In an ordination such as this, you have two sets of scores; i) one pertaining to the (dis)similarity of your samples in terms of species composition, and ii) one pertaining to the species and which species co-occur. You can't display both sets of information and retain the meaning of the scores on the one plot. Scaling controls what relationships are preserved (focussing on sites or species etc). Gabriel (forget the citation now but is was in Biometrika) suggests that scaling 3 (symmetric scaling) is optimal and to be preferred.
There is a discussion of the various scalings in the Design Decision vignette that you should read. If this is too complex, then perhaps start with Jan Leps and Petr Smilauer's book "Multivariate analysis of ecological data using Canoco", 2003, Cambridge University Press. HTH Gavin > code > > rm(list=ls()) > library(vegan) > library(MASS) > > data(varespec) > print(varespec) > str(varespec) > > > #PCA > vare.pca <- rda(varespec) > vare.pca > plot(vare.pca) > sum(apply(varespec, 2, var)) > biplot(vare.pca, scaling = -1) > > Elaine > > On Sat, Aug 14, 2010 at 10:48 AM, Ben Bolker <bbol...@gmail.com> wrote: > >> elaine kuo <elaine.kuo.tw <at> gmail.com> writes: >> >> > Pls kindly advise what scaling is in plot. >> > Sometime it could be negative but sometimes it might be positive >> > .(I guess it is the proportion between the plot and the margin) >> >> Your question is unclear. Please give more context and/or details. >> >> ______________________________________________ >> 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. >> > > [[alternative HTML version deleted]] > > ______________________________________________ > 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. > ______________________________________________ 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.
