tree.pred <- yourfunction works!
Thanks, Josh! On Wed, May 26, 2010 at 9:35 AM, Joshua Wiley <[email protected]>wrote: > If you use return you need to assign the results to an object. For > instance > > tree.pred <- yourfunction > > then tree.pred will contain whatever data you returned from your > function. If you truly want your function to assign objects > internally that are available in your general workspace, instead of > just returning the data you want try: > > assign(variablename, datayouwantout, envir=.GlobalEnv) > > this will make an assignment to the global environment rather than the > function's environment. In general this seems risky though as your > function could be overwriting data in your main workspace without you > knowing it. > > HTH, > > Josh > > > > On Wed, May 26, 2010 at 9:26 AM, Changbin Du <[email protected]> wrote: > > HI, Dear R community, > > > > I am writing the following function to create one data set(*tree.pred*) > and > > one vector(*valid.out*) from loops. Later, I want to use the data set > from > > this loop to plot curves. I have tried return, list, but I can not use > the > > *tree.pred* data and *valid.out* vector. > > > > > > auc.tree<- function(msplit,mbucket) { > > > > * tree.pred<-data.frame() > > valid.out<-vector()* > > > > > > for(i in 1:10) { > > cat('Fold ', i, '\n') > > > > out.fold.c <-((i-1)*c.each.part +1):(i*c.each.part) > > out.fold.n <-((i-1)*n.each.part +1):(i*n.each.part) > > > > train.cv <- n.cc[-out.fold.c, c(2:401, 418)] > > train.nv <- n.nn[-out.fold.n, c(2:401, 418)] > > > > train.v<-rbind(train.cv, train.nv) #training data for feature > > selection > > > > # grow tree > > fit.dimer <- rpart(out ~ ., method="class", data=train.v) > > > > at<-grep("<leaf>", fit.dimer$frame[, "var"], value=FALSE, > ignore.case=TRUE) > > > > varr<-as.character(unique(fit.dimer$frame[-at, "var"])) > > > > train.cc <- n.cc[-out.fold.c, ] > > valid.cc <- n.cc[out.fold.c, ] > > > > train.nn <- n.nn[-out.fold.n,] > > valid.nn <- n.nn[out.fold.n,] > > > > train<-rbind(train.cc, train.nn) #training data > > valid<-rbind(valid.cc, valid.nn) # validation data > > > > #creat data set contains the following variables > > myvar<-names(gh5_h) %in% c(varr, "num_cell","num_genes","position", > > "acid_per", "base_per", "charge_per", "hydrophob_per", "polar_per", > "out") > > > > train<-train[myvar] # update training set > > valid<-valid[myvar] > > > > control<-rpart.control(xval=10, cp=0.01, minsplit=5, minbucket=5) > #control > > the size of the initial tree > > tree.fit <- rpart(out ~ ., method="class", data=train, > > control=control) # model fitting > > p.tree<- prune(tree.fit, > > cp=tree.fit$cptable[which.min(tree.fit$cptable[,"xerror"]),"CP"]) # prune > > the tree > > > > > > #get the prediction for the valid data set. > > tree.pred.r <-predict(p.tree, newdata=valid, type="prob") > > valid.r<-valid$out > > > > tree.pred <-rbind(tree.pred, tree.pred.r) > > valid.out<-c(valid.out, valid.r) > > cat('Dim of tree.pred', dim(tree.pred), 'length of valid.out', > > length(valid.out), '\n' ) > > > > } > > *list(tree.pred) > > list(valid.out)* > > cat('Minsplit ', msplit, 'Minbucket', mbucket, '\n') > > cat('10-cross validation is done! \n') > > } > > > > > >> auc.tree(5, 5) # > > Fold 1 > > Dim of tree.pred 141 2 length of valid.out 141 > > Fold 2 > > Dim of tree.pred 282 2 length of valid.out 282 > > Fold 3 > > Dim of tree.pred 423 2 length of valid.out 423 > > Fold 4 > > Dim of tree.pred 564 2 length of valid.out 564 > > Fold 5 > > Dim of tree.pred 705 2 length of valid.out 705 > > Fold 6 > > Dim of tree.pred 846 2 length of valid.out 846 > > Fold 7 > > Dim of tree.pred 987 2 length of valid.out 987 > > Fold 8 > > Dim of tree.pred 1128 2 length of valid.out 1128 > > Fold 9 > > Dim of tree.pred 1269 2 length of valid.out 1269 > > Fold 10 > > Dim of tree.pred 1410 2 length of valid.out 1410 > > Minsplit 5 Minbucket 5 > > 10-cross validation is done! > > > > > > if use return, it will print on the screen, you still can not use it to > > plot. Can anyone help me with this, thanks so much! > > > > > > > > -- > > Sincerely, > > Changbin > > -- > > > > > > [[alternative HTML version deleted]] > > > > ______________________________________________ > > [email protected] mailing list > > https://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code. > > > > > > -- > Joshua Wiley > Senior in Psychology > University of California, Riverside > http://www.joshuawiley.com/ > -- Sincerely, Changbin -- [[alternative HTML version deleted]] ______________________________________________ [email protected] mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
