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.
On Wed, Aug 2, 2017 at 7:50 AM, Vincenzo Ellis <vincenzoael...@gmail.com>
> 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
> 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!
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