Re: [R] Trying to extract probabilities in CARET (caret) package with a glmStepAIC model
I corrected some of my syntax and changed the the glmStepAIC for glm and ti worked. I tried my command lines with the mdrr dataset (after doing the first cleaning steps as referred in the manual), the only difference is that I only took first two columns because it took too much time with one variable and I got the same resutls: "undefined columns selected". Here are the command lines: fitControlAUC <- trainControl(method = "cv", number = 10, classProbs = TRUE, summaryFunction = twoClassSummary, returnResamp = "all", verboseIter = FALSE) glmROCLum1 <- train(trainDescr[,(1:4)], trainMDRR, method = "glmStepAIC", tuneLength = 4, metric = "ROC", trControl = fitControlAUC) So I used glmStepAIC to find the right model and the to obtain the ROC results I used the glm method using the variables select by glmStepAIC. Thank you very much for your package help and interest. Best regards, J Toledo Here is my previous session Info R version 2.13.0 (2011-04-13)Platform: i386-pc-mingw32/i386 (32-bit) locale:[1] LC_COLLATE=Spanish_United States.1252 LC_CTYPE=Spanish_United States.1252 [3] LC_MONETARY=Spanish_United States.1252 LC_NUMERIC=C [5] LC_TIME=Spanish_United States.1252 attached base packages:[1] splines tcltk stats graphics grDevices utils datasets methods base other attached packages: [1] e1071_1.5-26class_7.3-3 caret_4.98 cluster_1.14.0 reshape_0.8.4 plyr_1.5.2 [7] lattice_0.19-26 Rcmdr_1.6-4 car_2.0-10 foreign_0.8-44 survival_2.36-9 nnet_7.3-1 [13] MASS_7.3-13 loaded via a namespace (and not attached):[1] grid_2.13.0 > Date: Sun, 28 Aug 2011 13:23:24 -0400 > Subject: Re: [R] Trying to extract probabilities in CARET (caret) package > with a glmStepAIC model > From: mxk...@gmail.com > To: tintin...@hotmail.com > CC: r-help@r-project.org > > Can you provide a reproducible example and the results of > sessionInfo()? What are the levels of your classes? > [[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.
Re: [R] Trying to extract probabilities in CARET (caret) package with a glmStepAIC model
Can you provide a reproducible example and the results of sessionInfo()? What are the levels of your classes? On Sat, Aug 27, 2011 at 10:43 PM, Jon Toledo wrote: > > Dear developers, > I have jutst started working with caret and all the nice features it offers. > But I just encountered a problem: > I am working with a dataset that include 4 predictor variables in Descr and a > two-category outcome in Categ (codified as a factor). > Everything was working fine I got the results, confussion matrix etc. > BUT for obtaining the AUC and predicted probabilities I had to add " > classProbs = TRUE," in the trainControl. Thereafter everytime I run train I > get this message: > "undefined columns selected" > > I copy the syntax: > fitControl <- trainControl(method = "cv", number = 10, classProbs = > TRUE,returnResamp = "all", verboseIter = FALSE) > glmFit <- train(Descr, Categ, method = "glmStepAIC",tuneLength = 4,trControl > = fitControl) > Thank you. > Best regards, > > Jon Toledo, MD > > Postdoctoral fellow > University of Pennsylvania School of Medicine > Center for Neurodegenerative Disease Research > 3600 Spruce Street > 3rd Floor Maloney Building > Philadelphia, Pa 19104 > > [[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. > -- Max __ 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.
[R] Trying to extract probabilities in CARET (caret) package with a glmStepAIC model
Dear developers, I have jutst started working with caret and all the nice features it offers. But I just encountered a problem: I am working with a dataset that include 4 predictor variables in Descr and a two-category outcome in Categ (codified as a factor). Everything was working fine I got the results, confussion matrix etc. BUT for obtaining the AUC and predicted probabilities I had to add " classProbs = TRUE," in the trainControl. Thereafter everytime I run train I get this message: "undefined columns selected" I copy the syntax: fitControl <- trainControl(method = "cv", number = 10, classProbs = TRUE,returnResamp = "all", verboseIter = FALSE) glmFit <- train(Descr, Categ, method = "glmStepAIC",tuneLength = 4,trControl = fitControl) Thank you. Best regards, Jon Toledo, MD Postdoctoral fellow University of Pennsylvania School of Medicine Center for Neurodegenerative Disease Research 3600 Spruce Street 3rd Floor Maloney Building Philadelphia, Pa 19104 [[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.
