[R] CCA with Vegan - Plot problem

[Gavin Simpson]

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
> 
> 
> 
> --
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> Sent from the R help mailing list archive at Nabble.com.
> 
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> 

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