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 tintin...@hotmail.com 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.
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.
[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.
