Performing CCA in R

stompper33 0 Newbie Poster

13 Years Ago

I know they say don't say please... or plead...but I'm sorry but I really need some help with this problem. I have tried to perform CCA in R and I can never do this successfully. Can someone please tell me what I'm doing wrong. I've attached my CCA R script file. I've also attached my data file I use that contains all my data I use for my analyzing.
**All attached files were saved as .txt This was the only way I could attach them. The file "all_Data01.txt" needs to be converted into a .csv file. Just rename it.****

If you can help I will really appreciate it. You will need to install the 'CCA' package in R before running it. I am also thinking maybe I may only be able to run the regularized CCA rather than Classical CCA. But I hope to run one or the other.
If anyone needs an easy example of CCA please follow the link below:
http://www.jstatsoft.org/v23/i12/paper (scroll to about the bottom of page 7 )

I've tried to follow the example as well and still have problems.

Thank You...Thank You

static-analysis

all_Data01.txt (21.69 KB)

The attachment preview is chopped off after the first 10 KB. Please download the entire file.

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performing_CCA_inR.txt (1.85 KB)

##############################################################
########### Performing CCA with Moth and Plant DATA	########
##############################################################
#First you need to load the CCA package in R

#We need to open csv file that contains ALL the data
#The data file I've attached is called "all_Data01.csv"
#The data contains moth specie names and plant data
#Plant data is Abbreviated with four letter names e.g."ABAM" and are
#in the first 71 columns. Followed by 493 species which are named
# by "S##"

all_data = read.csv(file.choose(),header=T)
#open all_Data01.csv


#The above line will give you a pop up window that
#allows you to choose which file you want open
#Be sure to open file titled "all_Data01.csv"

#View all the data
all_data

#Now we want to separate the data into mothdata and plantdata
plantdata <- all_data [1:20, 2:72]
mothdata <- all_data [1:20, 73:494]

#You can now view each separately
plantdata
mothdata

#Make two matrices to hold the separate data
X <- as.matrix(mothdata)
Y <- as.matrix(plantdata)

#Remove any columns with just 0s or 1s
NewX <- X[,colSums(X) != 0]
NewY <- Y[,colSums(Y) != 0]
NewX1 <- NewX[,colSums(NewX) != 20]
NewY1 <- NewY[,colSums(NewY) != 20]

#Perform Cross-Correlation on mothdata and plantdata
correl <- matcor (NewX1, NewY1)
img.matcor(correl, type=2)  			#you should get three different correlation matrices

#NOW we want to perform Classical CCA on our data. We will do this
#by using just a sample of the data from the mothdata

Xr <- as.matrix(NewX1[,sample(1:378,size=10)])
res.cc <- cc(Xr, NewY1)

#There should be two more lines that follow after the last line
#above. BUT I get an error after putting in
#res.cc <- cc(Xr, NewY1)

##I have also heard to try to normalize my data first. I have tried this also and still cannot get it.

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