[R] Matrix package: band matrix

Martin Maechler maechler at stat.math.ethz.ch
Sat Feb 21 00:51:38 CET 2009


>>>>> "KK" == Ken Knoblauch <ken.knoblauch at inserm.fr>
>>>>>     on Fri, 20 Feb 2009 14:11:55 +0000 (UTC) writes:

    KK> Thomas Lumley <tlumley <at> u.washington.edu> writes:
    >> I want to construct a symmetric band matrix in the Matrix
    >> package from a matrix where the first column contains
    >> data for the main diagonal, the second column has data
    >> for the first subdiagonal/superdiagonal and so on.
    >> 
    >> Since the Matrix will be 10^5 x 10^5 or so, with perhaps
    >> 10-20 non-zero elements above the diagonal per row, I
    >> can't do it by constructing a full matrix and then using
    >> the band() function to subset it to a band matrix.
    >> 
    >> Any suggestions?
    >> 
    >> -thomas
    >> 
    >> Thomas Lumley Assoc. Professor, Biostatistics tlumley
    >> <at> u.washington.edu University of Washington, Seattle
    >> 
    KK> I'm not expert but just looking at the package, perhaps
    KK> the spMatrix function (constructor) would do it.


    KK> spMatrix(5, 5, c(2:5, 1:5, 1:4), c(1:4, 1:5, 2:5), rnorm(13))

    KK> 5 x 5 sparse Matrix of class "dgTMatrix"
                                                             
    KK> [1,] -1.7109379 -0.5576860  .            .          .        
    KK> [2,] -0.3219899 -0.9294558  0.001323253  .          .        
    KK> [3,]  .          0.4099070  0.646068453  0.5388224  .        
    KK> [4,]  .          .         -1.007848357 -0.1117796 -0.5555834
    KK> [5,]  .          .          .           -0.6816979 -0.6052127

Yes, very good, Ken!

My solution uses the successor of spMatrix(), called 
sparseMatrix(), unless in the symmetric case, where it class
new("dsTMatrix", ...) directly:

bandSparse <- function(n, m = n, k, listDiag, symmetric = FALSE)
{
    ## Purpose: Compute a band-matrix by speciyfying its (sub-)diagonal(s)
    ## ----------------------------------------------------------------------
    ## Arguments: (n,m) : Matrix dimension
    ##		      k : integer vector of "diagonal numbers",  with identical
    ##                    meaning as in  band(*, k)
    ##          listDiag: list of (sub)diagonals
    ##         symmetric: if TRUE, specify only upper or lower triangle;
    ## ----------------------------------------------------------------------
    ## Author: Martin Maechler, Date: 20 Feb 2009, 22:42
    use.x <- !missing(listDiag)
    len.k <- length(k)
    stopifnot(is.list(listDiag),
	      k == as.integer(k), n == as.integer(n), m == as.integer(m))
    if(use.x && length(listDiag) != len.k)
	stop(sprintf("'listDiag' must have the same length (%d) as 'k'", len.k))
    k <- as.integer(k)
    n <- as.integer(n)
    m <- as.integer(m)
    stopifnot(n >= 0, m >= 0, -n+1 <= k, k <= m - 1)
    if(symmetric && any(k < 0) && any(k > 0))
	stop("for symmetric band matrix, only specify upper or lower triangle",
	     "\n hence, all k must have the same sign")
    dims <- c(n,m)

    k.lengths <- ## This is a bit "ugly"; I got the cases "by inspection"
	if(n >= m) {
	    ifelse(k >= m-n,  m - pmax(0,k), n+k)
	} else { ## n < m
	    ifelse(k >= -n+1, n + pmin(0,k), m-k)
	}
    i <- j <- integer(sum(k.lengths))
    if(use.x)
	x <- if(len.k > 0) # carefully getting correct type/mode
	    rep.int(listDiag[[1]][1], length(i))
    off.i <- 0L
    for(s in seq_len(len.k)) {
	kk <- k[s] ## *is* integer
	l.kk <- k.lengths[s] ## == length of (sub-)diagonal kk
	ii1 <- seq_len(l.kk)
	ind <- ii1 + off.i
	if(kk >= 0) {
	    i[ind] <- ii1
	    j[ind] <- ii1 + kk
	} else { ## k < 0
	    i[ind] <- ii1 - kk
	    j[ind] <- ii1
	}
	if(use.x) {
	    xx <- listDiag[[s]]
	    if(length(xx) < l.kk)
		warning(sprintf("the %d-th (sub)-diagonal (k = %d) is %s",
				s, kk, "too short; filling with NA's"))
	    x[ind] <- xx[ii1]
	}
	off.i <- off.i + l.kk
    }
    if(symmetric) { ## we should have smarter sparseMatrix()
        UpLo <- if(min(k) >= 0) "U" else "L"
	as(if(use.x) {
	    if(is.integer(x)) x <- as.double(x)
	    new("dsTMatrix", i= i-1L, j = j-1L, x = x, Dim= dims, uplo=UpLo) } else
	   new("nsTMatrix", i= i-1L, j = j-1L, Dim= dims, uplo=UpLo),
	   "CsparseMatrix")
    }
    else { ## general, not symmetric
	if(use.x)
	    sparseMatrix(i=i, j=j, x=x, dims=dims)
	else
	    sparseMatrix(i=i, j=j, dims=dims)
    }
}

if(FALSE) { ## Examples

    dList <- list(1:30, 10*(1:20), 100*(1:20))

    s1 <- bandSparse(13, k = -c(0:2, 6), lis = c(dList, dList[2]), symm=TRUE)
    s2 <- bandSparse(13, k =  c(0:2, 6), lis = c(dList, dList[2]), symm=TRUE)
    stopifnot(identical(s1, t(s2)), is(s1,"dsCMatrix"))

    n <- 1e6 ## is already biggish; MM sees top memory up to 1.1 GB;
             ## and it (the bandSparse() call) takes 1 or 2 minutes (slow NB)
    bk <- c(0:5, 7,11)
    bLis <- as.data.frame(matrix(1:8, 1e6, 8, byrow=TRUE))
    B <- bandSparse(1e6, k = bk, list = bLis)
    object.size(B) ## 100 mio Bytes
    Bs <- bandSparse(1e6, k = bk, list = bLis, symmetric=TRUE)
    object.size(Bs)## 100 mio Bytes
    gc()
    show(Bs[1:30, 1:15])
}



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