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read.matrix.csr <- function(file, fac = TRUE, ncol = NULL)
{
if(!require("methods")) stop("Could not load package 'methods'.")
if(!require("SparseM")) stop("Could not load package 'SparseM'.")
l <- strsplit(readLines(file(file)), "[ ]+")
## extract y-values, if any
y <- if (length(grep(":",l[[1]][1])))
NULL
else
sapply(l, function(x) x[1])
## x-values
rja <- do.call("rbind",
lapply(l, function(x)
do.call("rbind",
strsplit(if (is.null(y)) x else x[-1], ":")
)
)
)
ja <- as.integer(rja[,1])
ia <- cumsum(c(1, sapply(l, length) - !is.null(y)))
max.ja <- max(ja)
dimension <- c(length(l), if (is.null(ncol)) max.ja else max(ncol, max.ja))
x = methods::new("matrix.csr", ra = as.numeric(rja[,2]), ja = ja,
ia = as.integer(ia), dimension = as.integer(dimension))
if (length(y))
list(x = x, y = if (fac) as.factor(y) else as.numeric(y))
else x
}
## old version: slow, but uses less memory
# read.matrix.csr <- function (file, fac = TRUE, ncol = NULL)
# {
# library(methods)
# if (!require(SparseM))
# stop("Need `SparseM' package!")
# con <- file(file)
# open(con)
# y <- vector()
# ia <- 1
# ra <- ja <- c()
# i <- 1
# maxcol <- 1
# while (isOpen(con) & length(buf <- readLines(con, 1)) > 0) {
# s <- strsplit(buf, "[ ]+", extended = TRUE)[[1]]
# ## y
# if (length(grep(":", s[1])) == 0) {
# y[i] <- if (fac)
# s[1]
# else as.numeric(s[1])
# s <- s[-1]
# }
# ## x
# if (length(s)) {
# tmp <- do.call("rbind", strsplit(s, ":"))
# ra <- c(ra, as.numeric(tmp[, 2]))
# ja <- c(ja, as.numeric(tmp[, 1]))
# }
# i <- i + 1
# ia[i] <- ia[i - 1] + length(s)
# }
# dimension <- c(i - 1, if (is.null(ncol)) max(ja) else max(ncol, ja))
# x = new("matrix.csr", ra, as.integer(ja), as.integer(ia), as.integer(dimension))
# if (length(y))
# list(x = x, y = if (fac) as.factor(y) else y)
# else x
# }
write.matrix.csr <- function (x, file="out.dat", y=NULL) {
on.exit(sink())
if(!require("methods")) stop("Could not load package 'methods'.")
if (!is.null(y) & (length(y) != nrow(x)))
stop(paste("Length of y (=", length(y),
") does not match number of rows of x (=",
nrow(x), ")!", sep=""))
sink(file)
for (i in 1:nrow(x)) {
if (!is.null(y)) cat (y[i],"")
for (j in x@ia[i]:(x@ia[i+1] - 1))
cat(x@ja[j], ":", x@ra[j], " ", sep="")
cat("\n")
}
}
na.fail.matrix.csr <- function(object, ...) {
if(!require("methods")) stop("Could not load package 'methods'.")
if (any(is.na(object@ra)))
stop("missing values in object") else return(object)
}
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