[R] R help
Petr Savicky
savicky at cs.cas.cz
Sun Feb 19 20:35:32 CET 2012
On Sat, Feb 18, 2012 at 06:00:53PM -0500, li li wrote:
> Dear all,
> I need to generate numbers from multivariate normal with large dimensions
> (5,000,000).
Hi.
I am replying to your first email, since the other did not arrive
to my folder, possibly filtered out by a spam filter. I see them
at the web interface.
1. Error: cannot allocate vector of size 381.5 Mb
The error message makes sense. The matrix requires m*n*8/2^20 MB,
which is in your case
m <- 100000
n <- 500
m*n*8/2^20
[1] 381.4697
May be, you already have other large objects in the memory. Try to
minimize the number and size of objects, which you need simultaneously
in an R session.
2. Generating a multivariate normal distribution.
As Peter Dalgaard pointed out, a speed up is possible only
for special types of the covariance matrix Sigma. A general
way is to find a matrix A such that A A^t = Sigma. Then,
the vector A X, where X is from N(0,I) and I is an identity
matrix of an appropriate dimension, has covariance Sigma.
This is also the way, how mvtnorm package works.
A speed up is possible, if computing the product A X does not
require to have matrix A explicitly represented in memory.
The matrix A need not be a square matrix. In particular, the
previous case may be understood as using the matrix A, which
for a small m is as follows.
m <- 5
rho <- 0.5
A <- cbind(sqrt(rho), sqrt(1 - rho)*diag(m))
A
[,1] [,2] [,3] [,4] [,5] [,6]
[1,] 0.7071068 0.7071068 0.0000000 0.0000000 0.0000000 0.0000000
[2,] 0.7071068 0.0000000 0.7071068 0.0000000 0.0000000 0.0000000
[3,] 0.7071068 0.0000000 0.0000000 0.7071068 0.0000000 0.0000000
[4,] 0.7071068 0.0000000 0.0000000 0.0000000 0.7071068 0.0000000
[5,] 0.7071068 0.0000000 0.0000000 0.0000000 0.0000000 0.7071068
A %*% t(A)
[,1] [,2] [,3] [,4] [,5]
[1,] 1.0 0.5 0.5 0.5 0.5
[2,] 0.5 1.0 0.5 0.5 0.5
[3,] 0.5 0.5 1.0 0.5 0.5
[4,] 0.5 0.5 0.5 1.0 0.5
[5,] 0.5 0.5 0.5 0.5 1.0
This construction is conceptually possible also for a large m because
the structure of A allows to compute A X by simpler operations with
the vector X than an explicit matrix product. Namely, the expression
rnorm(1, sd=sqrt(rho)) + rnorm(m, sd=sqrt(1 - rho))
or, more clearly,
sqrt(rho) * rnorm(1) + sqrt(1 - rho) * rnorm(m)
is equivalent to the required A X, where X consists of rnorm(1)
and rnorm(m) together.
If you have a specific Sigma, describe it and we can discuss,
whether an appropriate A can be found.
Hope this helps.
Petr Savicky.
More information about the R-help
mailing list