Leon wrote: > Hi, > I am using rpart to do leave one out cross validation, but met some problem, > Data is a data frame, the first column is the subject id, the second column > is the group id, and the rest columns are numerical variables, > > >>Data[1:5,1:10] > > sub.id group.id X3262.345 X3277.402 X3369.036 X3439.895 X3886.935 X3939.054 > X3953.777 X3970.352 > 1 32613 HAM_TSP 417.7082 430.4895 619.4776 720.8246 1048.1290 374.4598 > 770.4653 646.8712 > 2 32616 HAM_TSP 2553.5913 1113.4997 225.5340 274.5644 1105.7908 363.4623 > 2380.1872 784.9196 > 3 32617 HAM_TSP 291.6596 314.7322 238.3287 315.8305 982.6276 299.5855 > 1059.1140 540.8592 > 4 32628 HAM_TSP 456.9504 508.2278 552.3632 719.9989 1306.6299 446.6184 > 1352.9955 867.4219 > 5 32629 HAM_TSP 898.8879 640.2680 342.5477 386.5816 811.6709 518.0244 > 715.9886 441.1622 > > Example, I use the first sample as test set, the rest as training set > > >>fit <- rpart(as.factor(Data[-1,2]) ~., Data[-1, -c(1:2 ) ], minbucket=2 ) > > >>predict(fit, Data[1,],type='prob') > > Error in predict.rpart(fit, Data[1, ]) : subscript out of bounds
rpart has only seen one class so far, hence the tree consists of the root only. Uwe Ligges > but when I changes the parameter of type into 'class' > it works well > > >>predict(fit, Data[1,-c(1:2)],type='class') > > [1] HTLV_Carrier > Levels: HAM_TSP HTLV_Carrier Leukemia Normal > > Could anyone tell me what is the problem with it? > > Thanks very much in advance! > > [[alternative HTML version deleted]] > > ______________________________________________ > R-help@stat.math.ethz.ch mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html