Ok..So here is an example of some of my code Sites,P1,P2,P3,P4,P5,P6,P7,S1,S2,S3,S4,S4,S5 trap01,0,1,0,1,1,0,1,1,0,0,0,0 trap02,0,1,0,0,0,0,0,0,1,1,0,0 trap03,0,1,0,1,1,1,1,1,0,0,0,1 trap04,0,1,0,0,0,0,0,0,1,1,0,0 trap05,0,1,0,0,0,1,1,1,1,0,0,1
So here is a SMALL example of what the code looks like. The first row is names of plant species and moth species. P1....P7 = plantSpecies, and S1...S5 = mothSpecies. And the each of the rows that follow are presence and absent data (1=present, 0=absent) for different trapping sites. (In reality there are like 71 plant species, and over 450 moth species and 20 trap sites) So I've been trying to run CCA on this for a long time and keep getting errors. I've been suggested to remove duplicate rows which I think I’ve done (using 'unique' command...BUT what I was wondering is how can any rows be duplicate if each row has a different trapID as the first item in each row...or does R know to ignore this??) I have also been suggested to remove any columns containing only 0s or 1s. I've done this also. Another suggestion was Normalizing the data which I can normalize it using "normalize"command but not sure if it is that simple. I am pasting my R script. The only reason why I wanted to post my entire data was because something is telling me with this small example data set that CCA may be able to run successfully and I just really wanted to see if anyone can really get it to go with my real data set. Like I said I've been trying this for awhile. I am able to get the preliminary stages of CCA to work (correlation matrices) but nothing else after that. So I will attach my example data set and my R script I use. I will also attach my REAL data as well for anyone who thinks they can solve this. It's probably something real minor or small...that I'm just not seeing. ***IN the R Script you will need to change the csv file it reads in to "example_data.csv" (this is the example data. ALSO the R script is ran for the REAL data so it will need to be changed to work with the example_data. While you're going through the script feel free to make note of errors I could of made when writing up the script******** Thanks...thanks!! http://r.789695.n4.nabble.com/file/n2329826/example_data.csv example_data.csv http://r.789695.n4.nabble.com/file/n2329826/Performing_CCA_Script Performing_CCA_Script http://r.789695.n4.nabble.com/file/n2329826/all_Data01.csv all_Data01.csv -- View this message in context: http://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329826.html Sent from the R help mailing list archive at Nabble.com. ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
