[R-sig-phylo] Comparing slopes from regressions and PIC regressions
Dear all I am currently analyzing a community dataset of two continuous traits survival and disease resistance. I ran two regressions: (1) considering each species independent data points, and (2) phylogenetic independent contrasts. Both regressions were significant. Blombergs K also significant and ~ 0.38, and 0.34, respectively. However, I am interested in the slope of these regressions. For regression 1, slope = 0.142, for regression 2 slope = 0.105. I am interested in saying how much (in %) the evolutionary relationships contributed to the slope. My question is: Can I say that evolutionary relationships accounted for 74% (0.105/0.142) of the observed slope? Or is it only 26%? Thanks in advance for your help, since I don't have any experience running these types of analyses. Best regards, Ana [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Comparing slopes from regressions and PIC regressions
Long story short, you don't want to think about it in those terms. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 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 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 Ana Longo [ana.lo...@gmail.com] Sent: Wednesday, January 18, 2012 7:20 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Comparing slopes from regressions and PIC regressions Dear all I am currently analyzing a community dataset of two continuous traits – survival and disease resistance. I ran two regressions: (1) considering each species independent data points, and (2) phylogenetic independent contrasts. Both regressions were significant. Blomberg’s K also significant and ~ 0.38, and 0.34, respectively. However, I am interested in the slope of these regressions. For regression 1, slope = 0.142, for regression 2 slope = 0.105. I am interested in saying how much (in %) the evolutionary relationships contributed to the slope. My question is: Can I say that evolutionary relationships accounted for 74% (0.105/0.142) of the observed slope? Or is it only 26%? Thanks in advance for your help, since I don't have any experience running these types of analyses. Best regards, Ana [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] Comparing slopes from regressions and PIC regressions
VERY synthetically The two r-squared are NOT comparable. Taking in to account phylogeny is useful just to partial out data non independence due to shared ancestry, and to perform better tests of significance but the r-sq could be higher or smaller just because of chance. Maybe someone can add more on this. best paolo Long story short, you don't want to think about it in those terms. Cheers, Ted Theodore Garland, Jr. Professor Department of Biology University of California, Riverside Riverside, CA 92521 Office Phone: (951) 827-3524 Wet Lab Phone: (951) 827-5724 Dry Lab Phone: (951) 827-4026 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 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 Ana Longo [ana.lo...@gmail.com] Sent: Wednesday, January 18, 2012 7:20 AM To: r-sig-phylo@r-project.org Subject: [R-sig-phylo] Comparing slopes from regressions and PIC regressions Dear all I am currently analyzing a community dataset of two continuous traits survival and disease resistance. I ran two regressions: (1) considering each species independent data points, and (2) phylogenetic independent contrasts. Both regressions were significant. Blombergs K also significant and ~ 0.38, and 0.34, respectively. However, I am interested in the slope of these regressions. For regression 1, slope = 0.142, for regression 2 slope = 0.105. I am interested in saying how much (in %) the evolutionary relationships contributed to the slope. My question is: Can I say that evolutionary relationships accounted for 74% (0.105/0.142) of the observed slope? Or is it only 26%? Thanks in advance for your help, since I don't have any experience running these types of analyses. Best regards, Ana [[alternative HTML version deleted]] ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Paolo Piras Center for Evolutionary Ecology and Dipartimento di Scienze Geologiche, Università Roma Tre Largo San Leonardo Murialdo, 1, 00146 Roma Tel: +390657338000 email: ppi...@uniroma3.it ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Re: [R-sig-phylo] randomizing clades within a node
Hi Juan, Juan Antonio Balbuena wrote on 13/01/2012 21:57: Hello I would very much appreciate if someone can help me with this one. I wish to compare two additive trees that are identical for some but not all the clades. So I use rtree of the ape package with, say, 10 tips to generate tree A. Then I wish to modify A to get tree B by randomizing the clades and patristic distances in a given number of nodes. If the number of nodes is, for instance, three, the 3 nodes furthest apart from the origin will be randomized. Then A and B will be compared. The whole procedure needs to be carried out a large number of times (10,000). The functions you need are extract.clade and bind.tree. The both have options to allow you to flexibly handle eventual root edges, so have a look at their help pages. HTH Emmanuel Any help would be much appreciated. Juan A. Balbuena -- Dr. Juan A. Balbuena Marine Zoology Unit Cavanilles Institute of Biodiversity and Evolutionary Biology University of Valencia http://www.uv.es/~balbuena http://www.uv.es/%7Ebalbuena P.O. Box 22085 http://www.uv.es/cavanilles/zoomarin/index.htm 46071 Valencia, Spain http://cetus.uv.es/mullpardb/index.html e-mail: j.a.balbu...@uv.es mailto:j.a.balbu...@uv.es tel. +34 963 543 658 fax +34 963 543 733 NOTE! For shipments by EXPRESS COURIER use the following street address: C/ Catedrático José Beltrán 2, 46980 Paterna (Valencia), Spain. ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo -- Emmanuel Paradis IRD, Jakarta, Indonesia http://ape.mpl.ird.fr/ ___ R-sig-phylo mailing list R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
