Hi Martin,
Thanks for the help. Just to make sure I understand correctly.
The below steps are for creating an example table similar to the one that I
read from file.
n <- 22638
m <- 80914
nnz <- 300000 # no idea if this is realistic for you
set.seed(101)
ex <- cbind(i = sample(n,nnz, replace=TRUE),
j = sample(m,nnz, replace=TRUE),
x = round(100 * rnorm(nnz)))
and I can understand the way sparseMatrix is initialized right now as
M <- sparseMatrix(i = ex[,"i"],
j = ex[,"j"],
x = ex[,"x"])
How ever, I couldn't understand the use of below commands.
MM. <- tcrossprod(M) # == MM' := M %*% t(M)
M.1 <- M %*% rep(1, ncol(M))
stopifnot(identical(drop(M.1), rowSums(M)))
Kindly let me know if I missed something.
Thanks
Pallavi
On Tue, Oct 27, 2009 at 4:12 PM, Martin Maechler <maech...@stat.math.ethz.ch
> wrote:
>
> PP> Hi all,
>
> PP> I used sparseM package for creating sparse Matrix and
> PP> followed below commands.
>
> I'd strongly recommend to use package 'Matrix' which is part of
> every R distribution (since R 2.9.0).
>
> PP> The sequence of commands are:
>
> >> ex <- read.table('fileName',sep=',')
> >> M <- as.matrix.csr(0,22638,80914)
> >> for (i in 1:nrow(ex)) { M[ex[i,1],ex[i,2]]<-ex[i,3]}
>
> This is very slow in either 'Matrix' or 'SparseM'
> as soon as nrow(ex) is non-small.
>
> However, there are very efficient ways to construct the sparse
> matrix directly from your 'ex' structure:
> In 'Matrix' you should use the sparseMatrix() function as you
> had proposed.
>
> Here I provide a reproducible example,
> using a random 'ex':
>
>
> n <- 22638
> m <- 80914
> nnz <- 300000 # no idea if this is realistic for you
>
> set.seed(101)
> ex <- cbind(i = sample(n,nnz, replace=TRUE),
> j = sample(m,nnz, replace=TRUE),
> x = round(100 * rnorm(nnz)))
>
> library(Matrix)
>
> M <- sparseMatrix(i = ex[,"i"],
> j = ex[,"j"],
> x = ex[,"x"])
> MM. <- tcrossprod(M) # == MM' := M %*% t(M)
>
> M.1 <- M %*% rep(1, ncol(M))
> stopifnot(identical(drop(M.1), rowSums(M)))
>
> ## .... and now do other stuff with your sparse matrix M
>
>
> PP> Even after 4 hours, I can still see the above command running. But,
> I am not
> PP> sure whether it got stuck some where.
>
> PP> Also, when I initialize matrix M and try to display the values, I
> can see
> PP> something like this
> PP> [1] 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
> 2 2 2 2
> PP> 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2
> 2 2 2 2
> PP> 2 2 2 2 2 2 2 2 2 2
> PP> [85] 2 2
>
> PP> And, after I stopped executing above initialize command from
> table(after 4
> PP> hours). I could see a different values.
>
> PP> Could some one kindly explain what these number are about and how
> can I test
> PP> that my command is running and not just stuck some where.
>
> PP> Also, it would be great if some one point me to a tutorial if any on
> sparse
> PP> matricies on R as I couldn't get one from internet.
>
> PP> Thanks
> PP> Pallavi
>
>
>
> PP> Pallavi Palleti wrote:
> >>
> >> Hi David,
> >>
> >> Thanks for your help. This is exactly what I want.
> >> But, I have number of rows of my matrix = 25k and columns size as
> 80k. So,
> >> when I define a matrix object, it is throwing an error saying can not
> >> allocate a vector of length (25K * 80k). I heard that, this data can
> still
> >> be loaded into R using sparseMatrix. However, I couldn't get a syntax
> for
> >> creating the same. Could someone kindly help me in this regard.
> >>
> >> Thanks
> >> Pallavi
> >>
> >>
> >> David Winsemius wrote:
> >>>
> >>>
> >>> On Oct 26, 2009, at 5:06 AM, Pallavi Palleti wrote:
> >>>
> >>>>
> >>>> Hi all,
> >>>>
> >>>> I am new to R and learning the same. I would like to create a
> sparse
> >>>> matrix
> >>>> from an existing file whose contents are in the format
> >>>> "rowIndex,columnIndex,value"
> >>>>
> >>>> for ex:
> >>>> 1,2,14
> >>>> 2,4,15
> >>>>
> >>>> I would like to create a sparse matrix by taking the above as
> input.
> >>>> However, I couldn't find an example where the data was being read
> >>>> from a
> >>>> file. I tried searching in R tutorial and also searched for the
> same
> >>>> in web
> >>>> but in vain. Could some one kindly help me how to give the above
> >>>> format as
> >>>> input in R to create a sparse matrix.
> >>>
> >>> ex <- read.table(textConnection("1,2,14
> >>> 2,4,15") , sep=",")
> >>> ex
> >>> # V1 V2 V3
> >>> #1 1 2 14
> >>> #2 2 4 15
> >>>
> >>> M <- Matrix(0, 20, 20)
> >>>
> >>> > M
> >>> #20 x 20 sparse Matrix of class "dsCMatrix"
> >>>
> >>> [1,] . . . . . . . . . . . . . . . . . . . .
> >>> [2,] . . . . . . . . . . . . . . . . . . . .
> >>> [3,] . . . . . . . . . . . . . . . . . . . .
> >>> snip
> >>>
> >>> for (i in 1:nrow(ex) ) { M[ex[i, 1], ex[i, 2] ] <- ex[i, 3] }
> >>>
> >>> > M
> >>> 20 x 20 sparse Matrix of class "dgCMatrix"
> >>>
> >>> [1,] . 14 . . . . . . . . . . . . . . . . . .
> >>> [2,] . . . 15 . . . . . . . . . . . . . . . .
> >>> [3,] . . . . . . . . . . . . . . . . . . . .
> >>> snip
> >>> >
> >>> --
> >>>
> >>> David Winsemius, MD
> >>> Heritage Laboratories
> >>> West Hartford, CT
> >>>
> >>> ______________________________________________
> >>> R-help@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.
> >>>
> >>>
> >>
> >>
>
> PP> --
> PP> View this message in context:
> http://www.nabble.com/Creating-a-sparse-matrix-from-a-file-tp26056334p26075036.html
> PP> Sent from the R help mailing list archive at Nabble.com.
>
> PP> ______________________________________________
> PP> R-help@r-project.org mailing list
> PP> https://stat.ethz.ch/mailman/listinfo/r-help
> PP> PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> PP> and provide commented, minimal, self-contained, reproducible code.
>
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