externalFormats function

Read and write external matrix formats

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

methods

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

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.

Returns

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).

Note

The Harwell-Boeing format is older and less flexible than the MatrixMarket format. The function writeHB was deprecated and has now been removed. Please use writeMM instead.

Note that these formats do not know anything about dimnames, hence these are dropped by writeMM().

A very simple way to export small sparse matrices S, is to use summary(S) which returns a data.frame with columns i, j, and possibly x, see summary in sparseMatrix-class, and an example below.

References

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

https://sparse.tamu.edu/

Examples

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")))
## https://math.nist.gov/MatrixMarket/data/Harwell-Boeing/counterx/counterx.htm
str(jgl   <- readMM(system.file("external/jgl009.mtx" , package = "Matrix")))

## 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 untar step:
u. <- url("https://www.cise.ufl.edu/research/sparse/RB/Boeing/msc00726.tar.gz")
str(sm <- readHB(gzcon(u.)))
}

data(KNex, package = "Matrix")
## 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, package = "Matrix")
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))