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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[R-sig-phylo] Phylogenetic quantile regression

[briansedio]

Hi Agus,

Did you ever figure out a way to do phylogenetic quantile regression?  I have 
searched and searched, and cannot find any tool or even literature on the 
topic.  I would ideally like to make it work in R.

Thanks for any update or information.

Brian Sedio
se...@si.edu
brianse...@gmail.com
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[R-sig-phylo] Frequency histograms in APE

[LUCAS A. (599841)]

Hi

(This is my first query to a group like this, so my apologies if the subject is 
a little basic)

I have a data set of insect COI barcodes, that i've aligned and edited in MEGA. 
 I've also generated the K2P distances in MEGA, producing a very large 
spreadsheet of intra and inter specific distances.

I'd like to generate a frequency distribution histogram of conspecific and 
heterospecific distances for selected sub groups of my data.  I understand this 
can be done in the APE package, but am struggling to understand the method from 
the documentation.  Can anyone advise?

Andrew Lucas


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

[Vincenzo Ellis]

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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