bigalgebra-package: Arithmetic routines for native R matrices and big.matrix...

In bigalgebra: 'BLAS' and 'LAPACK' Routines for Native R Matrices and 'big.matrix' Objects

Arithmetic routines for native R matrices and big.matrix objects.

Description

This package provides arithmetic functions for native R matrices and big.matrix objects.

Details

This package provides arithmetic functions for native R matrices and big.matrix objects.

The package defines a number of global options that begin with bigalgebra. They include:

Option	Default value
bigalgebra.temp_pattern	"matrix_"
bigalgebra.tempdir	tempdir
bigalgebra.mixed_arithmetic_returns_R_matrix	TRUE
bigalgebra.DEBUG	FALSE

The bigalgebra.tempdir option must be a function that returns a temporary directory path used to big matrix results of BLAS and LAPACK operations. The deault value is simply the default R tempdir function.

The bigalgebra.temp_pattern is a name prefix for file names of generated big matrix objects output as a result of BLAS and LAPACK operations.

The bigalgebra.mixed_arithmetic_returns_R_matrix option determines whether arithmetic operations involving an R matrix or vector and a big.matrix matrix or vector return a big matrix (when the option is FALSE), or return a normal R matrix (TRUE).

The package is built, by default, with R's native BLAS libraries, which use 32-bit signed integer indexing. The default build is limited to vectors of at most 2**31 - 1 entries and matrices with at most 2**31 - 1 rows and 2**31 - 1 columns (note that standard R matrices are limtied to 2**31 - 1 total entries).

The package includes a reference BLAS implementation that supports 64-bit integer indexing, relaxing the limitation on vector lengths and matrix row and column limits. Installation of this package with the 64-bit reference BLAS implementation may be performed from the command-line install:

REFBLAS=1 R CMD INSTALL bigalgebra

where "bigalgebra" is the source package (for example, bigalgebra_0.8.4.tar.gz).

The package may also be build with user-supplied external BLAS and LAPACK libraries, in either 32- or 64-bit varieties. This is an advanced topic that requires additional Makevars modification, and may include adjustment of the low-level calling syntax depending on the library used.

Feel free to contact us for help installing and running the package.

Author(s)

Frédéric Bertrand, Michael J. Kane, Bryan Lewis, John W. Emerson

Maintainer: Frédéric Bertrand <[e-mail]>

References

https://www.netlib.org/blas/

https://www.netlib.org/lapack/

See Also

bigmemory, big.matrix

Examples

# Testing the development of the user-friendly operators:
# if you have any problems, please email us!  - Jay & Mike 4/29/2010

library("bigmemory")
A <- big.matrix(5,4, type="double", init=0,
                dimnames=list(NULL, c("alpha", "beta")))
B <- big.matrix(4,4, type="double", init=0,
                dimnames=list(NULL, c("alpha", "beta")))

C <- A 
D <- A[] 

print(C - D)       # Compare the results (subtraction of an R matrix from a
                   # big.matrix)

# The next example illustrates mixing R and big.matrix objects. It returns by
# default (see # options("bigalgebra.mixed_arithmetic_returns_R_matrix")
D <- matrix(rnorm(16),4)
E <- A 

bigalgebra documentation built on Sept. 30, 2024, 9:42 a.m.