[R] X'W in Matrix
Rafael A Irizarry
ririzarr at jhsph.edu
Fri Jun 9 19:52:04 CEST 2006
Doug,
I did mean wX = crossprod(X, W). sorry about that.
Thanks for the suggestions and for the *very* useful package. Im still
smiling about inverting a 6000x6000 matrix in one second with on line of
R code.
Best wishes,
-r
Douglas Bates wrote:
> On 6/9/06, Rafael A. Irizarry <ririzarr at jhsph.edu> wrote:
>
>> Hi!
>>
>> I have used the Matrix package (Version: 0.995-10) successfully
>> to obtain the OLS solution for a problem where the design matrix X is
>> 44000x6000. X is very sparse (about 80000 non-zeros elements).
>>
>> Now I want to do WLS: (X'WX)^-1X'Wy
>>
>> I tried W=Diagonal(length(w),w) and
>> wX=solve(X,W)
>>
>> but after various minutes R gives a not enough
>> memory error (Im using a 64bit machine with 16Gigs of RAM).
>
>
> That's an interesting question, Rafael, and very timely. I happen to
> be visiting Martin Maechler this week and he mentioned to me just a
> few minutes ago that we should add the capability for sparse least
> squares calculations to the Matrix package.
>
> Just for clarification, did you really mean wX = solve(X, W) above or
> were you thinking of wX = crossprod(X, W)?
>
> I would suggest storing the square root of the diagonal matrix W as a
> sparse matrix
>
>> w <- abs(rnorm(88000))
>> ind <- seq(along = w) - 1:1
>> W <- as(new("dgTMatrix", i = ind, j = ind, x = sqrt(w), Dim =
>> c(length(w), length(w))), "dgCMatrix")
>> str(W)
>
> Formal class 'dgCMatrix' [package "Matrix"] with 6 slots
> ..@ i : int [1:88000] 0 1 2 3 4 5 6 7 8 9 ...
> ..@ p : int [1:88001] 0 1 2 3 4 5 6 7 8 9 ...
> ..@ Dim : int [1:2] 88000 88000
> ..@ Dimnames:List of 2
> .. ..$ : NULL
> .. ..$ : NULL
> ..@ x : num [1:88000] 0.712 0.989 1.032 0.348 0.573 ...
> ..@ factors : list()
>
> (The 1:1 expression in the calculation of ind is a cheap trick to get
> an integer value of 1 so that ind stays integer). Now you should be
> able to create wX <- W %*% X and wy <- W %*% y very quickly.
>
>
>
>> I ended up doing this:
>> wX=Matrix(as.matrix(X)*sqrt(w),sparse=TRUE)
>> coefs1=as.vector(solve(crossprod(wX),crossprod(X,w*y)))
>>
>> which takes about 1-2 minutes, but it seems a better way, using the
>> diagonal matrix, should exist. If there is I'd appreciate hearing it. If
>> not, Im happy waiting 1-2 minute x #of iters.
>>
>>
>> Thanks,
>> Rafael
>>
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