The R Project SVN R-packages

setAs("matrix", "dgeMatrix",
      function(from) .Call(dup_mMatrix_as_dgeMatrix, from))

setAs("dgeMatrix", "matrix",
      function(from) {
      array(from@x, dim = from@Dim, dimnames = from@Dimnames)
      })

## Group Methods, see ?Math (e.g.)

##  "Arith" is in ./Ops.R

setMethod("Math", signature(x = "dgeMatrix"),
      function(x) {
          x@x <- callGeneric(x@x)
          x
      })

##  "Math2" is in ./dMatrix.R

## "Summary"

## "Compare"  now happens in ./dMatrix.R

## -- end{group generics} -----------------------


##  "[" settings are "up in"  Matrix.R & denseMatrix.R


setMethod("as.vector", signature(x = "dgeMatrix", mode = "missing"),
          function(x, mode) x@x)

setMethod("norm", signature(x = "dgeMatrix", type = "missing"),
      function(x, type, ...) norm(x, type = "O", ...))
setMethod("norm", signature(x = "dgeMatrix", type = "character"),
      function(x, type, ...) .Call(dgeMatrix_norm, x, type),
      valueClass = "numeric")

setMethod("rcond", signature(x = "dgeMatrix", norm = "missing"),
      function(x, norm, ...) rcond(x, norm = "O", ...))
setMethod("rcond", signature(x = "dgeMatrix", norm = "character"),
      function(x, norm, ...)  {
          if({d <- dim(x); d[1] == d[2]})
          .Call(dgeMatrix_rcond, x, norm)
          else rcond(qr.R(qr(if(d[1] < d[2]) t(x) else x)), norm=norm, ...)
      },
      valueClass = "numeric")

##--- the same for "traditional"  'matrix':
setMethod("norm", signature(x = "matrix", type = "character"),
      function(x, type, ...) .Call(dgeMatrix_norm, as(x,"dgeMatrix"), type),
      valueClass = "numeric")

## for now:
if(!existsFunction("rcond", where=baseenv()))## later: (exists(getRversion() < "2.7.0")
## afterwards, this should continue using base::rcond
setMethod("rcond", signature(x = "matrix", norm = "character"),
      function(x, norm, ...) rcond(as(x,"dgeMatrix"), norm=norm, ...))


setMethod("t", signature(x = "dgeMatrix"), t_geMatrix)

## crossprod(x) & tcrossprod(x) :
setMethod("crossprod", signature(x = "dgeMatrix", y = "missing"),
      function(x, y = NULL) .Call(dgeMatrix_crossprod, x, FALSE),
      valueClass = "dpoMatrix")

setMethod("tcrossprod", signature(x = "dgeMatrix", y = "missing"),
      function(x, y = NULL) .Call(dgeMatrix_crossprod, x, TRUE),
      valueClass = "dpoMatrix")

if(FALSE) { ## this would mask 'base::tcrossprod'
setMethod("tcrossprod", signature(x = "matrix", y = "missing"),
      function(x, y = NULL)
          .Call(dgeMatrix_crossprod, as(x, "dgeMatrix"), TRUE),
      valueClass = "dpoMatrix")

setMethod("tcrossprod", signature(x = "numeric", y = "missing"),
      function(x, y = NULL) tcrossprod(as.matrix(as.double(x))))
}

## crossprod (x,y)
setMethod("crossprod", signature(x = "dgeMatrix", y = "dgeMatrix"),
      function(x, y = NULL) .Call(dgeMatrix_dgeMatrix_crossprod, x, y, FALSE),
      valueClass = "dgeMatrix")

setMethod("crossprod", signature(x = "dgeMatrix", y = "matrix"),
      function(x, y = NULL) .Call(dgeMatrix_matrix_crossprod, x, y, FALSE),
      valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "dgeMatrix", y = "numeric"),
      function(x, y = NULL)
      .Call(dgeMatrix_matrix_crossprod, x, as.matrix(as.double(y)), FALSE),
      valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "matrix", y = "dgeMatrix"),
      function(x, y = NULL) crossprod(as(x, "dgeMatrix"), y),
      valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "numeric", y = "dgeMatrix"),
      function(x, y = NULL) crossprod(as.matrix(as.double(x)), y),
      valueClass = "dgeMatrix")

## tcrossprod (x,y)
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "dgeMatrix"),
      function(x, y = NULL) .Call(dgeMatrix_dgeMatrix_crossprod, x, y, TRUE),
      valueClass = "dgeMatrix")

setMethod("tcrossprod", signature(x = "dgeMatrix", y = "matrix"),
      function(x, y = NULL) .Call(dgeMatrix_matrix_crossprod, x, y, TRUE),
      valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "numeric"),
      function(x, y = NULL)
      .Call(dgeMatrix_matrix_crossprod, x, rbind(as.double(y)), TRUE),
      valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "matrix", y = "dgeMatrix"),
      function(x, y = NULL) tcrossprod(as(x, "dgeMatrix"), y),
      valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "numeric", y = "dgeMatrix"),
      function(x, y = NULL) tcrossprod(rbind(as.double(x)), y),
      valueClass = "dgeMatrix")

## %*% methods
setMethod("%*%", signature(x = "dgeMatrix", y = "dgeMatrix"),
      function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
      valueClass = "dgeMatrix")

setMethod("%*%", signature(x = "dgeMatrix", y = "matrix"),
      function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
          valueClass = "dgeMatrix")

setMethod("%*%", signature(x = "matrix", y = "dgeMatrix"),
      function(x, y) .Call(dgeMatrix_matrix_mm, y, x, TRUE),
          valueClass = "dgeMatrix")

## DB: Should we retain these methods?  Does the shortcut save enough
## to justify additional signatures?
## dgeMatrix <-> numeric: conceptually dispatch to "matrix" one, but shortcut
setMethod("%*%", signature(x = "dgeMatrix", y = "numeric"),
      function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
      valueClass = "dgeMatrix")

setMethod("%*%", signature(x = "numeric", y = "dgeMatrix"),
      function(x, y)
      .Call(dgeMatrix_matrix_mm, y, rbind(x), TRUE),
      valueClass = "dgeMatrix")

setMethod("diag", signature(x = "dgeMatrix"),
      function(x, nrow, ncol) .Call(dgeMatrix_getDiag, x))

setMethod("chol", signature(x = "dgeMatrix"), cholMat)

setMethod("solve", signature(a = "dgeMatrix", b = "missing"),
      function(a, b, ...) .Call(dgeMatrix_solve, a),
      valueClass = "dgeMatrix")

setMethod("solve", signature(a = "dgeMatrix", b = "ddenseMatrix"),
      function(a, b, ...) .Call(dgeMatrix_matrix_solve, a, b),
      valueClass = "dgeMatrix")

setMethod("solve", signature(a = "dgeMatrix", b = "matrix"),
      function(a, b, ...) .Call(dgeMatrix_matrix_solve, a, b),
          valueClass = "dgeMatrix")

## not needed - method for numeric defined for Matrix class
## setMethod("solve", signature(a = "dgeMatrix", b = "numeric"),
##    function(a, b, ...)
##    .Call(dgeMatrix_matrix_solve, a, as.matrix(as.double(b))))

setMethod("lu", signature(x = "dgeMatrix"),
      function(x, ...) .Call(dgeMatrix_LU, x),
      valueClass = "denseLU")

setMethod("determinant", signature(x = "dgeMatrix", logarithm = "missing"),
      function(x, logarithm, ...)
      .Call(dgeMatrix_determinant, x, TRUE))

setMethod("determinant", signature(x = "dgeMatrix", logarithm = "logical"),
      function(x, logarithm, ...)
      .Call(dgeMatrix_determinant, x, logarithm))


setMethod("expm", signature(x = "dgeMatrix"),
      function(x) .Call(dgeMatrix_exp, x),
      valueClass = "dgeMatrix")

##-> ./colSums.R  for colSums,... rowMeans