[R-sig-eco] wascores() for metaMDS?
Hi sig-ecology! Here comes a probably stupid question... I am looking for smart ways to include information about underlying variables in MDS plots. In other words, after having computed an ordination with isoMDS or metaMDS from a community table, I would like to add something like species coefficients/loadings as vectors to the plot of sites. As no species coefficients exist in this case, the best I could come up with so far is simply vectors calculated from correlation coefficients of the individual species with the site scores (on two MDS axes). The function metaMDS allows to compute species scores using the function wascores() I have now pondered for 2 days how these scores are calculated and what their precise meaning would be. Would these species scores be appropriate to show as vectors in the MDS? Thanks for any answer... Gabriel Singer ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] wascores() for metaMDS?
Gabriel, On 19/08/09 12:40 PM, gabriel singer gabriel.sin...@univie.ac.at wrote: Hi sig-ecology! Here comes a probably stupid question... I am looking for smart ways to include information about underlying variables in MDS plots. In other words, after having computed an ordination with isoMDS or metaMDS from a community table, I would like to add something like species coefficients/loadings as vectors to the plot of sites. As no species coefficients exist in this case, the best I could come up with so far is simply vectors calculated from correlation coefficients of the individual species with the site scores (on two MDS axes). The function metaMDS allows to compute species scores using the function wascores() I have now pondered for 2 days how these scores are calculated and what their precise meaning would be. Would these species scores be appropriate to show as vectors in the MDS? Thanks for any answer... I think these were documented... Please point out the unclear parts of the documentation so that I can correct those. The wascores are Weighted Averages Scores and they are calculated like weighted averages, or similarly as species scores in correspondence analysis. This means that (with some scaling) they show the centroid (barycentre) of the species occurrence in the ordination graph. It is not appropriate to present these as arrows which indicate a linear increase to the direction of the arrow instead of the centre of abundance. Therefore the species scores can (and as default in metaMDS, will) be presented as points. If -- for any reason that is none of my business -- you want to get vectors of species, you can fit species as vectors. This happens with metaMDS or isoMDS like this: library(vegan) data(dune) m - metaMDS(dune) # or m - isoMDS(vegdist(dune)) vec - envfit(m, dune) plot(m, dis=site) # or with isoMDS: ordiplot(m) plot(vec) I promised that I won't comment on this, but still I must say that I cannot find a reason to do so. Please note that you can also use ordisurf to fit nonlinear species responses if you think that species are not points nor arrows. Vegan tutorial (from the Web) gives an example. Cheers, Jari Oksanen ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
Re: [R-sig-eco] Help with downloading package
Dear Leigh, You have 2 options: 1. build the MAC OS X package for yourself and install it, in this way you will be able to use the help files as usual, 2. unpack the .tar.gz and source all files in the /R directory (on how to do it at once see Example in help(source)). Cheers, Peter On Wed, Aug 19, 2009 at 3:58 PM, Leigh Fallleigh.f...@gmail.com wrote: Hey all, I have recently starting using R, so I'm still on the steep-learning curve of the program. I have been unable to install Diveristy.R from Dr. Pelissier's website (http://pelissier.free.fr/Diversity.html). I have downloaded the libraries ade4 and spdep (along with all the other packages needed to run spdep). I'm running R version 2.9.1 on a MAC OS X version 10.5.8. When I click on Package source (all platforms): diversity_1.5-9.tar.gzhttp://pelissier.free.fr/diversity/R-2.8.1/diversity_1.5-9.tar.gz from the website, a folder labeled diversity is downloaded onto my desktop. One question I have is where the package/folder/library should be downloaded. My other question is how to install it. I've tried to Package Installer-Local Binary Package and Local Source Package at the user level without success. I also just downloaded the tar.gz file directly to my desktop and then use the Package Installer, but again without success. I tried the install.packages command, but I don't know if I'm using it correctly. The solution is probably simple, but with my limited experience with writing code and programming, I'm not sure what I'm doing wrong. Any help will be appreciated!! Many thanks in advance!!! Cheers, Leigh -- Leigh M. Fall Ph.D. Candidate Dept. of Geology and Geophysics Texas AM University 3115 TAMU College Station, TX 77843 Phone: (979) 845-3071 E-mail: leigh.f...@gmail.com http://geoweb.tamu.edu/profile/LFall [[alternative HTML version deleted]] ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology ___ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology
