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Diff of /pkg/R/Matrix.R

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revision 1290, Thu Jun 8 09:30:21 2006 UTC revision 1799, Sat Mar 24 14:54:00 2007 UTC
# Line 1  Line 1 
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2    
3    
4    ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5    
6    setAs("Matrix", "sparseMatrix", function(from) as(from, "CsparseMatrix"))
7    setAs("Matrix", "CsparseMatrix", function(from) as_Csparse(from))
8    setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
9    
10    ## Maybe TODO:
11    ## setAs("Matrix", "nMatrix", function(from) ....)
12    
13    ## Most of these work; this is a last resort:
14    setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
15          function(from) .bail.out.2("coerce", class(from), class(to)))
16    setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
17    
18  ## ## probably not needed eventually:  ## ## probably not needed eventually:
19  ## setAs(from = "ddenseMatrix", to = "matrix",  ## setAs(from = "ddenseMatrix", to = "matrix",
20  ##       function(from) {  ##       function(from) {
# Line 12  Line 27 
27  ## for 'Matrix' objects, as.array() should be equivalent:  ## for 'Matrix' objects, as.array() should be equivalent:
28  setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))  setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
29    
30    ## head and tail apply to all Matrix objects for which subscripting is allowed:
31    setMethod("head", signature(x = "Matrix"), utils::head.matrix)
32    setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
33    
34    setMethod("drop", signature(x = "Matrix"),
35              function(x) if(all(dim(x) != 1)) x else drop(as(x, "matrix")))
36    
37  ## slow "fall back" method {subclasses should have faster ones}:  ## slow "fall back" method {subclasses should have faster ones}:
38  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),  setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
39            function(x) as.vector(as(x, "matrix")))            function(x) as.vector(as(x, "matrix")))
40    
41    ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
42    setMethod("as.numeric", signature(x = "Matrix"),
43              function(x, ...) as.numeric(as.vector(x)))
44    setMethod("as.logical", signature(x = "Matrix"),
45              function(x, ...) as.logical(as.vector(x)))
46    
47  ## Note that isSymmetric is *not* exported  
48  ## but that "base" has an isSymmetric() S3-generic since R 2.3.0  ## "base" has an isSymmetric() S3-generic since R 2.3.0
49  setMethod("isSymmetric", signature(object = "symmetricMatrix"),  setMethod("isSymmetric", signature(object = "symmetricMatrix"),
50            function(object,tol) TRUE)            function(object,tol) TRUE)
51  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
52            ## TRUE iff diagonal:            ## TRUE iff diagonal:
53            function(object,tol) isDiagonal(object))            function(object,tol) isDiagonal(object))
54    
 if(paste(R.version$major, R.version$minor, sep=".") < "2.3")  
     ## need a "matrix" method as in R 2.3 and later  
     setMethod("isSymmetric", signature(object = "matrix"),  
               function(object, tol = 100*.Machine$double.eps, ...)  
           {  
               ## pretest: is it square?  
               d <- dim(object)  
               if(d[1] != d[2]) return(FALSE)  
               ## for `broken' all.equal in R <= 2.2.x:  
               dn <- dimnames(object)  
               if(!identical(dn[1], dn[2])) return(FALSE)  
               test <-  
                   if(is.complex(object))  
                       all.equal.numeric(object, Conj(t(object)), tol = tol, ...)  
                   else              # numeric, character, ..  
                       all.equal(object, t(object), tol = tol, ...)  
               isTRUE(test)  
           })  
   
   
55  setMethod("isTriangular", signature(object = "triangularMatrix"),  setMethod("isTriangular", signature(object = "triangularMatrix"),
56            function(object, ...) TRUE)            function(object, ...) TRUE)
57    
# Line 56  Line 63 
63    
64  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
65            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
66    
67    setMethod("length", "Matrix", function(x) prod(dim(x)))
68    
69  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
70    
71    
72  ## not exported but used more than once for "dimnames<-" method :  ## not exported but used more than once for "dimnames<-" method :
73  ## -- or do only once for all "Matrix" classes ??  ## -- or do only once for all "Matrix" classes ??
74  dimnamesGets <- function (x, value) {  dimnamesGets <- function (x, value) {
# Line 75  Line 87 
87  setMethod("unname", signature("Matrix", force="missing"),  setMethod("unname", signature("Matrix", force="missing"),
88            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
89    
90    setMethod("all", signature(x = "Matrix"),
91              function(x, ..., na.rm) { x <- as(x, "lMatrix"); callGeneric()})
92    setMethod("any", signature(x = "Matrix"),
93              function(x, ..., na.rm) { x <- as(x, "lMatrix"); callGeneric()})
94    
95    setMethod("!", "Matrix", function(e1) !as(e1, "lMatrix"))
96    
97    
98    
99  Matrix <-  Matrix <-
100      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
101                sparse = NULL)                sparse = NULL, forceCheck = FALSE)
102  {  {
103      sparseDefault <- function(m)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
         prod(dim(m)) > 2*sum(as(m, "matrix") != 0)  
104    
105      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
106      if(is.null(sparse) && (i.M || is(data, "matrix")))  
107        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
108          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
109    
110        doDN <- TRUE
111      if (i.M) {      if (i.M) {
112            if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
113                warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
114          sM <- is(data,"sparseMatrix")          sM <- is(data,"sparseMatrix")
115          if((sparse && sM) || (!sparse && !sM))          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
116              return(data)              return(data)
117          ## else : convert  dense <-> sparse -> at end          ## else : convert  dense <-> sparse -> at end
118      }      }
# Line 97  Line 121 
121              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
122          else if (missing(ncol))          else if (missing(ncol))
123              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
124            if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
125                ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
126                if(is.null(sparse)) sparse1 <- sparse <- TRUE
127                ## will be sparse: do NOT construct full matrix!
128                data <- new(if(is.numeric(data)) "dgTMatrix" else
129                            if(is.logical(data)) "lgTMatrix" else
130                            stop("invalid 'data'"),
131                            Dim = as.integer(c(nrow,ncol)),
132                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
133                            else dimnames)
134            } else { ## normal case
135          data <- .Internal(matrix(data, nrow, ncol, byrow))          data <- .Internal(matrix(data, nrow, ncol, byrow))
136          if(is.null(sparse))          if(is.null(sparse))
137              sparse <- sparseDefault(data)              sparse <- sparseDefault(data)
138          dimnames(data) <- dimnames          dimnames(data) <- dimnames
139      } else if (!is.null(dimnames))          }
140          dimnames(data) <- dimnames          doDN <- FALSE
141        } else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
142            warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
143    
144      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
145        if (doDN && !is.null(dimnames))
146            dimnames(data) <- dimnames
147    
148      ## check for symmetric / triangular / diagonal :      ## check for symmetric / triangular / diagonal :
149      isSym <- isSymmetric(data)      isSym <- isSymmetric(data)
# Line 114  Line 153 
153      if(isDiag)      if(isDiag)
154          isDiag <- isDiagonal(data)          isDiag <- isDiagonal(data)
155    
 ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R  
   
156      ## Find proper matrix class 'cl'      ## Find proper matrix class 'cl'
157      cl <-      cl <-
158          if(isDiag)          if(isDiag && !isTRUE(sparse1))
159              "diagonalMatrix" # -> will automatically check for type              "diagonalMatrix" # -> will automatically check for type
160          else {          else {
161              ## consider it's type              ## consider it's type
# Line 159  Line 196 
196            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
197    
198  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
199            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
200    
201  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
202            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
   
203  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
204            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
205    
206    ## The as.matrix() promotion seems illogical to MM,
207    ## but is according to help(tcrossprod, package = "base") :
208    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
209              function(x, y = NULL) callGeneric(x, as.matrix(y)))
210    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
211              function(x, y = NULL)  callGeneric(as.matrix(x), y))
212    
213    ## maybe not optimal
214    setMethod("solve", signature(a = "Matrix", b = "missing"),
215              function(a, b, ...) solve(a, Diagonal(nrow(a))))
216    
217  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
218            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
219    ## when no sub-class method is found, bail out
220    setMethod("solve", signature(a = "Matrix", b = "matrix"),
221              function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
222    setMethod("solve", signature(a = "Matrix", b = "Matrix"),
223              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
224    
225  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
226  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 180  Line 232 
232            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
233  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
234            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
235    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
236              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
237    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
238              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
239    
240    ## cheap fallbacks
241    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
242              function(x, y = NULL) t(x) %*% y)
243    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
244              function(x, y = NULL) x %*% t(y))
245    
246  ## There are special sparse methods; this is a "fall back":  ## There are special sparse methods; this is a "fall back":
247  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
# Line 192  Line 254 
254                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
255    
256    
257    ## FIXME: All of these should never be called
258    setMethod("chol", signature(x = "Matrix"),
259              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
260    setMethod("determinant", signature(x = "Matrix"),
261              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
262    
263    setMethod("diag", signature(x = "Matrix"),
264              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
265  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
266            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
267    
268  ## Group Methods  setMethod("dim<-", signature(x = "Matrix", value = "ANY"),
269  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, value) {
270  ## "fallback":                if(!is.numeric(value) || length(value) != 2)
271  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),                    stop("dim(.) value must be numeric of length 2")
272            function(e1) {                if(prod(dim(x)) != prod(value <- as.integer(value)))
273                warning("inefficient method used for \"- e1\"")                    stop("dimensions don't match the number of cells")
274                0-e1                clx <- class(x)
275                  if(substring(clx,2) == "geMatrix") {
276                      x@Dim <- value
277                      if(length(x@factors) > 0)
278                          x@factors <- list()
279                      x
280                  } else if(extends(clx, "denseMatrix")) {
281                      x <- as_geSimpl2(x, clx)
282                      dim(x) <- value
283                  } else { ## FIXME: this is very inefficient for large sparse x
284                      Matrix(as.vector(x), value[1], value[2])
285                  }
286            })            })
287    
288  ## bail-outs:  ## MM: More or less "Cut & paste" from
289  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),  ## --- diff.default() from  R/src/library/base/R/diff.R :
290            function(e1, e2) {  setMethod("diff", signature(x = "Matrix"),
291                d <- dimCheck(e1,e2)            function(x, lag = 1, differences = 1, ...) {
292                .bail.out.2(.Generic, class(e1), class(e2))                if (length(lag) > 1 || length(differences) > 1 ||
293                      lag < 1 || differences < 1)
294                      stop("'lag' and 'differences' must be integers >= 1")
295                  xlen <- nrow(x)
296                  if (lag * differences >= xlen)
297                      return(x[,FALSE][0])  # empty of proper mode
298    
299                  i1 <- -1:-lag
300                  for (i in 1:differences)
301                      x <- x[i1, , drop = FALSE] -
302                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
303                  x
304            })            })
 setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),  
           function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  
 setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),  
           function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  
305    
306    
307    ## Group Methods
308    
309    ##-> see ./Ops.R
310    
311  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
312  ###  ###
# Line 235  Line 326 
326  ## select rows  ## select rows
327  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
328                           drop = "missing"),                           drop = "missing"),
329            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, drop) {
330                  if(nargs() == 1) { ## e.g. M[0] , M[TRUE],  M[1:2]
331                      if(any(i)) as.vector(x)[i] else as.vector(x[1,1])[FALSE]
332                  } else callGeneric(x, i=i, drop= TRUE)})
333    
334  ## select columns  ## select columns
335  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
336                           drop = "missing"),                           drop = "missing"),
# Line 249  Line 344 
344            function(x,i,j, drop)            function(x,i,j, drop)
345            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
346    
347  ##  "logical *vector* indexing, such as  M [ M >= 10 ] :  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
348  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  ## The following is *both* for    M [ <logical>   ]
349                           drop = "ANY"),  ##                 and also for   M [ <logical> , ]
350            function (x, i, j, drop) {  .M.sub.i.logical <- function (x, i, j, drop)
351    {
352        nA <- nargs()
353        if(nA == 2) { ##  M [ M >= 7 ]
354            ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
355                as(x, geClass(x))@x[as.vector(i)]                as(x, geClass(x))@x[as.vector(i)]
356                                          # -> error when lengths don't match          ## -> error when lengths don't match
357            })      } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
358            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
359    
360        } else stop("nargs() = ", nA,
361                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
362    }
363    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
364                             drop = "ANY"),
365              .M.sub.i.logical)
366  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
367                           drop = "ANY"),                           drop = "ANY"),
368            function (x, i, j, drop) as(x, geClass(x))@x[i])            .M.sub.i.logical)
369    
370    
371  ## "FIXME:"  ## A[ ij ]  where ij is (i,j) 2-column matrix :
372  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  .M.sub.i.2col <- function (x, i, j, drop)
373  ##  and                A[ LL ]  where LL is a logical *vector*  {
374  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?      nA <- nargs()
375        if(nA == 2) { ##  M [ cbind(ii,jj) ]
376            if(!is.integer(nc <- ncol(i)))
377                stop("'i' has no integer column number",
378                     " should never happen; please report")
379            if(is.logical(i))
380                return(.M.sub.i.logical(x,i,j,drop))
381            else if(!is.numeric(i) || nc != 2)
382                stop("such indexing must be by logical or 2-column numeric matrix")
383            m <- nrow(i)
384            if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
385            ## else
386            i1 <- i[,1]
387            i2 <- i[,2]
388            ## potentially inefficient -- FIXME --
389            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
390    
391        } else stop("nargs() = ", nA,
392                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
393    }
394    setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
395              .M.sub.i.2col)
396    
397    
398  ### "[<-" : -----------------  ### "[<-" : -----------------
# Line 274  Line 401 
401  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
402                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
403            function (x, value) {            function (x, value) {
404                x@x <- value                ## Fails for 'nMatrix' ... FIXME : make sure have method there
405                  x@x <- rep(value, length = length(x@x))
406                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
407                x                x
408            })            })
409    
410  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
411    ## ----------------   The cheap general method --- FIXME: provide special ones
412    .M.repl.i.2col <- function (x, i, j, value)
413    {
414        nA <- nargs()
415        if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value
416            if(!is.integer(nc <- ncol(i)))
417                stop("'i' has no integer column number",
418                     " should never happen; please report")
419            else if(!is.numeric(i) || nc != 2)
420                stop("such indexing must be by logical or 2-column numeric matrix")
421            if(is.logical(i)) {
422                message(".M.repl.i.2col(): drop 'matrix' case ...")
423                i <- c(i) # drop "matrix"
424                return( callNextMethod() )
425            }
426            if(!is.integer(i)) storage.mode(i) <- "integer"
427            if(any(i < 0))
428                stop("negative values are not allowed in a matrix subscript")
429            if(any(is.na(i)))
430                stop("NAs are not allowed in subscripted assignments")
431            if(any(i0 <- (i == 0))) # remove them
432                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
433            ## now have integer i >= 1
434            m <- nrow(i)
435            ## mod.x <- .type.kind[.M.kind(x)]
436            if(length(value) > 0 && m %% length(value) != 0)
437                warning("number of items to replace is not a multiple of replacement length")
438            ## recycle:
439            value <- rep(value, length = m)
440            i1 <- i[,1]
441            i2 <- i[,2]
442            ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
443            for(k in seq_len(m))
444                x[i1[k], i2[k]] <- value[k]
445    
446            x
447        } else stop("nargs() = ", nA,
448                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
449    }
450    
451    setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
452                                    value = "replValue"),
453              .M.repl.i.2col)
454    
455    
456    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
457                                    value = "Matrix"),
458                     function (x, i, j, value) {
459    ### *TEMPORARY* diagnostic output:
460    ##                  cat("<Matrix1>[i,j] <- <Matrix1>:\n<Matrix1> = x :")
461    ##                  str(x)
462    ##                  cat("<Matrix2> = value :")
463    ##                  str(value)
464    ##                  cat("i :"); if(!missing(i)) str(i) else cat("<missing>\n")
465    ##                  cat("j :"); if(!missing(j)) str(j) else cat("<missing>\n")
466    
467                         callGeneric(x=x, i=i, j=j, value = as.vector(value))
468                     })
469    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
470                                    value = "Matrix"),
471                     function (x, i, j, value)
472                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
473    
474    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
475                                    value = "matrix"),
476                     function (x, i, j, value)
477                     callGeneric(x=x, i=i, j=j, value = c(value)))
478    
479  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## (ANY,ANY,ANY) is used when no `real method' is implemented :
480  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
481                                  value = "ANY"),                                  value = "ANY"),
482            function (x, i, j, value) {            function (x, i, j, value) {
483                if(!is.atomic(value))                if(!is.atomic(value))
484                    stop("RHS 'value' must match matrix class ", class(x))                    stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
485                                   class(value),class(x)))
486                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
487            })            })
   
   
 ## The trivial methods :  
 setMethod("cbind2", signature(x = "Matrix", y = "NULL"),  
           function(x, y) x)  
 setMethod("cbind2", signature(x = "Matrix", y = "missing"),  
           function(x, y) x)  
 setMethod("cbind2", signature(x = "NULL", y="Matrix"),  
           function(x, y) x)  
   
 setMethod("rbind2", signature(x = "Matrix", y = "NULL"),  
           function(x, y) x)  
 setMethod("rbind2", signature(x = "Matrix", y = "missing"),  
           function(x, y) x)  
 setMethod("rbind2", signature(x = "NULL", y="Matrix"),  
           function(x, y) x)  
   
 ## Makes sure one gets x decent error message for the unimplemented cases:  
 setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),  
           function(x, y) {  
               rowCheck(x,y)  
               stop(gettextf("cbind2() method for (%s,%s) not-yet defined",  
                             class(x), class(y)))  
           })  
   
 ## Use a working fall back {particularly useful for sparse}:  
 ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones  
 setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),  
           function(x, y) {  
               colCheck(x,y)  
               t(cbind2(t(x), t(y)))  
           })  

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