[Rd] e1071: using svm with sparse matrices (PR#8527)
david.meyer at wu-wien.ac.at
Mon Feb 6 00:53:14 CET 2006
> First: this is not a bug, more a feature request.
[not in R as correctly pointed out, so just for the records:]
It _is_ a bug (in e1071), since svm() is indeed supposed to support
sparse data. The bug was introduced in 1.5-9 I think when support for
correct na-handling was added. The bug will be fixed in 1.5-13.
Thanks for pointing this out!
> Secondly, even if it was a bug, it is _not_ a bug in R, please read
> the posting rules for bugs. Now a member of R-core has to use
> valuable time to clean up after your bug report.
> Correspondence such as this such really be sent to the package
> maintainers (and - perhaps - a cc to R-devel).
> Having said all of this, of course it would be nice if svn supported
> sparse matrices.
> Libsvm, the `engine' underneath svm() in `e1071', uses a sparse
> representation of the data. I vaguely recall seeing Chih-Jen Lin's code
> that uses the SparseM package to pass sparse data to svm()... David would
> know best, of course.
> On Jan 27, 2006, at 2:02 AM, julien.gagneur at embl.de wrote:
> > Full_Name: Julien Gagneur
> > Version: 2.2.1
> > OS: Linux (Suse 9.3)
> > Submission from: (NULL) (18.104.22.168)
> > Using the SparseM library (SparseM_0.66)
> > and the e1071 library (e1071_1.5-12)
> > I fail using svm method with a sparse matrix. Here is a sample
> > example.
> > I experienced the same problem under Windows.
> >> library(SparseM)
> >  "SparseM library loaded"
> >> library("e1071")
> > Loading required package: class
> >> data(iris)
> >> attach(iris)
> >> M=as.matrix(iris[,1:4])
> >> Msparse=as.matrix.csr(M)
> >> Species=iris[,5]
> >> mod=svm(Msparse,Species)
> > Error in svm.default(Msparse, Species) : object "nac" not found
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