Thanks Dave,
I'll try Blomberg's K with small simulated fully-bifurcating trees of
simple shape (e.g. fully pectinate), where I can easily paint the tips
myself in what I believe to be a "maximally stratified manner" e.g.
010101010 to see if Blomberg's K does actually reach minimum (i.e. 0.00000
?) for such a distribution. If it does, great! This is the measure I need.
I still wonder though, for a complex tree structure in terms of
balance/shape somewhere intermediate between fully balanced and fully
pectinate; how does one arrive empirically at _the_ most optimal
stratified/even sampling ('painting') of tips if say only 25% of tips
are/can be 'painted'. I guess a lot depends on how one defines what 'even
sampling' on a phylogeny actually is, does it include branch lengths et
cetera...
I'll give it a try anyway,
Thanks again,
Ross
On 14 March 2017 at 14:33, David Bapst <dwba...@gmail.com> wrote:
> Ross,
>
> An interesting question. I understand it as that you want to test if
> the trait is overdispersed relative to phylogeny, which still makes me
> think that measures of 'phylogenetic signal' might be still be useful,
> even though the typical interpretation is 'signal' as 'heritability'.
> I would try some toy examples with smallish trees and artificial data
> and play with different signal measures; particularly your idea
> regarding that the variance is high at the level of closest
> relatedness suggests that you perhaps should investigate Blomberg's K
> as a measure, rather than Pagel's lambda:
>
> Blomberg, S. P., T. Garland, and A. R. Ives. 2003. Testing for
> phylogenetic signal in comparative data: behavioral traits are more
> labile. Evolution 57.
>
> However, your soft polytomies are worrisome; I suggest using the MPT
> or posterior tree sample, if such exists, or considering resolving
> those polytomies somehow.
>
> Cheers,
> -Dave
>
> On Tue, Mar 14, 2017 at 5:45 AM, Ross Mounce <ross.mou...@gmail.com>
> wrote:
> > Hi all,
> >
> > I'm interested in the distribution of a non-heritable binary
> > trait/observation across a large tree 1000+ tip tree. The tree is
> > non-distinct in shape and balance, it is neither fully pectinate nor
> fully
> > balanced. It has many soft polytomies too.
> >
> > I believe the distribution of this trait to be significantly stratified
> > such that just for the sake of explanation, every other tip is "present"
> > for the trait. So essentially I'm interested in testing the evenness of
> > distribution of "present" tips across the tree.
> >
> > In this instance it doesn't seem to me that I should be testing for
> > "phylogenetic signal" or using models that do that, nor am I testing the
> > randomicity of distribution of the trait.
> > Specifically, I want to test if the observed distribution is
> significantly
> > close to "perfect" stratification for the given number of "presences"
> > (which is ~33% of the tips of the tree), on the given fixed tree shape.
> >
> > TL;DR
> >
> > How can I meaningfully test the evenness of the distribution of a binary
> > trait across a tree, with R?
> >
> >
> > Any ideas?
> >
> > Thanks,
> >
> > Ross
> >
> >
> > --
> > --
> > -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> -/-/-/-/-/-/-/-
> > Ross Mounce, PhD
> > Software Sustainability Institute Fellow
> > Dept. of Plant Sciences, University of Cambridge
> > www.rossmounce.co.uk <http://rossmounce.co.uk/>
> > -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> -/-/-/-/-/-/-/-
> >
> > [[alternative HTML version deleted]]
> >
> > _______________________________________________
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>
>
>
> --
> David W. Bapst, PhD
> Adjunct Asst. Professor, Geology and Geol. Eng.
> South Dakota School of Mines and Technology
> 501 E. St. Joseph
> Rapid City, SD 57701
>
> http://webpages.sdsmt.edu/~dbapst/
> http://cran.r-project.org/web/packages/paleotree/index.html
>
--
--
-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-
Ross Mounce, PhD
Software Sustainability Institute Fellow 2016
Dept. of Plant Sciences, University of Cambridge
www.rossmounce.co.uk <http://rossmounce.co.uk/>
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