CCA with Vegan - Plot problem
On Fri, 2012-11-09 at 05:16 -0800, rumble14 wrote:
Thanks for replying. Apologies for not putting the code, I have not deviated from that used on the website I linked to.
Can you show the exact code you used please?
I am using:
#below is Species_1 etc
org <- read.table ("Organisms.S", header=TRUE, row.names=1)
#below is environmental variables
env<-read.table ("Environment.S, header=TRUE)
attach(env)
library(vegan)
cca.1<-(org~Temp+Water+etc)
cca.1
Don't do that - it is an abuse of the formula interface and an abomination to attach such objects to the search path. This isn't actually doing anything (well, it is, but it is not a CCA): cca.1<-(org~Temp+Water+etc) There is no function call. And your use of `+ etc` suggests this isn't the **actual** code you ran and I did ask for that. You should use: cca.1 <- cca(org ~ ., data = env) assuming you want all variables in `env` in the model - not that that is a good thing but that is a statistical issue not an R one! Can you show me - probably *off list* including the actual data files (which I promise to delete after we solve the problem) - the code you use and I can take a look but before you send anything to me in an email make sure you can paste the exact same code into R and have it run G
At this point I have noticed (this morning) that I should be getting the CCA come up here, and this is working with test data but not my actual data which is formatted in exactly the same way. If I type: cca(formula = org ~ Temp + Water+etc, data = org) at this point, I get what looks like but (you're right) might not be an output. For the graph I was then trying to use: cca1.plot <- plot(cca.1,choices=c(1,2)) at which point I get error messages.
Also, not sure why you are
attaching anything As I said, I'm quite new to R. It does so on the tutorial linked so had assumed it was to do with being able to access the parameters Temp etc. H -- View this message in context: http://r.789695.n4.nabble.com/CCA-with-Vegan-Plot-problem-tp4649012p4649045.html Sent from the R help mailing list archive at Nabble.com.
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