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 <vincenzoael...@gmail.com> 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/
