Friends Seems I've run into another snag. More of the nitty-gritty r-details I don't understand.
So, as I mentioned below, dataset[[var_sub]] seems to be understood well by the functions I previously used and I was able to run my loop successfully with the [[var_sub]] as a variable-substitution method. However, now I want to do the same with TukeyHSD, and this function does not play nice with this kind of syntax. So if I do fac<-as.factor(dataset$factor) res<-aov(dataset$var~dataset$factor) tuk<-TukeyHSD(res,"fac") things work fine. But if I try (similar to the script below which worked for ROCR functions): fac<-as.factor(dataset$factor) var_sub<-noquotes("var") res<-aov(dataset[[var_sub]]~dataset$factor) tuk<-TukeyHSD(res,"fac") TukeyHSD craps out with an error, even though "res" is identical in both cases, apart from the formula syntax. So, TukeyHSD seems to be picky about syntax. Is there any other way I can do variable substitution (so I can read variable names from my list) and get this loop to work for TukeyHSD? Thanks Jon Friends First, thanks to all for great feed-back. Open-source rocks! I have a workable solution to my question, attached below in case it might be of any use to anyone. I'm sure there are more elegant ways of doing this, so any further feedback is welcome! Things I've learned (for other noobs like me to learn from): 1) dataset[[j]] seems equivalent to dataset$var if j<-var, though quotes can mess you up, hence j<-noquote(varlist[i]) in the script (it also makes a difference that variables in varlist be stored as a space-separated string. tab- or line-break-separated lists don't seem to work, though a different method might handle that) dataset[["var"]] is "equivalent" to dataset$var given var does not contain any special characters. Otherwise j == "var" has to be TRUE. 2) Loops will abort if they encounter an error (like ROCR encountering a prediction that is singular). Error handling can be built in, but is a little tricky. I reduplicated the method with a function to test and advance the loop on failure. You can suppress error messages if you like) Not tricky, just use try(). 3) Some stats methods don't have NA handling built into them (eg: "prediction" in ROCR chokes if there are empty cells in the variables) hence it seems a good idea to strip these out before starting. The subsetting with na.omit does this ... given you know what you are doing (and omitting). 4) You reference pieces (slots) of results (S3/S4 objects) by using obj...@slot. The @ operator is defined for slots of *S4* classes. Best, Uwe Ligges > Hence, you pull out the the auc value in ROCR-"performance" by p...@y.value > in the script. you can see what slots are in an object by simply listing the > object contents at the command line>object. Thanks again for all the help! Jon Soli Deo Gloria Jon Erik Ween, MD, MS Scientist, Kunin-Lunenfeld Applied Research Unit Director, Stroke Clinic, Brain Health Clinic, Baycrest Centre Assistant Professor, Dept. of Medicine, Div. of Neurology University of Toronto Faculty of Medicine ...code ################################################################################ ## R script for automating stats crunching in large datasets ## ## Needs space separated list of variable names matching dataset column names ## ## You have to tinker with the code to customize for your application ## ## ## ## Jon Erik Ween MD, MSc, 26 Feb 2010 ## ################################################################################ library(ROCR) # Load stats package to use if not standard varslist<-scan("/Users/jween/Desktop/INCASvars.txt","list") # Read variable list results<-as.data.frame(array(,c(3,length(varslist)))) # Initialize results array, one type of stat at a time for now for (i in 1:length(varslist)){ # Loop throught the variables you want to process. Determined by varslist j<-noquote(varslist[i]) vars<-c(varslist[i],"Issue_class") # Variables to be analyzed temp<-na.omit(incas[vars]) # Have to subset to get rid of NA values causing ROCR to choke n<-nrow(temp) # Record how many cases the analysis ios based on. Need to figure out how to calc cases/controls #.table<-table(temp$SubjClass) # Maybe for later figure out cases/controls results[1,i]<-j # Name particular results column results[2,i]<-n # Number of subjects in analysis test<-try(aucval(i,j),silent=TRUE) # Error handling in case procedure craps oust so loop can continue. Supress annoying error messages if(class(test)=="try-error") next else # Run procedure only if OK, otherwise skip pred<-prediction(incas[[j]],incas$Issue_class); # Procedure perf<-performance(pred,"auc"); results[3,i]<-as.numeric(p...@y.values) # Enter result into appropriate row } write.table(results,"/Users/jween/Desktop/IncasRres_ Issue_class.csv",sep=",",col.names=FALSE,row.names=FALSE) # Write results to table rm(aucval,i,n,temp,vars,results,test,pred,perf,j,varslist) # Clean up aucval<-function(i,j){ # Function to trap errors. Should be the same as real procedure above pred<-prediction(incas[[j]],incas$Issue_class) # Don't put any real results here, they don't seem to be passed back perf<-performance(pred,"auc") } [[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.