Matrix: How create a _row-oriented_ sparse Matrix (=dgRMatrix)?

Henrik Bengtsson <henrik.bengtsson at gmail.com>
    on Tue, 19 Apr 2016 14:04:11 -0700 writes:

    > Using the Matrix package, how can I create a row-oriented sparse
    > Matrix from scratch populated with some data?  By default a
    > column-oriented one is created and I'm aware of the note that the
    > package is optimized for column-oriented ones, but I'm only interested
    > in using it for holding my sparse row-oriented data and doing basic
    > subsetting by rows (even using drop=FALSE).

    > Here is what I get when I set up a column-oriented sparse Matrix:

    >> Cc <- Matrix(0, nrow=5, ncol=5, sparse=TRUE)
    >> Cc[1:3,1] <- 1

A general ("teaching") remark :
The above use of Matrix() is seen in many places, and is fine
for small matrices and the case where you only use the `[<-`
method very few times (as above).
Also using  Matrix()  is nice when being introduced to using the
Matrix package.

However, for efficience in non-small cases, do use

   sparseMatrix()

directly to construct sparse matrices.

    >> Cc

    > 5 x 5 sparse Matrix of class "dgCMatrix"

    > [1,] 1 . . . .
    > [2,] 1 . . . .
    > [3,] 1 . . . .
    > [4,] . . . . .
    > [5,] . . . . .

    >> str(Cc)

    > Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
    > ..@ i       : int [1:3] 0 1 2
    > ..@ p       : int [1:6] 0 3 3 3 3 3
    > ..@ Dim     : int [1:2] 5 5
    > ..@ Dimnames:List of 2
    > .. ..$ : NULL
    > .. ..$ : NULL
    > ..@ x       : num [1:3] 1 1 1
    > ..@ factors : list()

    > When I try to do the analogue for a row-oriented matrix, I get a
    > "dgTMatrix", whereas I would expect a "dgRMatrix":

    >> Cr <- Matrix(0, nrow=5, ncol=5, sparse=TRUE)
    >> Cr <- as(Cr, "dsRMatrix")
    >> Cr[1,1:3] <- 1
    >> Cr

    > 5 x 5 sparse Matrix of class "dgTMatrix"

    > [1,] 1 1 1 . .
    > [2,] . . . . .
    > [3,] . . . . .
    > [4,] . . . . .
    > [5,] . . . . .

The reason for the above behavior has been

a) efficiency.  All the subassignment ( `[<-` ) methods for
   "RsparseMatrix" objects (of which "dsRMatrix" is a special case)
   are implemented via  TsparseMatrix.
b) because of the general attitude that Csparse (and Tsparse to
   some extent) are well supported in Matrix,
   and e.g. further operations on Rsparse matrices would *again*
   go via T* or C* sparse ones, I had decided to keep things Tsparse.

[...]

    > Trying with explicit coercion does not work:

    >> as(Cc, "dgRMatrix")

    > Error in as(Cc, "dgRMatrix") :
    > no method or default for coercing "dgCMatrix" to "dgRMatrix"

    >> as(Cr, "dgRMatrix")

    > Error in as(Cr, "dgRMatrix") :
    > no method or default for coercing "dgTMatrix" to "dgRMatrix"

The general philosophy in 'Matrix' with all the class
hierarchies and the many specific classes has been to allow and
foster coercing to abstract super classes,
i.e, to  "dMatrix"  or "generalMatrix", "triangularMatrix", or
then "denseMatrix", "sparseMatrix", "CsparseMatrix" or
"RsparseMatrix", etc

So in the above  as(*, "RsparseMatrix")   should work always.

As a summary, in other words,  for what you want,

   as(sparseMatrix(.....), "RsparseMatrix")

should give you what you want reliably and efficiently.

    > Am I doing some wrong here?  Or is this what means that the package is
    > optimized for the column-oriented representation and I shouldn't
    > really work with row-oriented ones?  I'm really only interested in
    > access to efficient Cr[row,,drop=FALSE] subsetting (and a small memory
    > footprint).

{ though you could equivalently use   Cc[,row, drop=FALSE]
  with a CsparseMatrix Cc := t(Cr),
  couldn't you ?
}

Martin Maechler  (maintainer of 'Matrix')
ETH Zurich