Hi Trey, On Mon, Apr 5, 2010 at 1:58 PM, Trey <trey3...@hotmail.com> wrote: > > Dr. Stevens, > > Hi, my name is Trey Scott, and I'm a grad student of Brian McCarthy's. He > referred me to you because of your expertise in handling complex R problems. > We were hoping you could help us solve a nagging problem that is prohibiting > me from producing graphicl output. > > Here is a simple mock-up of the matrix I'm using > > a b c d e f > 1i 1 4 7 9 2 5 > 2i 12 17 6 2 3 7 > 3i 2 5 8 1 3 2 > 1c 0 2 4 7 2 1 > 2c 0 1 4 6 9 10 > 3c 13 15 19 10 8 9 > > Where: 1i-3i are "infested" sites, and 1c-3c are "control sites". A-F are > species found at each site. I have several of these ordinations to perform > on different variables (BA, density, RIV, cover, etc..., all in different > matrices). I'm running NMDS (metaMDS) ordinations on each matrices, and > producing ordination graphs for each cloud of points. The problem I have is > that I cannot devise a way to split the cloud of points into infested and > control so that I can deduce any significant groupings. A simple difference > in symbols/color (Ex. gray triangles for infested, black circles for > control) would do. Also, I understand the use of pch/col/cex, I just need > to apply them to the "split". > > So: > > + How would I split these out in R after I run the metaMDS in vegan? > + What code would be necessary to bring this about? > > McCarthy and I are at the end of our preoverbial rope on this; nothing has > worked. > --
Was the solution I sent you the other day not helpful? http://n4.nabble.com/How-to-split-data-for-NMDS-plots-td1751101.html#a1751290 If not perhaps you can explain what went wrong. Also you can post a small example of your data using dput(). The best way that I have found to make ordination plots in vegan is to make them in pieces. Michael -- Michael Denslow I.W. Carpenter Jr. Herbarium [BOON] Department of Biology Appalachian State University Boone, North Carolina U.S.A. -- AND -- Communications Manager Southeast Regional Network of Expertise and Collections sernec.org 36.214177, -81.681480 +/- 3103 meters ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
