externalFormats: Read and write external matrix formats

Description

Read matrices stored in the Harwell-Boeing or MatrixMarket formats or write sparseMatrix objects to one of these formats.

Usage

readHB(file)
readMM(file)
writeMM(obj, file, ...)

Value

The readHB and readMM functions return an object that inherits from the "Matrix" class. Methods for the

writeMM generic functions usually return

NULL and, as a side effect, the matrix obj is written to file in the MatrixMarket format (writeMM).

Arguments

obj

a real sparse matrix

file

for writeMM - the name of the file to be written. For readHB and readMM the name of the file to read, as a character scalar. The names of files storing matrices in the Harwell-Boeing format usually end in ".rua" or ".rsa". Those storing matrices in the MatrixMarket format usually end in ".mtx".

Alternatively, readHB and readMM accept connection objects.

...

optional additional arguments. Currently none are used in any methods.

References

https://math.nist.gov/MatrixMarket/

https://sparse.tamu.edu/

Examples

Run this code

str(pores <- readMM(system.file("external/pores_1.mtx",
                                package = "Matrix")))
str(utm <- readHB(system.file("external/utm300.rua",
                               package = "Matrix")))
str(lundA <- readMM(system.file("external/lund_a.mtx",
                                package = "Matrix")))
str(lundA <- readHB(system.file("external/lund_a.rsa",
                                package = "Matrix")))
str(jgl009 <- ## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/counterx/counterx.html
        readMM(system.file("external/jgl009.mtx", package = "Matrix")))
if (FALSE) {
## NOTE: The following examples take quite some time
## ----  even on a fast internet connection:
if(FALSE) # the URL has been corrected, but we need an un-tar step!
str(sm <-
 readHB(gzcon(url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/msc00726.tar.gz"))))
}
data(KNex)
## Store as MatrixMarket (".mtx") file, here inside temporary dir./folder:
(MMfile <- file.path(tempdir(), "mmMM.mtx"))
writeMM(KNex$mm, file=MMfile)
file.info(MMfile)[,c("size", "ctime")] # (some confirmation of the file's)

## very simple export - in triplet format - to text file:
data(CAex)
s.CA <- summary(CAex)
s.CA # shows  (i, j, x)  [columns of a data frame]
message("writing to ", outf <- tempfile())
write.table(s.CA, file = outf, row.names=FALSE)
## and read it back -- showing off  sparseMatrix():
str(dd <- read.table(outf, header=TRUE))
## has columns (i, j, x) -> we can use via do.call() as arguments to sparseMatrix():
mm <- do.call(sparseMatrix, dd)
stopifnot(all.equal(mm, CAex, tolerance=1e-15))