Hi Gavin, thanks for your message. You are right. The function nmds is from library labdsv and not from vegan. My mistake.
Well, that's what I did: library(vegan) library(labdsv) nms.euc <- nmds(dis.euc,4) initial value 13.457832 iter 5 value 8.589716 iter 10 value 7.989993 iter 15 value 7.734503 iter 20 value 7.539719 iter 25 value 7.438721 final value 7.397254 converged plot(nms.euc) text(nms.euc$points[,1],nms.euc$points[,2],labels=row.names(nms.euc$points),pos=4,cex=0.7) # got overwritten labels identify(plot(nms.euc)) numeric(0) It seems that ordiplot is not suitable to nmds but only to cca and rda. But you understood exactly what I want. Your example showed for cca what I want for nmds plot. Best regards, Antonio Citando Gavin Simpson <[EMAIL PROTECTED]>: > On Wed, 2007-11-14 at 11:22 -0300, Antonio Olinto wrote: > > Hi, > > > > I'm using nmds command (library vegan) to analyze some fishing data. > > I doubt it - there is no nmds command. Do you mean metaMDS() ? This uses > isoMDS() from package MASS with some extra features. > > > > > I'd like to plot not only points, but also the names of species and > stations in > > a specified position. > > > > I used the command > > text(nmds$points[,1], nmds $points[,2],labels=row.names(nmds > > $points),pos=3,cex=0.5) > > > > But the labels are sometimes overlapped. > > > > Is there any way to use identify, or a similar command, to plot the row > names in > > a given position? Identify would be perfect but it indicates the row number > and > > I'd like to have the row name given in nmds$points. > > Have a look at ?orditorp in vegan for an alternative approach, but yes > you can use identify, but you have to capture the output of the plot > call and use that in your identify call: > > require(vegan) > data(varespec) > mod <- cca(varespec) > mod.plt <- plot(mod, display = "species", type = "p") > identify(mod.plt) > > See ?identify.ordiplot for more info. > > HTH > > > > > Many thanks, > > > > Antonio Olinto > > Sao Paulo Fisheries Institute > > Brasil > > > > > > > > > > > > > > ------------------------------------------------- > > BCMG Internet Webmail > > www.bcmg.com.br > > > > ______________________________________________ > > 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. > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > Dr. Gavin Simpson [t] +44 (0)20 7679 0522 > ECRC, UCL Geography, [f] +44 (0)20 7679 0565 > Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk > Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ > UK. WC1E 6BT. [w] http://www.freshwaters.org.uk > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > ------------------------------------------------- BCMG Internet Webmail www.bcmg.com.br ______________________________________________ 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.
