[R-sig-eco] simple question about CCA

[Simone Ruzza]

Dear all,

apologies for the simplicity of my question, maybe it has been asked
many times, but I am a total novice to CCA. I have performed a CCA
using a series of environmental variables that comprise a mixture of
categorical and non-categorical variables. What I do not understand is
why when I change the order of my variables and I plot the results, a
variable disappears from the CCA biplot i.e. the last one being
continuous variable. I realised that there might a very simple
question, so I would be happy even with a reference where to find an
answer. Below some code showing what is happening.

thanks in advance,

Simone



require(RCurl)
require(vegan)
x <- getURL("https://dl.dropboxusercontent.com/u/33966347/testdata.csv")
dat<- read.csv(text = x)


# example 1 x7 disappear from the plot (note that x5 and x6 are categorical)
ccatest<-cca(dat[8:144]~x1+x2+x3+x4+x5+x6+x7,data=dat)
plot(ccatest)

# example 2 x7 is present in the plot
ccatest1<-cca(dat[8:144]~x7+x1+x2+x3+x4+x5+x6,data=dat)
plot(ccatest1)