Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

[Emmanuel Paradis]

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

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Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

[Joe Felsenstein]

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

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Re: [R-sig-phylo] phylogenetic signal with sample sizes but no standard errors

[Theodore Garland]

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
>
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>
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