search for: rfimpute

I am having trouble with the rfImpute function in the randomForest package. Here is a sample... clunk.roughfix<-na.roughfix(clunk) > > clunk.impute<-rfImpute(CONVERT~.,data=clunk) ntree OOB 1 2 300: 26.80% 3.83% 85.37% ntree OOB 1 2 300: 18.56% 5.74% 51.22% Error in randomForest.defaul...

In trying to execute this line in R (Version 1.7.1 (2003-06-16), under windows XP pro), with the randomForest library (about two weeks old) loaded, the program crashed: bost4rf <- rfImpute(TargetDensity~.,data=bost4rf0) Specifically, an XP dialog box popped up, saying ?R for windows GUI front-end has encountered a problem and needs to close.? That was the dialog saying asking whether I wanted to send a report to Microsoft (which I chose not to do). When I clicked on ?To see what d...

Dear Administrator, I am using linux (suse 10.2). While attempting rfImpute, I am getting the following error message: > Members <- rfImpute(Status ~ ., data = Members) Error in .C("classRF", x = x, xdim = as.integer(c(p, n)), y = as.integer(y), : C symbol name "classRF" not in DLL for package "randomForest". I need the help to sor...

Hello everybody, this is my first request about R so I am sorry if I send it to a bad mail or if I am not very clear. So my problem is about the use of rfImpute from randomForest package. I am interested in imputations of missing values and I read that randomForest can make it. So i write the following code : set.seed(100); library(mlbench) library(randomForest) data(BreastCancer) summary(BreastCancer) data=BreastCancer[,-1] data=data[!is.na(data[,"B...

Hello R-user! I am running R 2.7.0 on a Power Book (Tiger). (I am still R and statistics beginner) I tried rfImpute (randomForest) and as far as I understood should it replace NA`s using a proximity matrix: > set.seed(100000) > Subset5Imputed<-rfImpute(Sex~., data=Subset5) ntree OOB 1 2 300: 11.78% 12.36% 11.21% ntree OOB 1 2 300: 12.07% 12.64% 11.49% ntree OOB...

Hi, In R, how to do missing value replacement for test data in randome forest in the way Breiman decribed. thanks in advance iris

Does anyone know a reason why, in principle, a call to randomForest cannot accept a data frame with missing predictor values? If each individual tree is built using CART, then it seems like this should be possible. (I understand that one may impute missing values using rfImpute or some other method, but I would like to avoid doing that.) If this functionality were available, then when the trees are being constructed and when subsequent data are put through the forest, one would also specify an argument for the use of surrogate rules, just like in rpart. I realize this...

...y. But I hesitate to duplicate a function that is already in the package, since I presume the na.roughfix should be as quick as possible and it should also be well "tailored" to the requirements of random forest. Has anyone else seen that this is really slow? (I haven't noticed rfImpute to be nearly as slow, but I cannot say for sure: my "predict" data sets are MUCH larger than my model data sets, so cleaning the prediction data set simply takes much longer.) If so, any ideas how to speed this up? Thanks!...

...ith na.omit in randomForest -- that wipes out any row with even one NA. If NAs are sprawled throughout your dataset, na.omit might end up killing a lot of rows. Here's my usual MO for missing values: 1) "impute" in Hmisc fills in gaps with the mean, median, most common value, etc. 2) rfImpute: fits a forest on the rows available and uses it to predict the missing values. 3) aregImpute: similar to rfImpute, but using a linear model. 4) You may want to consider using a single tree ("rpart" package) in this case instead of a forest. Single trees deal with missing values cleanly t...

I have a question regarding NA in randomForest (in R). I have a dataset which include both numerical and non-numerical variables, and the data includes some NA. I tried to use na.roughfix but then i get an error message "na.roughfix only works for numeric or factor". I also tried rfImpute but this does not work either because I have some NA in my response variable. Does anyone have som tips to how I can deal with this? [[alternative HTML version deleted]]

...> > Does anyone know a reason why, in principle, a call to randomForest > cannot accept a data frame with missing predictor values? If each > individual tree is built using CART, then it seems like this > should be possible. (I understand that one may impute missing values > using rfImpute or some other method, but I would like to avoid doing > that.) > > If this functionality were available, then when the trees are being > constructed and when subsequent data are put through the forest, one > would also specify an argument for the use of surrogate rules, just > lik...

So I have a very big matrix of about 900 by 400 and there are a couple of NA in the list. I have used the following functions to impute the missing data data(pc) pc.na<-pc pc.roughfix <- na.roughfix(pc.na) pc.narf <- randomForest(pc.na, na.action=na.roughfix) yet it does not replace the NA in the list. Presently I want to replace the NA with maybe the mean of the rows or columns or

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:

Dear All, I would like to use a randomForest algorithm on a dataset. The set is not particularly large/difficult to handle, but it has some missing values (both factors and numerical values). According to what I found https://stat.ethz.ch/pipermail/r-help/2005-September/078880.html https://stat.ethz.ch/pipermail/r-help/2007-January/123117.html the randomForest package has a problem with missing

...r extracting the importance measure. o The predict() method has an option to return predictions by the component trees. o There is a new getTree() function for looking at one of the trees in the forest. o For dealing with missing values in the predictor variables, there are na.roughfix() and rfImpute(), which correspond to the `missquick' and `missright' options in Breiman's V4/V5 code. Both works for classification as well as regression. o There is an experimental bias reduction step in regression (the corr.bias argument in randomForest) that could be very effective for some dat...

...r extracting the importance measure. o The predict() method has an option to return predictions by the component trees. o There is a new getTree() function for looking at one of the trees in the forest. o For dealing with missing values in the predictor variables, there are na.roughfix() and rfImpute(), which correspond to the `missquick' and `missright' options in Breiman's V4/V5 code. Both works for classification as well as regression. o There is an experimental bias reduction step in regression (the corr.bias argument in randomForest) that could be very effective for some dat...

A few days ago I asked whether there were options other than na.action=na.fail for the R port of Breiman?s randomForest; the function?s help page did not say anything about other options. I have since discovered that a pdf document called ?The randomForest Package? and made available by Andy Liaw (who made the tool available in R---thank you) does discuss an option. It is an implementation of

...n by n array of integers is erroneously allocated but not used (it's only used for proximity calculation, so not needed otherwise). * Updated combine() to conform to the new randomForest object. * na.roughfix() was not working correctly for matrices, which in turns causes problem in rfImpute(). Changes in 4.1-0: * In randomForest(), if sampsize is given, the sampling is now done without replacement, in addition to stratified by class. Therefore sampsize can not be larger than the class frequencies. * In classification randomForest, checks are added to avoid trees with onl...

...n by n array of integers is erroneously allocated but not used (it's only used for proximity calculation, so not needed otherwise). * Updated combine() to conform to the new randomForest object. * na.roughfix() was not working correctly for matrices, which in turns causes problem in rfImpute(). Changes in 4.1-0: * In randomForest(), if sampsize is given, the sampling is now done without replacement, in addition to stratified by class. Therefore sampsize can not be larger than the class frequencies. * In classification randomForest, checks are added to avoid trees with onl...

Dear all, Can anybody give me some hint on the following error msg I got with using randomForest? I have two-class classification problem. The data file "sample" is: ---------------------------------------------------------- udomain.edu udomain.hcs hpclass 1 1.0000 1 not 2 NA 2 not 3 NA 0.8 not 4 NA 0.2 hp 5 NA 0.9 hp ------------------------------------------------------------ The