In the words of Simpson (2007), "D'OH!" I knew it had to be something simple!
On 4/29/07, Gavin Simpson <[EMAIL PROTECTED]> wrote: > > On Sat, 2007-04-28 at 21:13 -0400, David L. Van Brunt, Ph.D. wrote: > > 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 reproducibility > > No differences between runs for me on FC4 using R 2.4.1 and 2.5.0 with: > > > require(randomForest) > Loading required package: randomForest > randomForest 4.5-18 > > *if* I reset the seed before each call to randomForest. > > Your example code doesn't seem to be resetting the random seed before > each run. As such, each run is using a different set of random variables > at each bootstrap sample. > > E.g. runs all same with reset seed: > > > set.seed(12) > > randomForest(Species ~ ., data=iris) > > Call: > randomForest(formula = Species ~ ., data = iris) > Type of random forest: classification > Number of trees: 500 > No. of variables tried at each split: 2 > > OOB estimate of error rate: 4% > Confusion matrix: > setosa versicolor virginica class.error > setosa 50 0 0 0.00 > versicolor 0 47 3 0.06 > virginica 0 3 47 0.06 > > set.seed(12) > > randomForest(x=iris[,1:4],y=iris[,5]) > > Call: > randomForest(x = iris[, 1:4], y = iris[, 5]) > Type of random forest: classification > Number of trees: 500 > No. of variables tried at each split: 2 > > OOB estimate of error rate: 4% > Confusion matrix: > setosa versicolor virginica class.error > setosa 50 0 0 0.00 > versicolor 0 47 3 0.06 > virginica 0 3 47 0.06 > > set.seed(12) > > randomForest(x=iris[,c(1:4)],y=iris[,5]) > > Call: > randomForest(x = iris[, c(1:4)], y = iris[, 5]) > Type of random forest: classification > Number of trees: 500 > No. of variables tried at each split: 2 > > OOB estimate of error rate: 4% > Confusion matrix: > setosa versicolor virginica class.error > setosa 50 0 0 0.00 > versicolor 0 47 3 0.06 > virginica 0 3 47 0.06 > > set.seed(12) > > randomForest(x=iris[,c(1,2,3,4)],y=iris[,5]) > > Call: > randomForest(x = iris[, c(1, 2, 3, 4)], y = iris[, 5]) > Type of random forest: classification > Number of trees: 500 > No. of variables tried at each split: 2 > > OOB estimate of error rate: 4% > Confusion matrix: > setosa versicolor virginica class.error > setosa 50 0 0 0.00 > versicolor 0 47 3 0.06 > virginica 0 3 47 0.06 > > HTH > > G > -- > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > Gavin Simpson [t] +44 (0)20 7679 0522 > ECRC [f] +44 (0)20 7679 0565 > UCL Department of Geography > Pearson Building [e] gavin.simpsonATNOSPAMucl.ac.uk > Gower Street > London, UK [w] http://www.ucl.ac.uk/~ucfagls/ > WC1E 6BT [w] http://www.freshwaters.org.uk/ > %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% > > -- --------------------------------------- David L. Van Brunt, Ph.D. mailto:[EMAIL PROTECTED] "If Tyranny and Oppression come to this land, it will be in the guise of fighting a foreign enemy." --James Madison [[alternative HTML version deleted]] ______________________________________________ R-help@stat.math.ethz.ch 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.
