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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 2036, Mon Aug 6 12:03:47 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    
48  ## Note that isSymmetric is *not* exported  ## "base" has an isSymmetric() S3-generic since R 2.3.0
 ## but that "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)
92              callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
93    
94    setMethod("any", signature(x = "Matrix"),
95              function(x, ..., na.rm)
96              callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
97    
98    ## NOTE:  "&" and "|"  are now in group "Logic" c "Ops" --> ./Ops.R
99    ##        "!" is in ./not.R
100    
101    
102  Matrix <-  Matrix <-
103      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
104                sparse = NULL)                sparse = NULL, forceCheck = FALSE)
105  {  {
106      sparseDefault <- function(m)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
         prod(dim(m)) > 2*sum(as(m, "matrix") != 0)  
107    
108      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
109      if(is.null(sparse) && (i.M || is(data, "matrix")))  
110        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
111          sparse <- sparseDefault(data)          sparse <- sparseDefault(data)
112    
113        doDN <- TRUE
114      if (i.M) {      if (i.M) {
115            if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
116                warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
117          sM <- is(data,"sparseMatrix")          sM <- is(data,"sparseMatrix")
118          if((sparse && sM) || (!sparse && !sM))          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
119              return(data)              return(data)
120          ## else : convert  dense <-> sparse -> at end          ## else : convert  dense <-> sparse -> at end
121      }      }
# Line 97  Line 124 
124              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
125          else if (missing(ncol))          else if (missing(ncol))
126              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
127            if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
128                ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
129                if(is.null(sparse)) sparse1 <- sparse <- TRUE
130                i.M <- sM <- TRUE
131                ## will be sparse: do NOT construct full matrix!
132                data <- new(if(is.numeric(data)) "dgTMatrix" else
133                            if(is.logical(data)) "lgTMatrix" else
134                            stop("invalid 'data'"),
135                            Dim = as.integer(c(nrow,ncol)),
136                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
137                            else dimnames)
138            } else { ## normal case
139          data <- .Internal(matrix(data, nrow, ncol, byrow))          data <- .Internal(matrix(data, nrow, ncol, byrow))
140          if(is.null(sparse))          if(is.null(sparse))
141              sparse <- sparseDefault(data)              sparse <- sparseDefault(data)
142          dimnames(data) <- dimnames          dimnames(data) <- dimnames
143      } else if (!is.null(dimnames))          }
144          dimnames(data) <- dimnames          doDN <- FALSE
145        } else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
146            warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
147    
148      ## 'data' is now a "matrix" or "Matrix"      ## 'data' is now a "matrix" or "Matrix"
149        if (doDN && !is.null(dimnames))
150            dimnames(data) <- dimnames
151    
152      ## check for symmetric / triangular / diagonal :      ## check for symmetric / triangular / diagonal :
153      isSym <- isSymmetric(data)      isSym <- isSymmetric(data)
# Line 114  Line 157 
157      if(isDiag)      if(isDiag)
158          isDiag <- isDiagonal(data)          isDiag <- isDiagonal(data)
159    
 ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R  
   
160      ## Find proper matrix class 'cl'      ## Find proper matrix class 'cl'
161      cl <-      cl <-
162          if(isDiag)          if(isDiag && !isTRUE(sparse1))
163              "diagonalMatrix" # -> will automatically check for type              "diagonalMatrix" # -> will automatically check for type
164          else {          else {
165              ## consider it's type              ## consider it's type
# Line 146  Line 187 
187                    }, sep="")                    }, sep="")
188          }          }
189    
190      ## Now coerce and return      ## Can we coerce and be done?
191        if(!canCoerce(data,cl)) { ## try to coerce ``via'' virtual classes
192            if(sparse && !sM)
193                data <- as(data, "sparseMatrix")
194            else if(!sparse && !is(data, "denseMatrix"))
195                data <- as(data, "denseMatrix")
196            if(isTri && !is(data, "triangularMatrix"))
197                data <- as(data, "triangularMatrix")
198            else if(isSym && !is(data, "symmetricMatrix"))
199                data <- as(data, "symmetricMatrix")
200        }
201        ## now coerce in any case .. maybe producing sensible error message:
202      as(data, cl)      as(data, cl)
203  }  }
204    
# Line 157  Line 209 
209    
210  setMethod("%*%", signature(x = "Matrix", y = "numeric"),  setMethod("%*%", signature(x = "Matrix", y = "numeric"),
211            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
   
212  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
213            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
214    
215    setMethod("%*%", signature(x = "Matrix", y = "matrix"),
216              function(x, y) callGeneric(x, Matrix(y)))
217    setMethod("%*%", signature(x = "matrix", y = "Matrix"),
218              function(x, y) callGeneric(Matrix(x), y))
219    
220    
221  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
222            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
   
223  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
224            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
225    
226    setMethod("crossprod", signature(x = "Matrix", y = "matrix"),
227              function(x, y) callGeneric(x, Matrix(y)))
228    setMethod("crossprod", signature(x = "matrix", y = "Matrix"),
229              function(x, y) callGeneric(Matrix(x), y))
230    
231    ## The as.matrix() promotion seems illogical to MM,
232    ## but is according to help(tcrossprod, package = "base") :
233    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
234              function(x, y = NULL) callGeneric(x, as.matrix(y)))
235    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
236              function(x, y = NULL)  callGeneric(as.matrix(x), y))
237    setMethod("tcrossprod", signature(x = "Matrix", y = "matrix"),
238              function(x, y) callGeneric(x, Matrix(y)))
239    setMethod("tcrossprod", signature(x = "matrix", y = "Matrix"),
240              function(x, y) callGeneric(Matrix(x), y))
241    
242    ## maybe not optimal
243    setMethod("solve", signature(a = "Matrix", b = "missing"),
244              function(a, b, ...) solve(a, Diagonal(nrow(a))))
245    
246  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
247            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, Matrix(b)))
248    setMethod("solve", signature(a = "Matrix", b = "matrix"),
249              function(a, b, ...) callGeneric(a, Matrix(b)))
250    setMethod("solve", signature(a = "matrix", b = "Matrix"),
251              function(a, b, ...) callGeneric(Matrix(a), b))
252    
253    ## when no sub-class method is found, bail out
254    setMethod("solve", signature(a = "Matrix", b = "matrix"),
255              function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
256    setMethod("solve", signature(a = "Matrix", b = "Matrix"),
257              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
258    setMethod("solve", signature(a = "Matrix", b = "matrix"),
259              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
260    setMethod("solve", signature(a = "matrix", b = "Matrix"),
261              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
262    
263  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
264  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 180  Line 270 
270            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
271  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
272            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
273    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
274              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
275    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
276              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
277    
278    ## cheap fallbacks
279    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
280              function(x, y = NULL) t(x) %*% y)
281    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
282              function(x, y = NULL) x %*% t(y))
283    
284  ## There are special sparse methods; this is a "fall back":  ## There are special sparse methods; this is a "fall back":
285  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
286                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
287            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
288                  if(is(X, "sparseMatrix"))
289                      warning("using slow kronecker() method")
290                X <- as(X, "matrix") ; Matrix(callGeneric()) })                X <- as(X, "matrix") ; Matrix(callGeneric()) })
291    
292  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
293                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
294            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
295                  if(is(Y, "sparseMatrix"))
296                      warning("using slow kronecker() method")
297                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
298    
299    
300    ## FIXME: All of these should never be called
301    setMethod("chol", signature(x = "Matrix"),
302              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
303    setMethod("determinant", signature(x = "Matrix"),
304              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
305    
306    setMethod("diag", signature(x = "Matrix"),
307              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
308  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
309            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
310    
311  ## Group Methods  setMethod("norm", signature(x = "Matrix", type = "character"),
312  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, type, ...) .bail.out.1(.Generic, class(x)))
313  ## "fallback":  setMethod("rcond", signature(x = "Matrix", type = "character"),
314  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),            function(x, type, ...) .bail.out.1(.Generic, class(x)))
315            function(e1) {  
316                warning("inefficient method used for \"- e1\"")  
317                0-e1  ## for all :
318    setMethod("norm", signature(x = "ANY", type = "missing"),
319              function(x, type, ...) norm(x, type = "O", ...))
320    setMethod("rcond", signature(x = "ANY", type = "missing"),
321              function(x, type, ...) rcond(x, type = "O", ...))
322    
323    
324    
325    
326    
327    ## MM: More or less "Cut & paste" from
328    ## --- diff.default() from  R/src/library/base/R/diff.R :
329    setMethod("diff", signature(x = "Matrix"),
330              function(x, lag = 1, differences = 1, ...) {
331                  if (length(lag) > 1 || length(differences) > 1 ||
332                      lag < 1 || differences < 1)
333                      stop("'lag' and 'differences' must be integers >= 1")
334                  xlen <- nrow(x)
335                  if (lag * differences >= xlen)
336                      return(x[,FALSE][0])  # empty of proper mode
337    
338                  i1 <- -1:-lag
339                  for (i in 1:differences)
340                      x <- x[i1, , drop = FALSE] -
341                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
342                  x
343            })            })
344    
345  ## bail-outs:  setMethod("image", "Matrix",
346  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),            function(x, ...) { # coercing to sparse is not inefficient,
347            function(e1, e2) {                ##               since we need 'i' and 'j' for levelplot()
348                d <- dimCheck(e1,e2)                x <- as(as(x, "sparseMatrix"), "dMatrix")
349                .bail.out.2(.Generic, class(e1), class(e2))                callGeneric()
350            })            })
 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)))  
351    
352    
353    ## Group Methods
354    
355    ##-> see ./Ops.R
356    ##         ~~~~~
357    ## For all  non-dMatrix objects, and note that  "all" and "any" have their own
358    setMethod("Summary", signature(x = "Matrix", na.rm = "ANY"),
359              function(x, ..., na.rm)
360              callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
361    
362    
363  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
364  ###  ###
# Line 235  Line 378 
378  ## select rows  ## select rows
379  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
380                           drop = "missing"),                           drop = "missing"),
381            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, drop) {
382                  if(nargs() == 1) { ## e.g. M[0] , M[TRUE],  M[1:2]
383                      if(any(i)) as.vector(x)[i] else as.vector(x[1,1])[FALSE]
384                  } else callGeneric(x, i=i, drop= TRUE)})
385    
386  ## select columns  ## select columns
387  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
388                           drop = "missing"),                           drop = "missing"),
# Line 249  Line 396 
396            function(x,i,j, drop)            function(x,i,j, drop)
397            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
398    
399  ##  "logical *vector* indexing, such as  M [ M >= 10 ] :  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
400  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  ## The following is *both* for    M [ <logical>   ]
401                           drop = "ANY"),  ##                 and also for   M [ <logical> , ]
402            function (x, i, j, drop) {  .M.sub.i.logical <- function (x, i, j, drop)
403    {
404        nA <- nargs()
405        if(nA == 2) { ##  M [ M >= 7 ]
406            ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
407                as(x, geClass(x))@x[as.vector(i)]                as(x, geClass(x))@x[as.vector(i)]
408                                          # -> error when lengths don't match          ## -> error when lengths don't match
409            })      } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
410            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
411    
412        } else stop("nargs() = ", nA,
413                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
414    }
415    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
416                             drop = "ANY"),
417              .M.sub.i.logical)
418  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
419                           drop = "ANY"),                           drop = "ANY"),
420            function (x, i, j, drop) as(x, geClass(x))@x[i])            .M.sub.i.logical)
421    
422    
423  ## "FIXME:"  ## A[ ij ]  where ij is (i,j) 2-column matrix :
424  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  .M.sub.i.2col <- function (x, i, j, drop)
425  ##  and                A[ LL ]  where LL is a logical *vector*  {
426  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?      nA <- nargs()
427        if(nA == 2) { ##  M [ cbind(ii,jj) ]
428            if(!is.integer(nc <- ncol(i)))
429                stop("'i' has no integer column number",
430                     " should never happen; please report")
431            if(is.logical(i))
432                return(.M.sub.i.logical(x,i,j,drop))
433            else if(!is.numeric(i) || nc != 2)
434                stop("such indexing must be by logical or 2-column numeric matrix")
435            m <- nrow(i)
436            if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
437            ## else
438            i1 <- i[,1]
439            i2 <- i[,2]
440            ## potentially inefficient -- FIXME --
441            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
442    
443        } else stop("nargs() = ", nA,
444                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
445    }
446    setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
447              .M.sub.i.2col)
448    
449    
450  ### "[<-" : -----------------  ### "[<-" : -----------------
# Line 274  Line 453 
453  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
454                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
455            function (x, value) {            function (x, value) {
456                x@x <- value                ## Fails for 'nMatrix' ... FIXME : make sure have method there
457                  x@x <- rep(value, length = length(x@x))
458                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
459                x                x
460            })            })
461    
462  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
463    ## ----------------   The cheap general method --- FIXME: provide special ones
464    .M.repl.i.2col <- function (x, i, j, value)
465    {
466        nA <- nargs()
467        if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value
468            if(!is.integer(nc <- ncol(i)))
469                stop("'i' has no integer column number",
470                     " should never happen; please report")
471            else if(!is.numeric(i) || nc != 2)
472                stop("such indexing must be by logical or 2-column numeric matrix")
473            if(is.logical(i)) {
474                message(".M.repl.i.2col(): drop 'matrix' case ...")
475                i <- c(i) # drop "matrix"
476                return( callNextMethod() )
477            }
478            if(!is.integer(i)) storage.mode(i) <- "integer"
479            if(any(i < 0))
480                stop("negative values are not allowed in a matrix subscript")
481            if(any(is.na(i)))
482                stop("NAs are not allowed in subscripted assignments")
483            if(any(i0 <- (i == 0))) # remove them
484                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
485            ## now have integer i >= 1
486            m <- nrow(i)
487            ## mod.x <- .type.kind[.M.kind(x)]
488            if(length(value) > 0 && m %% length(value) != 0)
489                warning("number of items to replace is not a multiple of replacement length")
490            ## recycle:
491            value <- rep(value, length = m)
492            i1 <- i[,1]
493            i2 <- i[,2]
494            ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
495            for(k in seq_len(m))
496                x[i1[k], i2[k]] <- value[k]
497    
498            x
499        } else stop("nargs() = ", nA,
500                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
501    }
502    
503    setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
504                                    value = "replValue"),
505              .M.repl.i.2col)
506    
507    
508    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
509                                    value = "Matrix"),
510                     function (x, i, j, value) {
511    ### *TEMPORARY* diagnostic output:
512    ##                  cat("<Matrix1>[i,j] <- <Matrix1>:\n<Matrix1> = x :")
513    ##                  str(x)
514    ##                  cat("<Matrix2> = value :")
515    ##                  str(value)
516    ##                  cat("i :"); if(!missing(i)) str(i) else cat("<missing>\n")
517    ##                  cat("j :"); if(!missing(j)) str(j) else cat("<missing>\n")
518    
519                         callGeneric(x=x, i=i, j=j, value = as.vector(value))
520                     })
521    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
522                                    value = "Matrix"),
523                     function (x, i, j, value)
524                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
525    
526    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
527                                    value = "matrix"),
528                     function (x, i, j, value)
529                     callGeneric(x=x, i=i, j=j, value = c(value)))
530    
531  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## (ANY,ANY,ANY) is used when no `real method' is implemented :
532  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
533                                  value = "ANY"),                                  value = "ANY"),
534            function (x, i, j, value) {            function (x, i, j, value) {
535                if(!is.atomic(value))                if(!is.atomic(value))
536                    stop("RHS 'value' must match matrix class ", class(x))                    stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
537                                   class(value),class(x)))
538                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
539            })            })
   
   
 ## 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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