similar to: 10-Fold Cross Validation AND Random Forest

Dear all, Does anybody can explain this: different results got when all the same parameters are used in the errorest() in library ipred, as the following? errorest(Species ~ ., data=iris, model=randomForest, estimator = "cv", est.para=control.errorest(k=3), mtry=2)$err [1] 0.03333333 > errorest(Species ~ ., data=iris, model=randomForest, estimator = "cv",

Hello! I'm Taeho, a graduate student in South Korea. In order to get .632+ bootstrap error using random forest, I have tried to use 'ipred' package; more specifically the function 'errorest' has been used. Following the guidelines, I made a simple command line like below: error<-errorest(class ~ ., data=data, model=randomForest, estimator = "632plus")$err

This post is NOT a question, but an answer. For readers please disregard all earlier posts by myself about this question. I'm posting for two reasons. First to say thanks, especially to Dimitris, for suggesting the use of errorest in the ipred library. Second, so that the solution to this problem is in the archives in case it gets asked again. If one wants to run a k-fold cross-validation

Greetings, I am having trouble calculating artificial neural network misclassification errors using errorest() from the ipred package. I have had no problems estimating the values with randomForest() or svm(), but can't seem to get it to work with nnet(). I believe this is due to the output of the predict.nnet() function within cv.factor(). Below is a quick example of the problem I'm

Dear List, I have a question regarding "ipred" package. Under 10-fold cv, for different knn ( = 1,3,...25), I am getting same misclassification errors: ############################################# library(ipred) data(iris) cv.k = 10 ## 10-fold cross-validation bwpredict.knn <- function(object, newdata) predict.ipredknn(object, newdata, type="class") for (i in

Dear all, Can I get the leave-one-out cross validation error of randomForest in R? I only found tune(), which got the 10-fold cross validation error. Thanks for any information. Xin LIU This e-mail is from ArraDx Ltd The e-mail and any files transmitted with it are confidentia...{{dropped}}

Hi, I am using errorest function from ipred package. I am hoping to perform "bootstrap 0.632+" and "bootstrap leave one out". According to the manual page for errorest, i use the following command: ce632[i]<-errorest(ytrain ~., data=mydata, model=lda, estimator=c("boot","632plus"), predict=mypredict.lda)$error It didn't work. I then tried the

Full_Name: Noel O'Boyle Version: 2.1.0 OS: Debian GNU/Linux Sarge Submission from: (NULL) (131.111.8.96) (1) Description of error The 10-fold CV option for the svm function in e1071 appears to give incorrect results for the rmse. The example code in (3) uses the example regression data in the svm documentation. The rmse for internal prediction is 0.24. It is expected the 10-fold CV rmse

1. This is _not_ a bug in R itself. Please don't use R's bug reporting system for contributed packages. 2. This is _not_ a bug in svm() in `e1071'. I believe you forgot to take sqrt. 3. You really should use the `tot.MSE' component rather than the mean of the `MSE' component, but this is only a very small difference. So, instead of spread[i] <- mean(mysvm$MSE), you

Hello all, I have become somewhat confused with options available for dealing with a highly unbalanced data set (10000 in one class, 50 in the other). As a summary I am unsure: a) if I am perform the two class weighting methods properly, b) if the data are too unbalanced and that this type of analysis is appropriate and c) if there is any interaction between the weighting for class imbalances

Dear all, can anybody help me with the program below? The function predict.lda seems to be defined but cannot be used by errortest. The R version is 1.7.1 Thanks in advance, Stefan ---------------- library("MASS"); library("ipred"); data(iris3); tr <- sample(1:50, 25); train <- rbind(iris3[tr,,1], iris3[tr,,2], iris3[tr,,3]); test <- rbind(iris3[-tr,,1],

Dear R-users, I'd like to estimate standard errors (for lda) and make a boxplot with the "632plus" and "boot" error estimators included in package ipred (method: errorest). The "boot" estimator returns only a standard deviation but not the whole error data. Thank you in advance, regards, Antoine

Hi All, I am looking for a reference that explains how the randomForest function in the randomForest package uses the classwt parameter. Here: http://tolstoy.newcastle.edu.au/R/e4/help/08/05/12088.html Andy Liaw suggests not using classwt. And according to: http://r.789695.n4.nabble.com/R-help-with-RandomForest-classwt-option-td817149.html it has "not been implemented" as of 2007.

Hello, I am using the R randomForest package to classify variable stars. I have a training set of 1755 stars described by (too) many variables. Some of these variables are highly correlated. I believe that I understand how randomForest works and how the variable importance are evaluated (through variable permutations). Here are my questions. 1) variable importance error? Is there any ways

Dear all, I have the following data set. V1 V2 V3 V4 V5 V6 V7 V8 V9 V10 alpha beta 1 11 1 11 1 11 1 11 1 11 alpha beta1 2 12 2 12 2 12 2 12 2 12 alpha beta1 3 13 3 13 3 13 3 13 3 13 alpha beta1 4 14 4 14 4 14 4 14 4 14 alpha beta1 5 15 5 15 5 15 5 15 5

Hi, I have been using some code for multivariate random forests. The output from this code is a list object with all the same values as from randomForest, but the model object is, of course, not of the class randomForest. So, I was hoping to modify the code for predict.randomForest to work for predicting the multivariate model to new data. This is my first attempt at modifying code from a

Didn't realize the message was cc'ed to R-help. Here's my reply... ________________________________ From: Liaw, Andy Sent: Thursday, June 18, 2009 11:35 AM To: 'Li GUO' Subject: RE: Can I estimate strength and correlation of Random Forest in R package " randomForest"? The strength and correlation among trees in a random forest are based on the predictions of

Hi, Can someone please offer me some guidance? I imported some data. One of the columns called "JOBTITLE" when imported was imported as a factor column with 416 levels. I subset the data in such a way that only 4 levels have data in "JOBTITLE" and tried running randomForest but it complained about "JOBTITLE" having more than 32 categories. I know that is the limit

Hi, I am having some trouble using R 2.13.1 for generating a pmml object of of class "c('randomForest.formula', 'randomForest')" I see that these methods are available: > methods(pmml) [1] pmml.coxph* pmml.hclust* pmml.itemsets* pmml.kmeans* pmml.ksvm* pmml.lm* pmml.multinom* pmml.nnet* pmml.rpart* [10] pmml.rsf* pmml.rules* pmml.survreg*

Hi users, I need to calculate .632 (and .632+) bootstrap and the cross-validation of area under curve (AUC) to compare my models. Is there any package for the same. I know about 'ipred' and using it i can calculate misclassification errors. Please help. It's urgent. -- View this message in context: