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

Description

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

Arguments

Author

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

Maintainer: Frédéric Bertrand <frederic.bertrand@utt.fr>

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.

References

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

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

Examples

Run this code


# 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