Re: [R] package:Matrix handling of data with identical indices

From: Douglas Bates <bates_at_stat.wisc.edu>
Date: Mon 10 Jul 2006 - 02:06:00 EST

The apparent contradiction here is again a case of inadequate documentation and checking.

Because the order of the triplets in the triplet form of a sparse matrix is essentially random it is permissible to have repeated indices. As you have seen, the interpretation of repeated indices is that the value at any index is the sum of the values in the triplets corresponding to that index.

 It is not permissible to have repeated indices in the compressed form. In the compressed form there is a well-defined ordering of the indices, first by columns then by row within column and the row indices must be increasing within columns.

Your matrix Mc should be flagged as invalid. Martin and I should discuss whether we want to add such a test to the validity method. It is not difficult to add the test but there will be a penalty in that it will slow down all operations on such matrices and I'm not sure if we want to pay that price to catch a rather infrequently occuring problem.

There is some documentation of the internal representations of these formats in the directory $R_LIB/Matrix/doc/UFSparse/. The User Guides in that directory are taken directly from the various sparse matrix packages that Tim Davis at the University of Florida has written. He has a book that is scheduled for publication this September

Tim Davis (2006), Direct Methods for Sparse Linear Systems, SIAM, Philadelphia, PA

I hope we will be able to refer to that book for details of the representation and algorithms.

On 7/8/06, Thaden, John J <ThadenJohnJ@uams.edu> wrote:
> In the Matrix package v. 0.995-11 I see that the dgTMatrix
> Class for compressed, sparse, triplet-form matrices handles
> Identically indexed data instances by summing their values,
> e.g.,
>
> library(Matrix)
> (Mt <- new("dgTMatrix",
> i = as.integer(c(0,0,1,1,4)),
> j = as.integer(c(0,1,2,2,4)),
> x = as.double(1:5),
> Dim = as.integer(c(5,5))))
> ## 5 x 5 sparse Matrix of class "dgTMatrix"
> ## [1,] 1 2 . . .
> ## [2,] . . 7 . . <--- 7 = 3 + 4.
> ## [3,] . . . . .
> ## [4,] . . . . .
> ## [5,] . . . . 5
>
> # If instead I make a dgCMatrix-class matrix, the first
> # instance is overwritten by the second, e.g.,
>
> library(Matrix)
> (Mc <- new("dgCMatrix",
> i = as.integer(c(0,0,1,1,4)),
> p = as.integer(c(0,1,2,4,5)),
> x = as.double(1:5),
> Dim = as.integer(c(5,5))))
> ## 5 x 5 sparse Matrix of class "dgCMatrix"
> ##
> ## [1,] 1 2 . .
> ## [2,] . . 4 . <-- the datum '3' has been lost.
> ## [3,] . . . .
> ## [4,] . . . .
> ## [5,] . . . 5
>
> # If one arrives at the dgCMatrix via the dgTMatrix class,
> # the summed value is of course preserved, e.g.,
>
> (Mtc <- as(Mt, "dgCMatrix"))
> ## 5 x 5 sparse Matrix of class "dgCMatrix"
> ##
> ## [1,] 1 2 . . .
> ## [2,] . . 7 . .
> ## [3,] . . . . .
> ## [4,] . . . . .
> ## [5,] . . . . 5
>
> As there is nothing inherent in either compressed, sparse,
> format that would prevent recognition and handling of
> duplicated index pairs, I'm curious why the dgCMatrix
> class doesn't also add x values in those instances?

> I wonder also if others might benefit also by being able
> to choose how these instances are handled, i.e.,
> whether they are summed, averaged or overwritten?
>
> -John Thaden, Ph.D.
> Research Assistant Professor of Geriatrics
> University of Arkansas for Medical Sciences
> Little Rock AR, USA
>
>
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