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]] > > > > _______________________________________________ > > 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/ > > > > -- > 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/> -/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/- [[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/