Hi, Comments inline:
On Tue, Nov 27, 2012 at 1:00 PM, Craig P O'Connell <coconne...@umassd.edu> wrote: > > > Dear all, > > I am having a recurring problem when I attempt to conduct a GLM. Here is > what I am attempting (with fake data): > First, I created a txt file, changed the directory in R (to the proper folder > containing the file) and loaded the file: > > #avoid<-read.table("avoid.txt",header=TRUE);avoid > # treatment feeding avoid noavoid > #1 control nofeed 1 357 > #2 control feed 2 292 > #3 control sat 4 186 > #4 proc nofeed 15 291 > #5 proc feed 25 288 > #6 proc sat 17 140 > #7 mag nofeed 87 224 > #8 mag feed 34 229 > #9 mag sat 46 151 > > I then try to "attach(avoid)" the data, but continue to get an error message > ( The following object(s) are masked _by_ .GlobalEnv :), so to fix this, I do > the following: > > #newavoid<-avoid > #newavoid (does this do anything?) It essentially makes a copy of `avoid` to `newavoid` -- what did you want it to do? That having been said, a good rule of thumb is to never use `attach`, so let's avoid it for now. > Lastly, I have several GLM's I wanted to conduct. Please see the following: > > #model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial) > > #model2=glm(cbind(avoid, noavoid)~feeding, familiy=binomial) > > #model3=glm(cbind(avoid, noavoid)~treatment+feeding, familiy=binomial) `cbind`-ing doesn't make much sense here. What is your target (y) variable here? are you trying to predict `avoid` or `noavoid` status? Let's assume you were "predicting" `noavoid` from just `treatment` and `feeding` (I guess you have more data (rows) than you show), you would build a model like so: R> model <- glm(noavoid ~ treatment + feeding, binomial, avoid) Or to be explicit about the parameters: R> model <- glm(noavoid ~ treatment + feeding, family=binomial, data=avoid) > It would be greatly appreciated if somebody can help me with my coding, as > you can see I am a novice but doing my best to learn. I figured if I can get > model1 to run, I should be able to figure out the rest of my models. Since you're just getting started, maybe it would be helpful for people writing documentation/tutorials/whatever what needs to be explained better. For instance, I'm curious why you thought to `cbind` in your first glm call, which was: model1<-glm(cbind(avoid, noavoid)~treatment,data=,family=binomial) What did you think `cbind`-ing was accomplishing for you? Is there an example somewhere that's doing that as the first parameter to a `glm` call? Also, why just have `data=<nothing>`? I'm not criticizing, just trying to better understand. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact ______________________________________________ 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.