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...nction get the message "predictors.gbm: no visible binding for global variable 'rel.inf'" predictors.gbm <- function(x, ...) { library(gbm) varList <- if(hasTerms(x)) predictors(x$terms) else colnames(x$data$x.order) relImp <- summary(x, plotit = FALSE) varUsed <- as.character(subset(relImp, rel.inf != 0)$var) basicVars(varList, varUsed) } So it didn't take the context into account that subset isn't (necessarily) looking in the global environment. Also, the package has a file splsda.R that has the message "splsda.default: no visi...

...1$SR <- as.factor(dat1$SR) > > > > dat1.rf <-randomForest(SR ~ X13+ X52+ X53+ X64+ X85+ X99+ X111+ > X142+ X157+ X158+ X162+ X169+ X200+ + X202+ 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 <...

Hello, I am a phd student in Bioinformatics and I am using the Random Forest package in order to classify my data, but I have some questions. Is there a function in order to visualize the trees, so as to get the rules? Also, could you please provide me with the code of "randomForest" function, as I would like to see how it works. I was wondering if I can get the classification having

...ta can now be calculated using the new function interaction.rsf(). This represents a third mode of operation for the application, and follows rsf.default (GROW) and predict.rsf (PREDICT). See the documentation for details. o An additional option in GROW mode can now be specified. The option 'varUsed' allows users to quantify which variables have been split upon within a single tree or over the entire forest. See the documentation for more details. o The ability to multiply impute data has been implemented. This involves imputing data while growing a forest and using the results to gro...

...ta can now be calculated using the new function interaction.rsf(). This represents a third mode of operation for the application, and follows rsf.default (GROW) and predict.rsf (PREDICT). See the documentation for details. o An additional option in GROW mode can now be specified. The option 'varUsed' allows users to quantify which variables have been split upon within a single tree or over the entire forest. See the documentation for more details. o The ability to multiply impute data has been implemented. This involves imputing data while growing a forest and using the results to gro...

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:

...y ntree matrix of terminal node indicators. This is ignored for regression. Changes in 4.2-1: * There is now a package name space. Only generics are exported. * Some function names have been changed: partial.plot -> partialPlot var.imp.plot -> varImpPlot var.used -> varUsed * There is a new option `replace' in randomForest() (default to TRUE) indicating whether the sampling of cases is with or without replacement. * In randomForest(), the `sampsize' option now works for both classification and regression, and indicate the number of cases to be dr...

...y ntree matrix of terminal node indicators. This is ignored for regression. Changes in 4.2-1: * There is now a package name space. Only generics are exported. * Some function names have been changed: partial.plot -> partialPlot var.imp.plot -> varImpPlot var.used -> varUsed * There is a new option `replace' in randomForest() (default to TRUE) indicating whether the sampling of cases is with or without replacement. * In randomForest(), the `sampsize' option now works for both classification and regression, and indicate the number of cases to be dr...