randomForest predictions are based on votes of individual trees, thus have little to do with error rates of individual trees.
Andy > -----Original Message----- > From: [EMAIL PROTECTED] > [mailto:[EMAIL PROTECTED] On Behalf Of Miklos Kiss > Sent: Saturday, July 19, 2008 10:47 PM > To: r-help@r-project.org > Subject: [R] confusion matrix in randomForest > > > I have a question on the output generated by randomForest in > classification > mode, specifically, the confusion matrix. The confusion > matrix lists the > various classes and how the forest classified each one, plus the > classification error. Are these numbers essentially averages > over all the > trees in the forest? If so, is there a way I can get the > standard deviation > values out of the randomForest, or do I have to evaluate each tree > individually? By way of illustration, let me show the > confusion matrix > using the iris data. The output below shows that the forest correctly > classified 47 versicolor irises, but this is the result for the entire > forest. I'd like to know if every tree will have 47 > correctly classified > versicolor irises, but I don't think it will. Same for the > class.error > value. Not every tree will have those exact same values, right? > > But this raises another question. For this example, I used > the entire data > set to generate the forest, and so I assume that the > confusion matrix is > based on OOB data, so if I created a training set and evaluated trees > individually in the test set I could get averages and > standard deviations on > the error rate. > > Any thoughts? Thanks in advance. > > -Miklos Z. Kiss > > > print(iris.rf) > Call: > randomForest(formula = Species ~ ., data = iris, importance > = TRUE, > keep.forest = TRUE) > Type of random forest: classification > Number of trees: 500 > No. of variables tried at each split: 2 > > OOB estimate of error rate: 5.33% > Confusion matrix: > setosa versicolor virginica class.error > setosa 50 0 0 0.00 > versicolor 0 47 3 0.06 > virginica 0 5 45 0.10 > -- > View this message in context: > http://www.nabble.com/confusion-matrix-in-randomForest-tp18550 873p18550873.html > Sent from the R help mailing list archive at Nabble.com. > > ______________________________________________ > 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:12}} ______________________________________________ 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.