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/
