Re: [R] How to Perform CCA in ??!! Help please
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. P1P7 = 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 normalizecommand 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.
Re: [R] How to Perform CCA in ??!! Help please
If you read your email back to yourself, you will notice that you never actually describe the problems you are having. There are people on this list who can help you, but you need to tell them what you need help with. We don't need your whole data set and script (in fact sending the whole shebang would be unhelpful). Instead, make sample data sets (just complex enough to illustrate your problems) and R code that you need help working out. We want to help you, but I JUST CAN'T GET IT is much to vague. Best, Ista On Wed, Aug 18, 2010 at 4:38 AM, stompper33 ascaldero...@gmail.com wrote: Performing CCA in R 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 can't attach any file...so Please email me and I'll attach the necessary files. (there's only two) the files will be my CCA R script file, and my data file I use that contains all my data I use for my analyzing. **The files I'll send you are .csv file and a R script. The file all_Data01.csv and Performing_CCA will be the file names PLEASE!! I AM DESPERATE! I'VE BEEN TRYING TO DO THIS FOR A COUPLE OF WEEKS AND I JUST CAN'T GET 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 -- View this message in context: http://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329336.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. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org __ 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.
Re: [R] How to Perform CCA in ??!! Help please
Hello Ista, I recently posted a new message on my own post that should clarify what you are talking about. Let me know if you can't see it. I been having problems post things on the forum. thanks On Wed, Aug 18, 2010 at 6:57 AM, Ista Zahn-2 [via R] ml-node+2329880-957103028-137...@n4.nabble.comml-node%2b2329880-957103028-137...@n4.nabble.com wrote: If you read your email back to yourself, you will notice that you never actually describe the problems you are having. There are people on this list who can help you, but you need to tell them what you need help with. We don't need your whole data set and script (in fact sending the whole shebang would be unhelpful). Instead, make sample data sets (just complex enough to illustrate your problems) and R code that you need help working out. We want to help you, but I JUST CAN'T GET IT is much to vague. Best, Ista On Wed, Aug 18, 2010 at 4:38 AM, stompper33 [hidden email]http://user/SendEmail.jtp?type=nodenode=2329880i=0 wrote: Performing CCA in R 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 can't attach any file...so Please email me and I'll attach the necessary files. (there's only two) the files will be my CCA R script file, and my data file I use that contains all my data I use for my analyzing. **The files I'll send you are .csv file and a R script. The file all_Data01.csv and Performing_CCA will be the file names PLEASE!! I AM DESPERATE! I'VE BEEN TRYING TO DO THIS FOR A COUPLE OF WEEKS AND I JUST CAN'T GET 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 -- View this message in context: http://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329336.htmlhttp://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329336.html?by-user=t Sent from the R help mailing list archive at Nabble.com. __ [hidden email] http://user/SendEmail.jtp?type=nodenode=2329880i=1mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- Ista Zahn Graduate student University of Rochester Department of Clinical and Social Psychology http://yourpsyche.org http://yourpsyche.org/?by-user=t __ [hidden email] http://user/SendEmail.jtp?type=nodenode=2329880i=2mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.htmlhttp://www.r-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. -- View message @ http://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329880.html To unsubscribe from How to Perform CCA in [R]??!! Help please, click herehttp://r.789695.n4.nabble.com/template/NodeServlet.jtp?tpl=unsubscribe_by_codenode=2329336code=YXNjYWxkZXJvbjAzQGdtYWlsLmNvbXwyMzI5MzM2fDExMzU0Njc1NzI=. -- View this message in context: http://r.789695.n4.nabble.com/How-to-Perform-CCA-in-R-Help-please-tp2329336p2329883.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] __ 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.
