[R] Matrix package: band matrix

Thomas Lumley tlumley at u.washington.edu
Sun Feb 22 12:00:52 CET 2009


Exactly what I wanted. Thanks much.

       -thomas


On Sat, 21 Feb 2009, Martin Maechler wrote:

>>>>>> "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])
> }
>
>
>
>

Thomas Lumley			Assoc. Professor, Biostatistics
tlumley at u.washington.edu	University of Washington, Seattle



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