#CANONICAL CORRESPONDENCE ANALYSIS
#EXAMPLE DATA FROM:
#http://www.xlstat.com/en/learning-center/tutorials/running-a-canonical-correspondence-analysis-cca-with-xlstat-ada.html

M=read.table("c:/DATA/Multivariate/CCAExample1.txt")
M

X=data.frame(M[,2:11],row.names=M$Site)
X

Y=data.frame(M[,12:14],row.names=M$Site)
Y

library(anacor)
library(vegan)

#USING {anacor}:
CCAas=anacor(X,row.covariates=Y,ndim=3,scaling=c("standard","standard"))
CCAas

#"STANDARD" SCORES:
summary(CCAas)

#USING {vegan}:
CCAv=cca(X,Y,scale=F)
CCAv
summary(CCAv)
scores(CCAv,scaling=1)

#"CENTROID" SCORES:
#USING {anacor}:
CCAac=anacor(X,row.covariates=Y,ndim=3,scaling=c("centroid","centroid"))
CCAac
summary(CCAac)
#USING {vegan}
scores(CCAv,scaling=2)

#PLOTTING WITH {anacor}:
CCAas=anacor(X,row.covariates=Y,ndim=2,scaling=c("standard","standard"))
plot(CCAas,plot.type="orddiag")
plot(CCAas)

CCAac=anacor(X,row.covariates=Y,ndim=2,scaling=c("centroid","centroid"))
plot(CCAac,plot.type="orddiag")
plot(CCAac)

#PLOTTING WITH {vegan}:
plot(CCAv,scaling=1)  
plot(CCAv,scaling=2) 
plot(CCAv,scaling=3)