[R] Binary Matrices

[Martin Maechler]

>>>>> "Mark" == Mark Edmondson-Jones <Mark.Edmondson-jones at nottingham.ac.uk>
>>>>>     on Wed, 13 Apr 2005 15:40:26 +0100 writes:

    Mark> 1000x1000 is only indicative.  I need to generate
    Mark> larger (adjacency) matrices using a variety of models.

    Mark> Most are sparse, with a high proportion of zeros and
    Mark> so SparseM sounds very promising.  I will investigate.

As others have said, you can use either 'SparseM' or 'Matrix'.
The latter has also good code for sparse matrices, and actually
I know that Doug Bates was going to implement sparse logical
matrices in the next few days.
Those actually need (quite) a bit less space than sparse double
matrices, since you only need to store the indices of the TRUE
entries.

Martin


    >>>> "Liaw, Andy" <andy_liaw at merck.com> 13/04/2005 >>>


    >> -----Original Message-----
    >> From: Uwe Ligges
    >> 
    >> Mark Edmondson-Jones wrote:
    >> 
    >> > I'm wanting to perform analysis (e.g. using eigen()) of 
    >> binary matrices - i.e. matrices comprising 0s and 1s.
    >> > 
    >> > For example:
    >> > 
    >> > n<-1000
    >> > test.mat<-matrix(round(runif(n^2)),n,n)
    >> > eigen(test.mat,only.values=T)
    >> > 
    >> > Is there a more efficient way of setting up test.mat, as 
    >> each cell only requires a binary digit?  I imagine R is 
    >> setting up a structure which could contain n^2 floats.
    >> 
    >> No. In principle you could use logicals,

    Mark> ... but that doesn't save any memory:

    >> object.size(integer(1e6))
    Mark> [1] 4000028
    >> object.size(logical(1e6))
    Mark> [1] 4000028

    >> but that does not help for further calculations in eigen().

    Mark> Besides, if the problem size is really 1000 x 1000, one matrix in 
    Mark> double precision is only 8MB.  As Reid said, if the matrix is sparse,
    Mark> there's probably a lot more saving in both memory and computation
    Mark> by using SparseM and Matrix packages.

    Mark> Cheers,
    Mark> Andy

 
    >> Uwe Ligges
    >> 
    >> 
    >> > Thanks in advance for any help.
    >> > 
    >> > Regards,
    >> > Mark
    >> > 
    >> > 
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