On Fri, 2012-11-09 at 00:51 -0800, rumble14 wrote: > Hi, > I've just started using R and am having some problems with CCA using vegan. > > I'm looking at abundance p/m2 (hence decimals) vs environmental variables > and have been using > http://ecology.msu.montana.edu/labdsv/R/labs/lab12/lab12.html to guide me > through. > > My organism data looks like this: > Sample "Species_1" "Species_2" "Species_3" etc > Sample_1 0 0.12432 0.3456 > etc > > and is in a .csv file > > My environment data (.csv again) looks like this: > Temp Water etc > 18 33.3 > etc > > I can get vegan to run the CCA with no problems but when I enter > > >cca1.plot <- plot(cca.1,choices=c(1,2)) > > I get the following error message: > > Error in function (formula, data = NULL, subset = NULL, na.action = na.fail, > : > invalid type (list) for variable 'org' > > ('org' is the name of my organism file once attached).
Somewhat frustratingly you have covered everything *but* how you created `cca.1` and whilst you might presume that because an error was not thrown everything worked out OK with that procedure, the failing `plot()` call suggests otherwise. Can you show the exact code you used please? Also, not sure why you are attaching anything - it is not required for most R usage and certainly not for using cca() in vegan. G > I'd appreciate some help. If I haven't given enough detail, please let me > know. I've tested the example data given on the website and it works so am > obviously missing something I shouldn't be. > > Cheers, > Heather > > > > -- > View this message in context: > http://r.789695.n4.nabble.com/CCA-with-Vegan-Plot-problem-tp4649012.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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 %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% ______________________________________________ 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.
