The Blomberg et al (2003) randomization test is implemented in the picante package, with the function phylosignal(). It may be implemented elsewhere as well.
Best, Gene -- Gene Hunt Curator, Department of Paleobiology National Museum of Natural History Smithsonian Institution [NHB, MRC 121] P.O. Box 37012 Washington DC 20013-7012 Phone: 202-633-1331 Fax: 202-786-2832 http://paleobiology.si.edu/staff/individuals/hunt.cfm On 4/25/12 11:29 AM, "Theodore Garland Jr" <[email protected]> wrote: >I would suggest the randomization test in Blomberg et al. (2003). This >will give a valid significance test of the null hypothesis of no >phylogenetic signal. By itself, it does not give a measure of the >strength (or amount) of phylogenetic signal. Not sure if it is implented >in r. If not, I can send our Matlab code. > >Cheers, >Ted > >Theodore Garland, Jr. >Professor >Department of Biology >University of California, Riverside >Riverside, CA 92521 >Office Phone: (951) 827-3524 >Home Phone: (951) 328-0820 >Facsimile: (951) 827-4286 = Dept. office (not confidential) >Email: [email protected] >http://www.biology.ucr.edu/people/faculty/Garland.html > >Experimental Evolution: Concepts, Methods, and Applications of Selection >Experiments. 2009. >Edited by Theodore Garland, Jr. and Michael R. Rose >http://www.ucpress.edu/book.php?isbn=9780520261808 >(PDFs of chapters are available from me or from the individual authors) > >________________________________________ >From: [email protected] >[[email protected]] on behalf of Nina Hobbhahn >[[email protected]] >Sent: Wednesday, April 25, 2012 1:55 AM >To: [email protected] >Subject: [R-sig-phylo] Normality requirement for assessment of lambda >with phylosig (phytools) and fitContinuous (geiger) > >Dear fellow list users, > >I would like to assess the magnitude of phylogenetic signal in two sets >of continuous data. Set 1 contains numerous zeros and is therefore >non-normal. Set 2 contains very little variation and is non-normal due to >underdispersion. Given that both data sets are largely immune to >transformations to normality, I am wondering whether the lambda estimates >for untransformed data derived from phylosig and fitContinuous will be >meaningful? If not, can you recommend transformations or other methods of >phylogenetic-signal assessment that would be preferable? > >Thank you very much, > >Nina > > > >Dr. Nina Hobbhahn >Post-doctoral fellow >Lab of Prof. S. D. Johnson >School of Life Sciences >University of KwaZulu-Natal >Private Bag X01 >Scottsville, Pietermaritzburg, 3201 >South Africa > > > [[alternative HTML version deleted]] > >_______________________________________________ >R-sig-phylo mailing list >[email protected] >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > >_______________________________________________ >R-sig-phylo mailing list >[email protected] >https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
