setAs("matrix", "dgeMatrix", function(from) .Call(dup_mMatrix_as_dgeMatrix, from)) if(FALSE)## the above is MUCH faster than setAs("matrix", "dgeMatrix", function(from) { new("dgeMatrix", x = as.double(from), Dim = as.integer(dim(from)), Dimnames = .M.DN(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) 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", type = "missing"), function(x, type, ...) rcond(x, type = "O", ...)) setMethod("rcond", signature(x = "dgeMatrix", type = "character"), function(x, type, ...) .Call(dgeMatrix_rcond, x, type), valueClass = "numeric") 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) callGeneric(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) callGeneric(as(x, "dgeMatrix"), y), valueClass = "dgeMatrix") setMethod("crossprod", signature(x = "numeric", y = "dgeMatrix"), function(x, y = NULL) callGeneric(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) callGeneric(as(x, "dgeMatrix"), y), valueClass = "dgeMatrix") setMethod("tcrossprod", signature(x = "numeric", y = "dgeMatrix"), function(x, y = NULL) callGeneric(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 = n) .Call(dgeMatrix_getDiag, x)) setMethod("chol", signature(x = "dgeMatrix", pivot = "ANY"), 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