On Tue, 4 Oct 2005, Weiwei Shi wrote: > Hi, Jim: > I tried your code and get the following error: > trn1<-read.table('trn1.svm', header=F, na.string='.', sep='|') > Med<-apply(trn1, 2, median, na.rm=T) > Ind<-which(is.na(trn1), arr.ind=T) > trn1[Ind]<-Med[Ind[,'col']] > Error in "[<-.data.frame"(`*tmp*`, Ind, value = c(1.00802124455, > 1.00802124455, : > only logical matrix subscripts are allowed in replacement > > > I cannot figure out why.
Read the help for "[<-.data.frame" to be told the answer. A data frame (as given by read.table) is not a matrix, as the example presumably was. Indexing whole matrices at once is efficient, but it hides loops for data frames. You will not do better than looping over columns for a data frame, but you certainly do not need to loop over rows which is very inefficient. Something like trn2 <- trn1 for(i in names(trn2)) { Med <- median(trn2[[i]], na.rm = TRUE) trn2[i, is.na(trn2[[i]])] <- Med } > > Thanks for help, > > On 9/27/05, jim holtman <[EMAIL PROTECTED]> wrote: >> >> Use 'which(...arr.ind=T)' >> > x.1 >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] >> [1,] 6 10 3 4 10 7 9 8 4 10 >> [2,] 8 7 4 7 4 8 3 NA 3 4 >> [3,] 7 7 10 10 3 5 3 2 2 2 >> [4,] 3 4 5 10 10 2 6 9 4 5 >> [5,] 3 5 9 5 6 NA 3 NA 6 7 >> [6,] 9 6 10 5 10 4 2 10 NA 5 >> [7,] 5 2 5 10 3 7 6 4 6 8 >> [8,] 2 6 1 8 9 2 7 8 3 8 >> [9,] 9 1 4 9 8 10 2 NA 1 7 >> [10,] 2 4 8 7 NA 4 3 NA 5 5 >>> x.4 >> [1] 5.5 5.5 5.0 7.5 8.0 5.0 3.0 8.0 4.0 6.0 >>> Med <- apply(x.1, 2, median, na.rm=T) # get median >>> Ind <- which(is.na(x.1), arr.ind=T) # determine which are NA >>> x.1[Ind] <- Med[Ind[,'col']] # replace with median >>> x.1 >> [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8] [,9] [,10] >> [1,] 6 10 3 4 10 7 9 8 4 10 >> [2,] 8 7 4 7 4 8 3 8 3 4 >> [3,] 7 7 10 10 3 5 3 2 2 2 >> [4,] 3 4 5 10 10 2 6 9 4 5 >> [5,] 3 5 9 5 6 5 3 8 6 7 >> [6,] 9 6 10 5 10 4 2 10 4 5 >> [7,] 5 2 5 10 3 7 6 4 6 8 >> [8,] 2 6 1 8 9 2 7 8 3 8 >> [9,] 9 1 4 9 8 10 2 8 1 7 >> [10,] 2 4 8 7 8 4 3 8 5 5 >>> >> >> >> On 9/27/05, Weiwei Shi <[EMAIL PROTECTED]> wrote: >> >>> Hi, >>> I have the following codes to replace missing using median, assuming >>> missing >>> only occurs on continuous variables: >>> >>> trn1<-read.table('trn1.fv', header=F, na.string='.', sep='|') >>> >>> # median >>> m.trn1<-sapply(1:ncol(trn1), function(i) median(trn1[,i], na.rm=T)) >>> >>> #replace >>> trn2<-trn1 >>> for (each in 1:nrow(trn1)){ >>> index.missing=which(is.na(trn1[each,])) >>> trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing]) >>> } >>> >>> >>> Anyone can suggest some ways to improve it since replacing 10 takes 1.5sec: >>>> system.time(for (each in 1:10){index.missing=which(is.na >>> (trn1[each,])); >>> trn2[each,]<-replace(trn1[each,], index.missing, m.trn1[index.missing >>> ]);}) >>> [1] 1.53 0.00 1.53 0.00 0.00 >>> >>> >>> Another general question is >>> are there some packages in R doing missing handling? >>> >>> Thanks, >>> >>> -- >>> Weiwei Shi, Ph.D >>> >>> "Did you always know?" >>> "No, I did not. But I believed..." >>> ---Matrix III >>> >>> [[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 >>> >> >> >> >> -- >> Jim Holtman >> Cincinnati, OH >> +1 513 247 0281 >> >> What the problem you are trying to solve? > > > > > -- > Weiwei Shi, Ph.D > > "Did you always know?" > "No, I did not. But I believed..." > ---Matrix III > > [[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 > -- Brian D. Ripley, [EMAIL PROTECTED] Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ University of Oxford, Tel: +44 1865 272861 (self) 1 South Parks Road, +44 1865 272866 (PA) Oxford OX1 3TG, UK Fax: +44 1865 272595 ______________________________________________ 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