Hello, The library picante in R implements Blomberg et al (2003) K estimate, Liam's phytools package does as well. Phytools has the added advantage, if I remember correctly, of allowing users to estimate K including within species variation.
Cheers Alejandro On 25, Apr 2012, at 5:29 PM, Theodore Garland Jr 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 __________________________________ Alejandro Gonzalez Voyer Post-doc Estación Biológica de Doñana Consejo Superior de Investigaciones Científicas (CSIC) Av Américo Vespucio s/n 41092 Sevilla Spain Tel: + 34 - 954 466700, ext 1749 E-mail: [email protected] Web site (Under construction): Personal page: http://consevol.org/members/alejandro.html Group page: http://consevol.org/index.html For PDF copies of papers see: http://csic.academia.edu/AlejandroGonzalezVoyer [[alternative HTML version deleted]]
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