However, calculating a K statistic is strange when the data are not thought of as continuous-valued and/or evolving similar to Brownian motion. The randomization test is OK, however.
Cheers, Ted From: Alejandro Gonzalez [alejandro.gonza...@ebd.csic.es] Sent: Wednesday, April 25, 2012 8:46 AM To: Theodore Garland Jr Cc: Nina Hobbhahn; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) 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: tgarl...@ucr.edu 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: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org] on behalf of Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 1:55 AM To: r-sig-phylo@r-project.org 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 R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org 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: alejandro.gonza...@ebd.csic.es 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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
