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\name{externalFormats}
\title{Read and write external matrix formats}
%
\docType{methods}
\keyword{connection}
\keyword{file}
\keyword{methods}
\keyword{utilities}
%
\alias{readHB}
\alias{readMM}
%\alias{writeHB}
\alias{writeMM}
%
\alias{writeMM,CsparseMatrix-method}
\alias{writeMM,sparseMatrix-method}
%
\description{
Read matrices stored in the Harwell-Boeing or MatrixMarket formats
or write \code{\linkS4class{sparseMatrix}} objects to one of these
formats.
}
\usage{
readHB(file)
readMM(file)
writeMM(obj, file, \dots)
}
\arguments{
\item{obj}{a real sparse matrix}
\item{file}{for \code{writeMM} - the name of the file to be written.
For \code{readHB} and \code{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 \code{".rua"} or \code{".rsa"}.
Those storing matrices in the MatrixMarket format usually end in
\code{".mtx"}.
Alternatively, \code{readHB} and \code{readMM} accept connection objects.}
\item{\dots}{optional additional arguments. Currently none are used in
any methods.}
}
\value{
The \code{readHB} and \code{readMM} functions return an object that
inherits from the \code{"\linkS4class{Matrix}"} class. Methods for the
\code{writeMM} generic functions usually return
\code{\link{NULL}} and, as a side effect, the matrix \code{obj} is
written to \code{file} in the MatrixMarket format (writeMM).
}
\note{
The Harwell-Boeing format is older and less flexible than the
MatrixMarket format. The function \code{writeHB} was deprecated and
has now been removed. Please use \code{writeMM} instead.
Note that these formats do \emph{not} know anything about
\code{\link{dimnames}}, hence these are dropped by \code{writeMM()}.
A very simple way to export small sparse matrices \code{S}, is to use
\code{summary(S)} which returns a \code{\link{data.frame}} with
columns \code{i}, \code{j}, and possibly \code{x}, see \code{summary} in
\code{\link{sparseMatrix-class}}, and an example below.
}
\references{
\url{https://math.nist.gov/MatrixMarket/}
\url{https://sparse.tamu.edu/}% was https://www.cise.ufl.edu/research/sparse/matrices/
}
\examples{
\dontshow{ % for R_DEFAULT_PACKAGES=NULL
library(utils, pos = "package:base", verbose = FALSE)
}
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))
}
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