search for: mdsplot

...atrix is approximately 133000 by 133000 which is quite large. To train a random forest on this large a dataset I have to use my institutions high performance computer. Using this setup I was able to train a randomForest with the proximity argument set to TRUE. At this point I wanted to construct an MDSplot using the following: MDSplot(nech.rf, nech.d$pd.fl, palette=c(1,2,3), pch=as.numeric(nech.d$pd.fl)) where "nech.rf" is the randomForest object and "nech.d$pd.fl" is the classification factor. Now with the architecture listed below, I've been waiting for approximately 2 day...

I am using randomForest to classify (relapse vs non-relapse) patients. I have built a forest using a training data and now want to predict classes in a test dataset. Instead of using the resulting randomForest object. I was wondering if there is a way to use the MDSplot. From looking at the MDS plot it seems like I could draw some lines through the plot to define 'high risk', 'intermediate' and 'low risk' groups with higher accuracy than what can be achieved with the forest itself. I have two questions: 1) Is this approach advisable? 2) Ho...

...t a plot with a straight line (a completely flat response). Similarly, If I set a categorical variable as predictor, I get a barplot with all the bar with the same height. I suppose I'm doing something wrong here because all other analysis on the same rforest object seem correct (e.g. varImp or MDSplot). Is it possible it is related to some option set in random forest object? Can somebody see the problem here? Thanks for your time -- View this message in context: http://r.789695.n4.nabble.com/Partial-dependence-plot-in-randomForest-package-all-flat-responses-tp4650470.html Sent from the R help...

Hi, i try several possibilities adn looking in the archive, but didn't getting success to install j.lindsey's usefuel "library repeated" on my linux (suse9.0 with kernel 2.6.7,R.1.9.1) P.S. Windows, works fine Many thanks for help Christian chris at linux:/space/downs> R CMD INSTALL - l /usr/lib/R/library repeated WARNING: invalid package '-' WARNING:

...02+ X203+ X205+ X206+ X209+ X210+ X225+ X269+ X283+ X290+ X432+ X434+ X455+ X467+ X512, data=dat1, importance=TRUE, + proximity=TRUE, varUsed=TRUE, ntree=5000, varImpPlot=TRUE) > > > print(dat1.rf) > varImpPlot(dat1.rf) > > varUsed(dat1.rf, by.tree=FALSE, count=TRUE) > > MDSplot(dat1.rf, dat1$SR, palette=rep(1, 2), + pch=as.numeric(dat1$SR)) > > > path3 <- "C:\\Users..." > path4 <- "..." > name2 <- "..." > > # reading in the test dataset > actualFileName2 <- paste(path3, path4, name2, ".txt", sep...

Hello, supposing that I have two or three clear categories for my data, lets say pet preferece across fish, cat, dog. Lets say most people rate their preference as being mostly one of the categories. I want to do pca on the data to see three 'groups' of people, one group for fish, one for cat and one for dog. I would like to see the odd person who likes both or all three in the