search for: errorest

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", est.para=control.errorest(k=3),...

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&qu...

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 experien...

...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 seq(1,25,2)){ set.seed(19) a<-errorest(Species ~ ., data=iris, model=ipredknn, estimator="cv", est.para=control.errorest(k=cv.k), predict=bwpredict.knn, nk = i)$err print(a) } [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [1] 0.02666667 [...

...53.00000 182 1 428.8740 130.8020 -328.00000 183 1 287.5540 98.0767 34.00000 Since predict.lda does not return simply the classification it is wrapped, as in the docs: mypredict.lda <- function(object, newdata) predict(object, newdata = newdata)$class In trying errorest() I get the message > errorest(class ~ hydrophobicity + charge, data=d, model=lda, predict=mypredict.lda) Error in cv.numeric(y, formula, data, model = model, predict = predict, : predict does not return numerical values even though a "manual" lda seems to provide the co...

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 using specified folds, and get misclassification error and root mean squared error this is what you do. Below is a script that will d...

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

...is3[tr,,2], iris3[tr,,3]); test <- rbind(iris3[-tr,,1], iris3[-tr,,2], iris3[-tr,,3]); cl <- factor(c(rep("s",25), rep("c",25), rep("v",25))); z <- lda(train, cl); predict(z, test)$class; data.frame(class=cl, train); flowers <- data.frame(class=cl, train); errorest(class ~ ., data=flowers, model=lda, estimator="cv", predict=predict.lda); Error-Message is : Error: Object "predict.lda" not found

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 however, I got an error message saying that: randomForest.default(m, y, ...) : Can't have empty c...

Hi, I am wondering what does "mypredict.lda<-function(object, newdata)predict(object, newdata=newdata)$class" actually do? I run a few errorest commands in the same function on the same dataset using the same classifier lda. The only difference is some use "cv", other use "boot" and "632plus". They all share one mypredict.lda. Will it cause any problem? Regards, justin

...le regression data in the svm documentation. The rmse for internal prediction is 0.24. It is expected the 10-fold CV rmse should be bigger, but the result obtained using the "cross=10" option is 0.07. When the 10-fold CV is conducted either 'by hand' (not shown below) or using the errorest function in ipred (shown below) the answer is closer to 0.27, a more reasonable value. (2) Description of system I'm using the Debian Sarge version of R: R : Copyright 2005, The R Foundation for Statistical Computing Version 2.1.0 (2005-04-18), ISBN 3-900051-07-0 svm is in the e1071 p...

Sorry for the repeat. The PRESS statistic is defined as sum(y-yhat(i))^2, where yhat(i) denotes the ith predicted value using all the data except the ith case (as used typically in linear models). Thanks again Jacob Jacob L van Wyk Department of Mathematics and Statistics Rand Afrikaans University P O Box 524 Auckland Park 2006 South Africa Tel: +27-11-489-3080 Fax: +27-11-489-2832

...umentation. The rmse for internal prediction is 0.24. It > is expected the > 10-fold CV rmse should be bigger, but the result obtained > using the "cross=10" > option is 0.07. When the 10-fold CV is conducted either 'by > hand' (not shown > below) or using the errorest function in ipred (shown below) > the answer is > closer to 0.27, a more reasonable value. > > (2) Description of system > > I'm using the Debian Sarge version of R: > R : Copyright 2005, The R Foundation for Statistical Computing > Version 2.1.0 (2005-04-18),...

...;s not something I can do from scratch on my own. So I have spent all this morning trying to find a good example script of 10-Fold Cross-validation and RandomForest where the ratio of classes is maintained. I have done multiple google searches. The only thing I came across was the ipred package and errorest. But when I was going through the?errorest examples I did not see examples of actual classification output only error rates. So I turn to you guys. Do you have a script I can refer to and learn off of to accomplish what I need to accomplish? Dan [[alternative HTML version deleted]]

Can someone help me with performing leave-out-one cross validation using R (model built is a Cox model)? Thanks. --------------------------------------------- David Verbel, MPH Senior Biostatistician Aureon Biosciences 28 Wells Avenue Yonkers, NY 10701 Phone: (914) 377-4021 Fax: (914) 377-4001 --------------------------------------------- [[alternative HTML version deleted]]

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}}

How to select training data set and test data set from the original data for performing cross-validation --------------------------------- [[alternative HTML version deleted]]

...on of various classifiers based solely on LOOCV classification errors may not be reliable." the authors use random splitting to determine the number of PLS components in GPLS, but I'm still not sure how to choose the right number of PLS components for my data set. I used the function errorest() from package ipred to estimate the error rates und gpls() with Firth procedure switched on. The attached PDF Graphik illustrates the problem for my data set. S_n is the model sensitivity and S_p the model specifity. With 4 component I get the best crossvalidation error rate 17% and with 5 co...

Hi Everyone, I am new in using R and I was wondering if anybody knows how to do a leave-one-out cross-validation in R. Thanks Charles Découvrez les photos les plus intéressantes du jour. [[alternative HTML version deleted]]

Dear, I wanna make cross-validation for the species data of species distribution models. Please kindly suggest any package containing cross validation suiting the purpose. Thank you. Elaine [[alternative HTML version deleted]]