CCA with Vegan - Plot problem
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.
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