite infects. I have a phylogeny for the > parasites and I have tabulated the number of host species each parasite > infects from the literature. However, some parasites are well sampled > (estimates from 20+ studies) and many are poorly sampled (estimates from > one study). So I would like to incorporate sampling error into the > calculation. > > I know that the phylosig function in phytools can do this, but it's not > clear to me how to estimate appropriate standard errors for these data. > > In the literature, people have dealt with this by testing for phylogenetic > signal in the residuals of a regression between number of host species a > parasite infects and the number of studies of the parasite. > > I'm wondering if there is another way to go about it, perhaps by weighting > species by sample size in the calculation of phylogenetic signal. Does > anyone know of a way to do something like this? Or do you think my best bet > is to just work with the residuals from a regression with sample size? > > Thanks for any feedback! > > Vincenzo > > [[alternative HTML version deleted]] > > ___ > 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-ph...@r-project.org/ > [[alternative HTML version deleted]] ___ 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-project.org/
[R-sig-phylo] phylogenetic signal with sample sizes but no standard errors
Dear list users, I'm interested in testing for phylogenetic signal in a trait of parasites: the number of host species a parasite infects. I have a phylogeny for the parasites and I have tabulated the number of host species each parasite infects from the literature. However, some parasites are well sampled (estimates from 20+ studies) and many are poorly sampled (estimates from one study). So I would like to incorporate sampling error into the calculation. I know that the phylosig function in phytools can do this, but it's not clear to me how to estimate appropriate standard errors for these data. In the literature, people have dealt with this by testing for phylogenetic signal in the residuals of a regression between number of host species a parasite infects and the number of studies of the parasite. I'm wondering if there is another way to go about it, perhaps by weighting species by sample size in the calculation of phylogenetic signal. Does anyone know of a way to do something like this? Or do you think my best bet is to just work with the residuals from a regression with sample size? Thanks for any feedback! Vincenzo [[alternative HTML version deleted]] ___ 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-project.org/