Read over the Blomberg et al. (2003) paper. K is intended for continuous-valued traits and/or those evolving similar to Brownian motion. You could report it if you wished, but I would add that caveat if you do.
The randomization test should be robust in any case. Cheers, Ted From: Nina Hobbhahn [n.hobbh...@gmail.com] Sent: Wednesday, April 25, 2012 9:19 AM To: Theodore Garland Jr Cc: Alejandro Gonzalez; Hunt, Gene; Enrico Rezende; r-sig-phylo@r-project.org Subject: Re: [R-sig-phylo] Normality requirement for assessment of lambda with phylosig (phytools) and fitContinuous (geiger) Thanks all for your helpful contributions! I will use phylosignal. Ted, I'm not sure I understand your last comment, "when the data are not though of as continuous-valued and/or evolving similar to Brownian motion". What do you mean by that? Also, are you suggesting that I report the presence/absence of phylogenetic signal, but not the value of the K statistic? Many thanks again, Nina On 2012-04-25, at 5:54 PM, Theodore Garland Jr wrote: > 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 _______________________________________________ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
