The R Project SVN R-packages

### Simple fallback methods for all dense matrices
### These are "cheap" to program, but potentially far from efficient;
### Methods for specific subclasses will overwrite these:

setAs("ANY", "denseMatrix", function(from) Matrix(from, sparse=FALSE))


## dense to sparse:
setAs("denseMatrix", "dsparseMatrix",
## MM thought that  as() will take the ``closest'' match; but that fails!
##      function(from) as(as(from, "dgeMatrix"), "dsparseMatrix"))
      function(from) as(as(from, "dgeMatrix"), "dgCMatrix"))

setAs("denseMatrix", "CsparseMatrix",
      function(from) {
          cl <- class(from)
      notGen <- !is(from, "generalMatrix")
      if (notGen) { ## e.g. for triangular | symmetric
              ## FIXME: this is a *waste* in the case of packed matrices!
          if     (extends(cl, "dMatrix")) from <- as(from, "dgeMatrix")
          else if(extends(cl, "lMatrix")) from <- as(from, "lgeMatrix")
          else if(extends(cl, "zMatrix")) from <- as(from, "zgeMatrix")
          else stop("undefined method for class ", cl)
      }
      .Call(dense_to_Csparse, from)
      })

setAs("denseMatrix", "TsparseMatrix",
      function(from) as(as(from, "CsparseMatrix"), "TsparseMatrix"))


setMethod("show", signature(object = "denseMatrix"),
          function(object) prMatrix(object))
##- ## FIXME: The following is only for the "dMatrix" objects that are not
##- ##        "dense" nor "sparse" -- i.e. "packed" ones :
##- ## But these could be printed better -- "." for structural zeros.
##- setMethod("show", signature(object = "dMatrix"), prMatrix)
##- ## and improve this as well:
##- setMethod("show", signature(object = "pMatrix"), prMatrix)
##- ## this should now be superfluous [keep for safety for the moment]:

## Using "index" for indices should allow
## integer (numeric), logical, or character (names!) indices :

## use geClass() when 'i' or 'j' are missing:
## since  symmetric, triangular, .. will not be preserved anyway:
setMethod("[", signature(x = "denseMatrix", i = "index", j = "missing",
             drop = "logical"),
      function (x, i, drop) {
          r <- as(x, "matrix")[i, , drop=drop]
          if(is.null(dim(r))) r else as(r, geClass(x))
      })

setMethod("[", signature(x = "denseMatrix", i = "missing", j = "index",
             drop = "logical"),
      function (x, j, drop) {
          r <- as(x, "matrix")[, j, drop=drop]
          if(is.null(dim(r))) r else as(r, geClass(x))
      })

setMethod("[", signature(x = "denseMatrix", i = "index", j = "index",
             drop = "logical"),
      function (x, i, j, drop) {
          r <- callGeneric(x = as(x, "matrix"), i=i, j=j, drop=drop)
          if(is.null(dim(r))) r else as_geClass(r, class(x))
      })

## Now the "[<-" ones --- see also those in ./Matrix.R
## It's recommended to use setReplaceMethod() rather than setMethod("[<-",.)
## even though the former is currently just a wrapper for the latter

## FIXME: 1) These are far from efficient
## -----  2) value = "numeric" is only ok for "ddense*"
setReplaceMethod("[", signature(x = "denseMatrix", i = "index", j = "missing",
                value = "numeric"),
         function (x, i, value) {
             r <- as(x, "matrix")
             r[i, ] <- value
             as(r, geClass(x))
         })

setReplaceMethod("[", signature(x = "denseMatrix", i = "missing", j = "index",
                value = "numeric"),
         function (x, j, value) {
             r <- as(x, "matrix")
             r[, j] <- value
             as(r, geClass(x))
         })

setReplaceMethod("[", signature(x = "denseMatrix", i = "index", j = "index",
                value = "numeric"),
         function (x, i, j, value) {
             r <- as(x, "matrix")
             r[i, j] <- value
             as_geClass(r, class(x)) ## was as(r, class(x))
         })


setMethod("isSymmetric", signature(object = "denseMatrix"),
      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"))
          isTRUE(all.equal(as(object, "dgeMatrix"),
                   as(t(object), "dgeMatrix"), tol = tol))
          else if (is(object, "lMatrix"))# not possible currently
          ## test for exact equality; FIXME(?): identical() too strict?
          identical(as(object, "lgeMatrix"),
                as(t(object), "lgeMatrix"))
          else if (is(object, "zMatrix"))
                  stop("'zMatrix' not yet implemented")
          else if (is(object, "iMatrix"))
                  stop("'iMatrix' not yet implemented")
      })

setMethod("isTriangular", signature(object = "triangularMatrix"),
      function(object, ...) TRUE)

setMethod("isTriangular", signature(object = "denseMatrix"), isTriMat)

setMethod("isDiagonal", signature(object = "denseMatrix"), .is.diagonal)

.as.dge.Fun <- function(x, na.rm = FALSE, dims = 1) {
    x <- as(x, "dgeMatrix")
    callGeneric()
}
setMethod("colSums",  signature(x = "denseMatrix"), .as.dge.Fun)
setMethod("colMeans", signature(x = "denseMatrix"), .as.dge.Fun)
setMethod("rowSums",  signature(x = "denseMatrix"), .as.dge.Fun)
setMethod("rowMeans", signature(x = "denseMatrix"), .as.dge.Fun)