similar to: Extracting the MSE and % Variance from RandomForest

When you have fairly large data, _do not use the formula interface_, as a couple of copies of the data would be made. Try simply: Myforest.rf <- randomForest(Mydata[, -46], Mydata[,46], ntrees=100, mtry=7) [Note that you don't need to set proximity (not proximities) or importance to FALSE, as that's the default already.] You might also want to use

Alternatively, if you can arrive at a sensible ordering of the levels you can declare them ordered factors and make the computation feasible once again. Bill Venables. -----Original Message----- From: r-help-bounces at stat.math.ethz.ch [mailto:r-help-bounces at stat.math.ethz.ch] On Behalf Of Torsten Hothorn Sent: Monday, 5 April 2004 4:27 PM To: David L. Van Brunt, Ph.D. Cc: R-Help Subject:

Dear Random Forests gurus, I have a question about R^2 provided by randomForest (for regression). I don't succeed in finding this information. In the help file for randomForest under "Value" it says: rsq: (regression only) - "pseudo R-squared'': 1 - mse / Var(y). Could someone please explain in somewhat more detail how exactly R^2 is calculated? Is "mse"

"classwt" in the current version of the randomForest package doesn't work too well. (It's what was in version 3.x of the original Fortran code by Breiman and Cutler, not the one in the new Fortran code.) I'd advise against using it. "sampsize" and "strata" can be use in conjunction. If "strata" is not specified, the class labels will be used.

I've run the function randomForest with importance=T. All my variables (predictors and the dependent variable) are numeric. rf<-randomForest(formula, data=mydata, importance=T, etc.) my results object "rf" contains predictor importances: rf$importance I am seeing two columns: %IncMSE IncNodePurity V1 -0.01683558 58.10910 V2 0.04000299 71.27579 V3 0.01974636

Sorry for the repost, but I've really been looking, and can't find any syntax direction on this issue... Just browsing the documentation, and searching the list came up short... I have some unbalanced data and was wondering if, in a "0" v "1" classification forest, some combo of these options might yield better predictions when the proportion of one class is low (less

Just out of curiosity, I took the default "iris" example in the RF helpfile... but seeing the admonition against using the formula interface for large data sets, I wanted to play around a bit to see how the various options affected the output. Found something interesting I couldn't find documentation for... Just like the example... > set.seed(12) # to be sure I have

Andy; Well, that about does it.... I'm copying this one back to the list for the benefit of those who may hit this thread while searching the archives. Your changes to the code run just fine on the my Windows machine, but gives the vector length error on the G4 whether I'm using the OS X build of R (as in Raqua) or the X11 build (for Darwin). It is worth noting that I have nearly twice

I?ve been using Frank Harrell?s rms package to do bootstrap model validation. Is it the case that the optimum penalization may still give a model which is substantially overfitted? I calculated corrected R^2, optimism in R^2, and corrected slope for various penalties for a simple example: x1 <- rnorm(45) x2 <- rnorm(45) x3 <- rnorm(45) y <- x1 + 2*x2 + rnorm(45,0,3) ols0 <- ols(y

Full_Name: David L. Van Brunt Version: 1.8-1.9 beta OS: OS X 10.3 Submission from: (NULL) (68.74.58.109) As posted on R-Help (after which another user replicated the problem): --------------- This is the conclusion from a prior thread ([R] " cannot allocate vector of length 1072693248") which ended with no other answer but that there must be a problem in the OS X version of R, or in

Dear Researches, I am using RF (in regression way) for analize several metrics extract from image. I am tuning RF setting a loop using different range of mtry, tree and nodesize using the lower value of MSE-OOB mtry from 1 to 5 nodesize from1 to 10 tree from 1 to 500 using this paper as refery Palmer, D. S., O'Boyle, N. M., Glen, R. C., & Mitchell, J. B. O. (2007). Random Forest Models

I have a question about predictor importances in randomForest. Once I've run randomForest and got my object, I get their importances: rfresult$importance I also get the "standard errors" of the permutation-based importance measure: rfresult$importanceSD I have 2 questions: 1. Because I am dealing with regressions, I am getting an importance object (rfresult$importance) with two

Sir, This query is related to randomForest regression using R. I have a dataset called qsar.arff which I use as my training set and then I run the following function - rf=randomForest(x=train,y=trainy,xtest=train,ytest=trainy,ntree=500) where train is a matrix of predictors without the column to be predicted(the target column), trainy is the target column.I feed the same data

All -- I have been trying to work with the 'Party' package using R v2.15.1 and have cobbled together a (somewhat) functioning code from examples on the web. I need to run a series of unbiased, conditional, cForest tests on several subsets of data which I have made into a loop. The results ideally will be saved to an output file in matrix form. The two questions regarding the script in

Hi everyone, I have another "Random Forest" package question: - my (presumably incorrect) understanding of the varImpPlot is that it should plot the "% increase in MSE" and "IncNodePurity" exactly as can be found from the "importance" section of the model results. - However, the plot does not, in fact, match the "importance"

Hi all, When running a randomForest run using the following command: forestplas=randomForest(Prev~.,data=plas,ntree=200000) print(forestplas) I get the following result: Call: randomForest(formula = Prev ~ ., data = plas, ntree = 2e+05, importance = TRUE) Type of random forest: regression Number of trees: 2e+05 No. of variables tried at each split: 5

I have been using random forest on a data set with 226 sites and 36 explanatory variables (continuous and categorical). When I use "tune.randomforest" to determine the best value to use in "mtry" there is a fairly consistent and steady decrease in MSE, with the optimum of "mtry" usually equal to 1. Why would that occur, and what does it signify? What I would

I am combining many different random forest objects run on the same data set using the combine ( ) function. After combining the forests I am not sure whether the variable importance, local importance, and rsq predictors are recalculated for the new random forest object or are calculated individually for each tree ensemble? Is it possible to calculate these predictors for the new random forest

Dear R-users, While making a prediction using the randomForest function (package randomForest) I'm getting the following error message: "Error in predict.randomForest(model, newdata = CV) : No forest component in the object" Here's my complete code. For reproducing this task, please find my 2 data sets attached ( http://www.nabble.com/file/p17855119/data.rar data.rar ).

Dear R users: I have been trying to figure out how to include string variables in a for loop to run multiple random forests with little success. The current code returns the following error: Error in trafo(data = data, numeric_trafo = numeric_trafo, factor_trafo = factor_trafo, : data class character is not supported In addition: Warning message: In storage.mode(RET@predict_trafo) <-