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 Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
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