No. Tree-based methods are invariant to monotone transformations in the predictors, because they only use ranks. Rotation can matter, though. Andy
-----Original Message----- From: Michael [mailto:[EMAIL PROTECTED] Sent: Friday, March 10, 2006 8:11 PM To: Liaw, Andy Cc: [email protected] Subject: Re: [R] how to use the randomForest and rpart function? Thanks a lot Andy, Do I need to have centering and scaling before sending data into rpart and randomForest? I knew for LDA and QDA, it does not matter... And for ridge, it matters; Thanks a lot! Michael. On 3/8/06, Liaw, Andy <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > wrote: The algorithm has something slicker than cross-validation. That's the whole OOB business mentioned in the R News article. The number of trees isn't really a parameter, as it doesn't hurt to have `too many trees' (other than wasting computing resources). Some people routinely run more than 10,000 trees just to make sure. Some times mtry does matter (though that's more of an exception than the rule). I can find pathological cases where mtry=1 is the best, or mtry=number of covariates (bagging) is best, but when given a real data, one almost never have any idea. Andy -----Original Message----- From: Michael [mailto:[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> ] Sent: Wednesday, March 08, 2006 8:22 PM To: Liaw, Andy Cc: [email protected] <mailto:[email protected]> Subject: Re: [R] how to use the randomForest and rpart function? Hi Andy, Does the randomForest have a Cross Validation built-in to decide what is the best number of trees or I have to find the best number manually by myself? Thanks a lot! Michael. On 3/7/06, Liaw, Andy <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > wrote: Yes, I do know. That's why I pointed you to the reference linked from the help page. BTW, there's also an R News article describing the initial version of the package. Have you perused that? Andy -----Original Message----- From: Michael [mailto: <mailto:[EMAIL PROTECTED]> [EMAIL PROTECTED] Sent: Tuesday, March 07, 2006 9:27 PM To: Liaw, Andy Cc: [email protected] <mailto:[email protected]> Subject: Re: [R] how to use the randomForest and rpart function? It did not have a legend showing on which color is for class1, which color is for class2, etc... I've read the R-help page. It lists a lot of options, but it did not say which ones are the key parameters that people use most for improving performance... Do you know? On 3/7/06, Liaw, Andy <[EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > wrote: As ?plot.randomForest says, it plots error rates. In addition to overall error rates, it also plots error rates for each class. As to the options in randomForest, read about the options in the help page and the reference linked from the help page. Andy From: Michael > > When I plot the randomForest object, it shows a graph with 3 > lines, green, red and black, what's the meaning of these three lines? > > On 3/7/06, Michael < [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> > wrote: > > > > Hi all, > > > > I am trying to play around with the randomForest function for > > classification. I know its performance is great. > > > > I am currently using the default options. > > > > It has many options. > > > > How do I further tweak the options so that I can make its > performance > > even better? > > > > What are the options that are mostly used? > > > > Thanks a lot! > > > > M > > > > [[alternative HTML version deleted]] > > ______________________________________________ > [email protected] <mailto:[email protected]> mailing list > https://stat.ethz.ch/mailman/listinfo/r-help <https://stat.ethz.ch/mailman/listinfo/r-help> > PLEASE do read the posting guide! > http://www.R-project.org/posting-guide.html <http://www.r-project.org/posting-guide.html> > > ---------------------------------------------------------------------------- -- Notice: This e-mail message, together with any attachments, contains information of Merck & Co., Inc. 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