Dear Roi, perhaps you could consider paper Zapata, F. and I. Jimenez. 2012. Species Delimitation: Inferring Gaps in Morphology across Geography. Systematic Biology 61:179-194. ( http://sysbio.oxfordjournals.org/content/61/2/179) where the authors introduce tolerance regions of multivariate normal distributions. Associated are also some R scripts which I have modified to be applicable for >2 dimensional case. I could provide you with them if you were interested. Best wishes, Ondřej
On 16 September 2014 12:00, <r-sig-phylo-requ...@r-project.org> wrote: > Send R-sig-phylo mailing list submissions to > r-sig-phylo@r-project.org > > To subscribe or unsubscribe via the World Wide Web, visit > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > or, via email, send a message with subject or body 'help' to > r-sig-phylo-requ...@r-project.org > > You can reach the person managing the list at > r-sig-phylo-ow...@r-project.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of R-sig-phylo digest..." > > > Today's Topics: > > 1. points overlap in multidimensional space (Roi Holzman) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 16 Sep 2014 12:28:05 +0300 > From: Roi Holzman <roi.holz...@gmail.com> > To: r-sig-phylo@r-project.org > Subject: [R-sig-phylo] points overlap in multidimensional space > Message-ID: <a52d461b-9eb8-4c4f-8072-f084e1f23...@gmail.com> > Content-Type: text/plain; charset="UTF-8" > > fellow R-sig-phylo users- > I know this is not strictly a phylogenetic question, but I was hoping > someone can help > > I have a 6 diminutional morphospace of observed traits (6 traits, 110 > observations) and another morphospace of simulated traits (same > dimensions). I want to quantify the overlap between the two morphospaces. > my original idea was to produce a kernel density estimation using one > matrix, and ask how many points from the other matrix fall within a a > certain contour (say the 50% contour). I used package ?ks? to produce a > kernel, as following: > > > library(ks) > > set.seed(8192) > > x1 <- rmvnorm.mixt(110, mus=rep(0,6), diag(6)) > > > set.seed(4192) > > x2 <- rmvnorm.mixt(110, mus=rep(0,6), diag(6)) > > > > fhat <- kde(x1, eval.points=x1) > > ct <- contourLevels(fhat, cont=50) > > but I could not figure out the second part, e.g. how many points from x2 > fall within the kde that was calculated based on x1 . any ideas? maybe I > should approach this differently? I already tried reducing dimensionality > using PCA, and I could reduce the data to 3x110, but not less > > many thanks! > > Roi > > Roi Holzman, Ph.D. > Department of Zoology, Tel Aviv University > and the Inter-University Institute for Marine Sciences in Eilat > Tel. (972)-8-6360-134 > holz...@post.tau.ac.il > http://iui-eilat.ac.il/People/AcademicStaffProfile.aspx?sid=106 > > > > > > [[alternative HTML version deleted]] > > > > ------------------------------ > > _______________________________________________ > R-sig-phylo mailing list > R-sig-phylo@r-project.org > https://stat.ethz.ch/mailman/listinfo/r-sig-phylo > > > End of R-sig-phylo Digest, Vol 80, Issue 4 > ****************************************** > -- Ondřej Mikula Institute of Animal Physiology and Genetics Academy of Sciences of the Czech Republic Veveri 97, 60200 Brno, Czech Republic Institute of Vertebrate Biology Academy of Sciences of the Czech Republic Studenec 122, 67502 Konesin, Czech Republic [[alternative HTML version deleted]] _______________________________________________ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
