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[matrix] Diff of /pkg/R/Matrix.R
 [matrix] / pkg / R / Matrix.R

# Diff of /pkg/R/Matrix.R

revision 1551, Tue Sep 12 16:39:13 2006 UTC revision 1660, Thu Nov 2 11:05:35 2006 UTC
# Line 6  Line 6
6  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8
9    ## Most of these work; this is a last resort:
10  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
11        function(from) .bail.out.2("coerce", class(from), class(to)))        function(from) .bail.out.2("coerce", class(from), class(to)))
12    setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
13
14  ## ## probably not needed eventually:  ## ## probably not needed eventually:
15  ## setAs(from = "ddenseMatrix", to = "matrix",  ## setAs(from = "ddenseMatrix", to = "matrix",
# Line 81  Line 83
83          prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)          prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)
84
85      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
86      if(is.null(sparse) && (i.M || is(data, "matrix")))
87        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
88          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
89
90      doDN <- TRUE      doDN <- TRUE
# Line 96  Line 99
99              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
100          else if (missing(ncol))          else if (missing(ncol))
101              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
102          if(length(data) == 1 && !is.na(data) && data == 0 &&          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
103             !identical(sparse, FALSE)) {              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
104                if(is.null(sparse)) sparse1 <- sparse <- TRUE
if(is.null(sparse)) sparse <- TRUE
105              ## will be sparse: do NOT construct full matrix!              ## will be sparse: do NOT construct full matrix!
106              data <- new(if(is.numeric(data)) "dgTMatrix" else              data <- new(if(is.numeric(data)) "dgTMatrix" else
107                          if(is.logical(data)) "lgTMatrix" else                          if(is.logical(data)) "lgTMatrix" else
# Line 127  Line 129
129      if(isDiag)      if(isDiag)
130          isDiag <- isDiagonal(data)          isDiag <- isDiagonal(data)
131
### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R

132      ## Find proper matrix class 'cl'      ## Find proper matrix class 'cl'
133      cl <-      cl <-
134          if(isDiag)          if(isDiag && !isTRUE(sparse1))
135              "diagonalMatrix" # -> will automatically check for type              "diagonalMatrix" # -> will automatically check for type
136          else {          else {
137              ## consider it's type              ## consider it's type
# Line 172  Line 172
172            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
173
174  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
175            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
176
177  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
178            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
# Line 188  Line 188
188
189  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
190            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
191    ## when no sub-class method is found, bail out
192    setMethod("solve", signature(a = "Matrix", b = "matrix"),
193              function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
194
195  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
196  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 221  Line 224
224                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
225
226
227    ## FIXME: All of these should never be called
228    setMethod("chol", signature(x = "Matrix"),
229              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
230    setMethod("determinant", signature(x = "Matrix"),
231              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
232
233  setMethod("diag", signature(x = "Matrix"),  setMethod("diag", signature(x = "Matrix"),
234            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
235  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
# Line 235  Line 244
244                0-e1                0-e1
245            })            })
246
247  ## bail-outs:  ## old-style matrices are made into new ones
248  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),  setMethod("Ops", signature(e1 = "Matrix", e2 = "matrix"),
249              function(e1, e2) callGeneric(e1, Matrix(e2)))
250    ##          callGeneric(e1, Matrix(e2, sparse=is(e1,"sparseMatrix"))))
251    setMethod("Ops", signature(e1 = "matrix", e2 = "Matrix"),
252              function(e1, e2) callGeneric(Matrix(e1), e2))
253
254    ## bail-outs -- on highest possible level, hence "Ops", not "Compare"/"Arith" :
255    setMethod("Ops", signature(e1 = "Matrix", e2 = "Matrix"),
256            function(e1, e2) {            function(e1, e2) {
257                d <- dimCheck(e1,e2)                d <- dimCheck(e1,e2)
258                .bail.out.2(.Generic, class(e1), class(e2))                .bail.out.2(.Generic, class(e1), class(e2))
259            })            })
260  setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),  setMethod("Ops", signature(e1 = "Matrix", e2 = "ANY"),
261            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
262  setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),  setMethod("Ops", signature(e1 = "ANY", e2 = "Matrix"),
263            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
264
265
# Line 314  Line 330
330  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
331                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
332            function (x, value) {            function (x, value) {
333                  ## Fails for 'nMatrix' ... FIXME : make sure have method there
334                x@x <- value                x@x <- value
335                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
336                x                x
337            })            })
338
339  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
340                                    value = "Matrix"),
341                     function (x, i, j, value)
342                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
343    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
344                                    value = "matrix"),
345                     function (x, i, j, value)
346                     callGeneric(x=x, i=i, j=j, value = c(value)))
347
348  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## (ANY,ANY,ANY) is used when no `real method' is implemented :
349  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
350                                  value = "ANY"),                                  value = "ANY"),
351            function (x, i, j, value) {            function (x, i, j, value) {
352                if(!is.atomic(value))                if(!is.atomic(value))
353                    stop("RHS 'value' must match matrix class ", class(x))                    stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
354                                   class(value),class(x)))
355                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
356            })            })
357

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