Hi Andy, I have used predict before and in fact when I do that to the train set I get a perfect model (i.e. ROC right angle curve in upper left quadrant) which just looks like it overfit the data. This is not the case with the test set were I get auc of .77.
I wanted to attempt a couple of calibration techniques I learned from Max Kuhn's Applied Predictive Modeling book. He uses a train set to do this. But with what I have now with the train set there is nothing to calibrate. That's why I thought I would use the original probabilities from the randomForest model that was used to create fm$predicted (fm is my randomForest model). I am still fairly new at predictive modeling and it could be the case that maybe I am not understanding something basic here. Thanks. Dan -----Original Message----- From: Liaw, Andy [mailto:andy_l...@merck.com] Sent: Monday, December 02, 2013 8:40 AM To: arun; R help; Lopez, Dan Subject: RE: [R] How do I extract Random Forest Terms and Probabilities? #2 can be done simply with predict(fmi, type="prob"). See the help page for predict.randomForest(). Best, Andy -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of arun Sent: Tuesday, November 26, 2013 6:57 PM To: R help Subject: Re: [R] How do I extract Random Forest Terms and Probabilities? Hi, For the first part, you could do: fmi2 <- fmi attributes(fmi2$terms) <- NULL capture.output(fmi2$terms) #[1] "Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width" A.k. On Tuesday, November 26, 2013 3:55 PM, "Lopez, Dan" <lopez...@llnl.gov> wrote: Hi R Experts, I need your help with two question regarding randomForest. 1. When I run a Random Forest model how do I extract the formula I used so that I can store it in a character vector in a dataframe? For example the dataframe might look like this if I am running models using the IRIS dataset #ModelID,Type, #001,RF,Species ~ Sepal.Length + Sepal.Width + Petal.Length + Petal.Width fmi<-randomForest(Species~.,iris,mtry=3,ntry=500) #I know one place where the information is in fmi$terms but not sure how to extract just the formula info. Or perhaps there is somewhere else in fmi that I could get this? 2. How do I get the probabilities (probability-like values) from the model that was run? I know for the test set I can use predict. And I know to extract the classifications from the model I use fmi$predicted. But where are the probabilities? Dan Workforce Analyst HRIM - Workforce Analytics & Metrics LLNL [[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-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. Notice: This e-mail message, together with any attachme...{{dropped:10}} ______________________________________________ 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.
