The logistic regression in Ives & Garland is implemented in the phyloglm function, from the R package “phylolm". Cécile
> On Jan 26, 2016, at 10:43 AM, Theodore Garland Jr <theodore.garl...@ucr.edu> > wrote: > > You might also want to read about the background, starting with these two > papers, both available at my website: > > Ives, A. R., and T. Garland, Jr. 2010. Phylogenetic logistic regression for > binary dependent variables. Systematic Biology 59:9-26. > > Ives, A. R., and T. Garland, Jr. 2014. Phylogenetic regression for binary > dependent variables. Pages 231-261 in Modern Phylogenetic Comparative > Methods and Their Application in Evolutionary Biology: Concepts and Practice, > L. Z. Garamszegi, ed. Springer: Heidelberg. > > Cheers, > Ted > > Theodore Garland, Jr., Professor > Department of Biology > University of California, Riverside > Riverside, CA 92521 > Office Phone: (951) 827-3524 > Facsimile: (951) 827-4286 (not confidential) > Email: tgarl...@ucr.edu > http://www.biology.ucr.edu/people/faculty/Garland.html > http://scholar.google.com/citations?hl=en&user=iSSbrhwAAAAJ > > Director, UCR Institute for the Development of Educational Applications > > Editor in Chief, Physiological and Biochemical Zoology > > Fail Lab: Episode One > http://testtube.com/faillab/zoochosis-episode-one-evolution > http://www.youtube.com/watch?v=c0msBWyTzU0 > > ________________________________________ > From: R-sig-phylo [r-sig-phylo-boun...@r-project.org] on behalf of Florian > Boucher [floflobouc...@gmail.com] > Sent: Tuesday, January 26, 2016 8:34 AM > To: Knappová Jana > Cc: r-sig-phylo@r-project.org > Subject: Re: [R-sig-phylo] multiple regression with binomial distribution > > Hi Jana, > > If your data are proportions, you might want to model their logit, ie > log(X/(1-X)), rather than their raw value. You can then use PGLS in the > same manner as you did. An ML value of 0 for lambda indicates that you are > actually fitting a non-phylogenetic model, but it is safer to allow for > lambda to vary in case there would be signal in the residuals of the > regression. > If your data are 0/1, then you should rather use phylogenetic logistic > regression. This is implemented for example in the 'phyloglm' function in > the R package 'phylolm'. > > Cheers, > Florian > > 2016-01-26 16:16 GMT+01:00 Knappová Jana <jana.knapp...@ibot.cas.cz>: > >> Hi everyone, >> >> I am not very familiar with phylogenetics, but i would like to incorporate >> it somehow into my work and i appreciate any suggestions. >> >> Is it possible to use any kind of phylogenetically informed analysis in >> case of multiple regression (one response ~ multiple predictors) in case I >> assume binomial distribution of response variable? I try to explain species >> occurrence (proportional data) by a couple of species traits. >> >> I tried pgls function from "caper" R package, but I am not sure about it. >> Generally, it seems that there is not strong signal in my data, when I used >> lambda="ML" than lambda was set to zero. >> >> Thanks >> >> Jana Knappová >> Botanický ústav AV ČR, v. v. i. | Institute of Botany of the CAS >> Zámek 1, 252 43 Průhonice | Zamek 1, CZ-25243 Pruhonice >> Česká republika | Czech Republic >> jana.knapp...@ibot.cas.cz >> www.ibot.cas.cz >> www.pruhonickypark.cz >> Telefon: 271015401, 737375227 | Phone: +420-271015401, 737375227 >> Fax: 271015105 | Fax: +420-271015105 >> _______________________________________________ >> 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/ > > > > > -- > Florian Boucher > Postdoctoral researcher, Institute of Systematic Botany, Zürich _______________________________________________ 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/
