Yes, that's part of the intention anyway. One can also use them to do clustering.
Best, Andy -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Massimo Bressan Sent: Monday, December 02, 2013 6:34 AM To: r-help@r-project.org Subject: [R] interpretation of MDS plot in random forest Given this general example: set.seed(1) data(iris) iris.rf <- randomForest(Species ~ ., iris, proximity=TRUE, keep.forest=TRUE) #varImpPlot(iris.rf) #varUsed(iris.rf) MDSplot(iris.rf, iris$Species) I’ve been reading the documentation about random forest (at best of my - poor - knowledge) but I’m in trouble with the correct interpretation of the MDS plot and I hope someone can give me some clues What is intended for “the scaling coordinates of the proximity matrix”? I think to understand that the objective is here to present the distance among species in a parsimonious and visual way (of lower dimensionality) Is therefore a parallelism to what are intended the principal components in a classical PCA? Are the scaling coordinates DIM 1 and DIM2 the eigenvectors of the proximity matrix? If that is correct, how would you find the eigenvalues for that eigenvectors? And what are the eigenvalues repreenting? What are saying these two dimensions in the plot about the different iris species? Their relative distance in terms of proximity within the space DIM1 and DIM2? How to choose for the k parameter (number of dimensions for the scaling coordinates)? And finally how would you explain the plot in simple terms? Thank you for any feedback Best regards ______________________________________________ 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 attachments, contains information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, New Jersey, USA 08889), and/or its affiliates Direct contact information for affiliates is available at http://www.merck.com/contact/contacts.html) that may be confidential, proprietary copyrighted and/or legally privileged. It is intended solely for the use of the individual or entity named on this message. If you are not the intended recipient, and have received this message in error, please notify us immediately by reply e-mail and then delete it from your system. ______________________________________________ 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.
