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

# View of /pkg/R/sparseMatrix.R

Mon Sep 11 22:13:07 2006 UTC (12 years, 5 months ago) by maechler
File size: 11941 byte(s)
`new nMatrix and subclasses; lsparse change to have x slot; many consequences`
```### 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 !

##-> see als ./dMatrix.R, ./ddenseMatrix.R  and  ./lMatrix.R

setAs("ANY", "sparseMatrix", function(from) as(from, "CsparseMatrix"))

## "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) "nsTMatrix" else "ngTMatrix")
}
})

setAs("graph", "CsparseMatrix",
function(from) as(as(from, "graphNEL"), "CsparseMatrix"))

setAs("graphNEL", "CsparseMatrix",
function(from) {
nd <- nodes(from)
dm <- rep.int(length(nd), 2)
symm <- edgemode(from) == "undirected"

## 	  if(graph.has.weights(from)) {
##               .bail.out.2(.Generic, class(from), to)
## 	      ## symm <- symm && <weights must also be symmetric>: improbable
## 	      ## if(symm) new("dsTMatrix", .....) else
## 	      ##new("dgTMatrix", )
## 	  }
## 	  else { ## no weights: 0/1 matrix -> logical
edges <- lapply(from@edgeL[nd], "[[", "edges")
lens <- unlist(lapply(edges, length))
nnz <- sum(unlist(lens))  # number of non-zeros
i <- unname(unlist(edges) - 1:1) # row indices (0-based)
j <- rep.int(0:(dm[1]-1), lens) # column indices (0-based)
if(symm) {                    # ensure upper triangle
tmp <- i
flip <- i > j
i[flip] <- j[flip]
j[flip] <- tmp[flip]
dtm <- new("nsTMatrix", i = i, j = j, Dim = dm,
Dimnames = list(nd, nd), uplo = "U")
} else {
dtm <- new("ngTMatrix", i = i, j = j, Dim = dm,
Dimnames = list(nd, nd))
}
as(dtm, "CsparseMatrix")
## 	  }
})

setAs("sparseMatrix", "graph", function(from) as(from, "graphNEL"))
setAs("sparseMatrix", "graphNEL",
function(from) as(as(from, "TsparseMatrix"), "graphNEL"))

Tsp2grNEL <- function(from) {
d <- dim(from)
if(d[1] != d[2])
stop("only square matrices can be used as incidence matrices for graphs")
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)) { # either "symmetricMatrix" or otherwise
##-> undirected graph: every edge only once!
if(!is(from, "symmetricMatrix")) {
## a general matrix which happens to be symmetric
## ==> remove the double indices
from <- tril(from)
}
## every edge is there only once, either upper or lower triangle
ft1 <- cbind(from@i + 1:1, from@j + 1:1)
## not yet: graph::ftM2graphNEL(.........)
ftM2graphNEL(ft1, W = from@x, V= rn, edgemode= "undirected")

} else { ## not symmetric

## not yet: graph::ftM2graphNEL(.........)
ftM2graphNEL(cbind(from@i + 1:1, from@j + 1:1),
W = from@x, V= rn, edgemode= "directed")
}

}
setAs("TsparseMatrix", "graphNEL", Tsp2grNEL)

### 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 <- paste(.M.kind(x,cl), "gTMatrix", sep='')
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 <- paste(.M.kind(x,cl), "gTMatrix", sep='')
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 <- paste(.M.kind(x,cl), "gTMatrix", sep='')
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 = "nsparseMatrix", e2 = "missing"),
function(e1) callGeneric(as(e1, "dgCMatrix")))
setMethod("-", signature(e1 = "pMatrix", e2 = "missing"),
function(e1) callGeneric(as(e1, "ngTMatrix")))

## Group method  "Arith"

## have CsparseMatrix methods (-> ./Csparse.R )
## which may preserve "symmetric", "triangular" -- simply defer to those:

setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
signature(e1 = "sparseMatrix", e2 = "sparseMatrix"),
function(e1, e2) callGeneric(as(e1, "CsparseMatrix"),
as(e2, "CsparseMatrix")))
setMethod("Arith",
signature(e1 = "sparseMatrix", e2 = "numeric"),
function(e1, e2) callGeneric(as(e1, "CsparseMatrix"), e2))
setMethod("Arith",
signature(e1 = "numeric", e2 = "sparseMatrix"),
function(e1, e2) callGeneric(e1, as(e2, "CsparseMatrix")))

setMethod("Math",
signature(x = "sparseMatrix"),
function(x) callGeneric(as(x, "CsparseMatrix")))

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

## FIXME(?) -- ``merge this'' (at least ``synchronize'') with
## - - -   prMatrix() from ./Auxiliaries.R
prSpMatrix <- function(object, digits = getOption("digits"),
maxp = getOption("max.print"), zero.print = ".")
{
stopifnot(is(object, "sparseMatrix"))
d <- dim(object)
if(prod(d) > maxp) { # "Large" => will be "cut"
## only coerce to dense that part which won't be cut :
nr <- maxp %/% d[2]
m <- as(object[1:max(1, nr), ,drop=FALSE], "Matrix")
} else {
m <- as(object, "matrix")
}
logi <- is(object,"lsparseMatrix") || is(object,"nsparseMatrix")
if(logi)
x <- array(character(length(m)), dim(m), dimnames=dimnames(m))
else {
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 " "
if(logi) {
x[!m] <- zero.print
x[m] <- "|"
} else { # non logical
## show only "structural" zeros as 'zero.print', not all of them..
## -> cannot use 'm'
iN0 <- 1:1 + encodeInd(non0ind(object), nr = nrow(x))
if(length(iN0)) x[-iN0] <- zero.print else x[] <- zero.print
}
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, maxp = maxp)
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 if (is(object, "nMatrix"))
## test for exact equality; FIXME(?): identical() too strict?
identical(as(object, "ngCMatrix"),
as(t(object), "ngCMatrix"))
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)
})

setMethod("diag", signature(x = "sparseMatrix"),
function(x, nrow, ncol = n) diag(as(x, "CsparseMatrix")))

## .as.dgT.Fun
setMethod("colSums",  signature(x = "sparseMatrix"), .as.dgT.Fun)
setMethod("colMeans", signature(x = "sparseMatrix"), .as.dgT.Fun)
## .as.dgC.Fun
setMethod("rowSums", signature(x = "sparseMatrix"), .as.dgC.Fun)
setMethod("rowMeans", signature(x = "sparseMatrix"),.as.dgC.Fun)
```