R help - May 2010 - how to Store loop output from a function

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
--

Changbin Du
DOE Joint Genome Institute
Bldg 400 Rm 457
2800 Mitchell Dr
Walnut Creet, CA 94598
Phone: 925-927-2856

	[[alternative HTML version deleted]]

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 <changbind at gmail.com>
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
> --
>
> Changbin Du
> DOE Joint Genome Institute
> Bldg 400 Rm 457
> 2800 Mitchell Dr
> Walnut Creet, CA 94598
> Phone: 925-927-2856
>
> ? ? ? ?[[alternative HTML version deleted]]
>
> ______________________________________________
> R-help at r-project.org 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/