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[matrix] View of /pkg/R/sparseMatrix.R
 [matrix] / pkg / R / sparseMatrix.R

# View of /pkg/R/sparseMatrix.R

Thu May 18 06:47:09 2006 UTC (13 years, 1 month ago) by maechler
File size: 9432 byte(s)
`some  "sparse <-> graph"  updates`
```### Define Methods that can be inherited for all subclasses

### Idea: Coercion between *VIRTUAL* classes -- as() chooses "closest" classes
### ----  should also work e.g. for  dense-triangular --> sparse-triangular !
## setAs("denseMatrix", "sparseMatrix",
##        function(from) {
##            as(as(from, "dgeMatrix")
##        })

## setAs("dMatrix", "lMatrix",
##       function(from) {
##       })

## "graph" coercions -- this needs the graph package which is currently
##  -----               *not* required on purpose
## Note: 'undirected' graph <==> 'symmetric' matrix

## Add some utils that may no longer be needed in future versions of the 'graph' package
graph.has.weights <- function(g) "weight" %in% names(edgeDataDefaults(g))

graph.wgtMatrix <- function(g)
{
## Purpose: work around "graph" package's  as(g, "matrix") bug
## ----------------------------------------------------------------------
## Arguments: g: an object inheriting from (S4) class "graph"
## ----------------------------------------------------------------------
## Author: Martin Maechler, based on Seth Falcon's code;  Date: 12 May 2006

## MM: another buglet for the case of  "no edges":
if(numEdges(g) == 0) {
p <- length(nd <- nodes(g))
return( matrix(0, p,p, dimnames = list(nd, nd)) )
}
## Usual case, when there are edges:
if(has.w) {
w <- unlist(edgeData(g, attr = "weight"))
has.w <- any(w != 1)
} ## now 'has.w' is TRUE  iff  there are weights != 1
m <- as(g, "matrix")
## now is a 0/1 - matrix (instead of 0/wgts) with the 'graph' bug
if(has.w) { ## fix it if needed
tm <- t(m)
tm[tm != 0] <- w
t(tm)
}
else m
}

setAs("graphAM", "sparseMatrix",
function(from) {
symm <- edgemode(from) == "undirected" && isSymmetric(from@adjMat)
## This is only ok if there are no weights...
if(graph.has.weights(from)) {
as(graph.wgtMatrix(from),
if(symm) "dsTMatrix" else "dgTMatrix")
}
else { ## no weights: 0/1 matrix -> logical
as(as(from, "matrix"),
if(symm) "lsTMatrix" else "lgTMatrix")
}
})

## FIXME: in the case of NEL or other sparse graphs, we really should *NOT* go
##        via a *dense* adjacency matrix as we do here :
setAs("graph", "sparseMatrix",
function(from) as(as(from, "graphAM"), "sparseMatrix"))
## but rather
if(FALSE) { #------------------------- NOT YET -----------------
setAs("graph", "sparseMatrix",
function(from) as(as(from, "graphNEL"), "sparseMatrix"))

setAs("graphNEL", "sparseMatrix",
function(from) {
nd <- nodes(from)
symm <- edgemode(from) == "undirected"
if(graph.has.weights(from)) {
## symm <- symm && <weights must also be symmetric>: improbable
## if(symm) new("dsTMatrix", .....) else
new("dgTMatrix", .....)
}
else { ## no weights: 0/1 matrix -> logical
if(symm) new("lsTMatrix", .....)
else     new("lgTMatrix", .....)
}
})
}# not yet

setAs("sparseMatrix", "graph", function(from) as(from, "graphNEL"))
setAs("sparseMatrix", "graphNEL",
function(from) as(as(from, "TsparseMatrix"), "graphNEL"))
setAs("TsparseMatrix", "graphNEL",
function(from) {
d <- dim(from)
if(d[1] != d[2])
stop("only square matrices can be used as incidence matrices for grphs")
n <- d[1]
if(n == 0) return(new("graphNEL"))
if(is.null(rn <- dimnames(from)[[1]]))
rn <- as.character(1:n)
from <- uniq(from) ## Need to 'uniquify' the triplets!
if(isSymmetric(from)) { # because it's "dsTMatrix" or otherwise
upper <- from@i <= from@j
ft1 <- cbind(from@i + 1:1, from@j + 1:1)
graph::ftM2graphNEL(rbind(ft1, ft1[, 2:1]),
W = from@x, V=rn, edgemode="undirected")

} else { ## not symmetric

graph::ftM2graphNEL(cbind(from@i + 1:1, from@j + 1:1),
W = from@x, V=rn, edgemode="directed")
}
## stop("'dgTMatrix -> 'graphNEL' method is not yet implemented")
})

### Subsetting -- basic things (drop = "missing") are done in ./Matrix.R

### FIXME : we defer to the "*gT" -- conveniently, but not efficient for gC !

## [dl]sparse -> [dl]gT   -- treat both in one via superclass
##                        -- more useful when have "z" (complex) and even more

setMethod("[", signature(x = "sparseMatrix", i = "index", j = "missing",
drop = "logical"),
function (x, i, j, drop) {
cl <- class(x)
viaCl <- if(is(x,"dMatrix")) "dgTMatrix" else "lgTMatrix"
x <- callGeneric(x = as(x, viaCl), i=i, drop=drop)
## try_as(x, c(cl, sub("T","C", viaCl)))
if(is(x, "Matrix") && extends(cl, "CsparseMatrix"))
as(x, sub("T","C", viaCl)) else x
})

setMethod("[", signature(x = "sparseMatrix", i = "missing", j = "index",
drop = "logical"),
function (x, i, j, drop) {
cl <- class(x)
viaCl <- if(is(x,"dMatrix")) "dgTMatrix" else "lgTMatrix"
x <- callGeneric(x = as(x, viaCl), j=j, drop=drop)
## try_as(x, c(cl, sub("T","C", viaCl)))
if(is(x, "Matrix") && extends(cl, "CsparseMatrix"))
as(x, sub("T","C", viaCl)) else x
})

setMethod("[", signature(x = "sparseMatrix",
i = "index", j = "index", drop = "logical"),
function (x, i, j, drop) {
cl <- class(x)
viaCl <- if(is(x,"dMatrix")) "dgTMatrix" else "lgTMatrix"
x <- callGeneric(x = as(x, viaCl), i=i, j=j, drop=drop)
## try_as(x, c(cl, sub("T","C", viaCl)))
if(is(x, "Matrix") && extends(cl, "CsparseMatrix"))
as(x, sub("T","C", viaCl)) else x
})

## setReplaceMethod("[", signature(x = "sparseMatrix", i = "index", j = "missing",
##                                 value = "numeric"),
##                  function (x, i, value) {

##                      stop("NOT YET")

##                      as(r, class(x))
##                  })

## setReplaceMethod("[", signature(x = "sparseMatrix", i = "missing", j = "index",
##                                 value = "numeric"),
##                  function (x, j, value) {

##                      stop("NOT YET")

##                      as(r, class(x))
##                  })

## setReplaceMethod("[", signature(x = "sparseMatrix", i = "index", j = "index",
##                                 value = "numeric"),

##                      stop("NOT YET")

##                      as(r, class(x))
##                  })

setMethod("-", signature(e1 = "sparseMatrix", e2 = "missing"),
function(e1) { e1@x <- -e1@x ; e1 })
## with the following exceptions:
setMethod("-", signature(e1 = "lsparseMatrix", e2 = "missing"),
function(e1) callGeneric(as(e1, "dgCMatrix")))
setMethod("-", signature(e1 = "pMatrix", e2 = "missing"),
function(e1) callGeneric(as(e1, "lgTMatrix")))

### --- show() method ---

prSpMatrix <- function(object, zero.print = ".")
{
stopifnot(is(object, "sparseMatrix"))
m <- as(object, "matrix")
x <- apply(m, 2, format)
if(is.null(dim(x))) {# e.g. in  1 x 1 case
dim(x) <- dim(m)
dimnames(x) <- dimnames(m)
}
x <- emptyColnames(x)
if(is.logical(zero.print))
zero.print <- if(zero.print) "0" else " "
## FIXME: show only "structural" zeros as 'zero.print', not all of them..
x[m == 0.] <- zero.print
if(is(object,"lsparseMatrix"))
x[m] <- "|"
print(noquote(x))
invisible(object)
}

setMethod("show", signature(object = "sparseMatrix"),
function(object) {
d <- dim(object)
cl <- class(object)
cat(sprintf('%d x %d sparse Matrix of class "%s"\n', d[1], d[2], cl))
maxp <- getOption("max.print")
if(prod(d) <= maxp)
prSpMatrix(object)
else { ## d[1] > maxp / d[2] >= nr : -- this needs [,] working:
nr <- maxp %/% d[2]
n2 <- ceiling(nr / 2)
nR <- d[1] # nrow
prSpMatrix(object[seq(length = min(nR, max(1, n2))), drop = FALSE])
cat("\n ..........\n\n")
prSpMatrix(object[seq(to = nR, length = min(max(1, nr-n2), nR)),
drop = FALSE])
invisible(object)
}
})

## not exported:
setMethod("isSymmetric", signature(object = "sparseMatrix"),
function(object, tol = 100*.Machine\$double.eps) {
## pretest: is it square?
d <- dim(object)
if(d[1] != d[2]) return(FALSE)
## else slower test
if (is(object, "dMatrix"))
## use gC; "T" (triplet) is *not* unique!
isTRUE(all.equal(as(object, "dgCMatrix"),
as(t(object), "dgCMatrix"), tol = tol))
else if (is(object, "lMatrix"))
## test for exact equality; FIXME(?): identical() too strict?
identical(as(object, "lgCMatrix"),
as(t(object), "lgCMatrix"))
else stop("not yet implemented")
})

setMethod("isTriangular", signature(object = "sparseMatrix"),
function(object, upper = NA)
isTriC(as(object, "CsparseMatrix"), upper))

setMethod("isDiagonal", signature(object = "sparseMatrix"),
function(object) {
gT <- as(object, "TsparseMatrix")
all(gT@i == gT@j)
})

```