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Diff of /pkg/R/Matrix.R

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revision 1455, Mon Aug 28 15:35:44 2006 UTC revision 2039, Mon Aug 6 18:49:27 2007 UTC
# Line 3  Line 3 
3    
4  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5    
6  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))  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))  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 19  Line 28 
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:  ## head and tail apply to all Matrix objects for which subscripting is allowed:
31  ## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {  setMethod("head", signature(x = "Matrix"), utils::head.matrix)
32      setMethod("head", signature(x = "Matrix"), utils:::head.matrix)  setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
33      setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)  
34  ## } else { # R 2.4.0 and newer  setMethod("drop", signature(x = "Matrix"),
35  ##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)            function(x) if(all(dim(x) != 1)) x else drop(as(x, "matrix")))
 ##     setMethod("tail", signature(x = "Matrix"), utils::tail.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"),
# Line 38  Line 45 
45            function(x, ...) as.logical(as.vector(x)))            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 77  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 96  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, forceCheck = FALSE)                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      doDN <- TRUE
114      if (i.M && !forceCheck) {      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 119  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 && data == 0 && !identical(sparse,FALSE)) {          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
128              if(is.null(sparse)) sparse <- TRUE              ## 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!              ## will be sparse: do NOT construct full matrix!
132              data <- new(if(is.numeric(data)) "dgTMatrix" else              data <- new(if(is.numeric(data)) "dgTMatrix" else
133                          if(is.logical(data)) "lgTMatrix" else                          if(is.logical(data)) "lgTMatrix" else
# Line 135  Line 142 
142              dimnames(data) <- dimnames              dimnames(data) <- dimnames
143          }          }
144          doDN <- FALSE          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))      if (doDN && !is.null(dimnames))
150          dimnames(data) <- dimnames          dimnames(data) <- dimnames
# Line 148  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 180  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 191  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(as.matrix(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
225    
226    setMethod("crossprod", signature(x = "Matrix", y = "matrix"),
227              function(x, y = NULL) callGeneric(x, Matrix(y)))
228    setMethod("crossprod", signature(x = "matrix", y = "Matrix"),
229              function(x, y = NULL) callGeneric(Matrix(x), y))
230    
231  ## The as.matrix() promotion seems illogical to MM,  ## The as.matrix() promotion seems illogical to MM,
232  ## but is according to help(tcrossprod, package = "base") :  ## but is according to help(tcrossprod, package = "base") :
233  setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),  setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
234            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
235  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),  setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
236            function(x, y = NULL)  callGeneric(as.matrix(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
237    setMethod("tcrossprod", signature(x = "Matrix", y = "matrix"),
238              function(x, y = NULL) callGeneric(x, Matrix(y)))
239    setMethod("tcrossprod", signature(x = "matrix", y = "Matrix"),
240              function(x, y = NULL) 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), class(b)))
256    
257  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
258  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 235  Line 279 
279  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
280                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
281            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
282                  if(is(X, "sparseMatrix"))
283                      warning("using slow kronecker() method")
284                X <- as(X, "matrix") ; Matrix(callGeneric()) })                X <- as(X, "matrix") ; Matrix(callGeneric()) })
285    
286  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
287                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
288            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
289                  if(is(Y, "sparseMatrix"))
290                      warning("using slow kronecker() method")
291                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
292    
293    
294    ## FIXME: All of these should never be called
295    setMethod("chol", signature(x = "Matrix"),
296              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
297    setMethod("determinant", signature(x = "Matrix"),
298              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
299    
300  setMethod("diag", signature(x = "Matrix"),  setMethod("diag", signature(x = "Matrix"),
301            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))            function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
302  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
303            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
304    
305  ## Group Methods  setMethod("norm", signature(x = "Matrix", type = "character"),
306  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, type, ...) .bail.out.1(.Generic, class(x)))
307  ## "fallback":  setMethod("rcond", signature(x = "Matrix", type = "character"),
308  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),            function(x, type, ...) .bail.out.1(.Generic, class(x)))
309            function(e1) {  
310                warning("inefficient method used for \"- e1\"")  
311                0-e1  ## for all :
312    setMethod("norm", signature(x = "ANY", type = "missing"),
313              function(x, type, ...) norm(x, type = "O", ...))
314    setMethod("rcond", signature(x = "ANY", type = "missing"),
315              function(x, type, ...) rcond(x, type = "O", ...))
316    
317    
318    
319    
320    
321    ## MM: More or less "Cut & paste" from
322    ## --- diff.default() from  R/src/library/base/R/diff.R :
323    setMethod("diff", signature(x = "Matrix"),
324              function(x, lag = 1, differences = 1, ...) {
325                  if (length(lag) > 1 || length(differences) > 1 ||
326                      lag < 1 || differences < 1)
327                      stop("'lag' and 'differences' must be integers >= 1")
328                  xlen <- nrow(x)
329                  if (lag * differences >= xlen)
330                      return(x[,FALSE][0])  # empty of proper mode
331    
332                  i1 <- -1:-lag
333                  for (i in 1:differences)
334                      x <- x[i1, , drop = FALSE] -
335                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
336                  x
337            })            })
338    
339  ## bail-outs:  setMethod("image", "Matrix",
340  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),            function(x, ...) { # coercing to sparse is not inefficient,
341            function(e1, e2) {                ##               since we need 'i' and 'j' for levelplot()
342                d <- dimCheck(e1,e2)                x <- as(as(x, "sparseMatrix"), "dMatrix")
343                .bail.out.2(.Generic, class(e1), class(e2))                callGeneric()
344            })            })
 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)))  
345    
346    
347    ## Group Methods
348    
349    ##-> see ./Ops.R
350    ##         ~~~~~
351    ## For all  non-dMatrix objects, and note that  "all" and "any" have their own
352    setMethod("Summary", signature(x = "Matrix", na.rm = "ANY"),
353              function(x, ..., na.rm)
354              callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
355    
356    
357  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
358  ###  ###
# Line 287  Line 372 
372  ## select rows  ## select rows
373  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
374                           drop = "missing"),                           drop = "missing"),
375            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, drop) {
376                  if(nargs() == 1) { ## e.g. M[0] , M[TRUE],  M[1:2]
377                      if(any(i)) as.vector(x)[i] else as.vector(x[1,1])[FALSE]
378                  } else callGeneric(x, i=i, drop= TRUE)})
379    
380  ## select columns  ## select columns
381  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
382                           drop = "missing"),                           drop = "missing"),
# Line 301  Line 390 
390            function(x,i,j, drop)            function(x,i,j, drop)
391            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
392    
393  ##  "logical *vector* indexing, such as  M [ M >= 10 ] :  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
394  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  ## The following is *both* for    M [ <logical>   ]
395                           drop = "ANY"),  ##                 and also for   M [ <logical> , ]
396            function (x, i, j, drop) {  .M.sub.i.logical <- function (x, i, j, drop)
397    {
398        nA <- nargs()
399        if(nA == 2) { ##  M [ M >= 7 ]
400            ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
401                as(x, geClass(x))@x[as.vector(i)]                as(x, geClass(x))@x[as.vector(i)]
402                ## -> error when lengths don't match                ## -> error when lengths don't match
403            })      } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
404            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
405    
406  ## FIXME: The following is good for    M [ <logical>   ]      } else stop("nargs() = ", nA,
407  ##        *BUT* it also triggers for   M [ <logical> , ] where it is *WRONG*                  ".  Extraneous illegal arguments inside '[ .. ]' ?")
408  ##       using nargs() does not help: it gives '3' for both cases  }
409  if(FALSE)  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
410                             drop = "ANY"),
411              .M.sub.i.logical)
412  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
413                           drop = "ANY"),                           drop = "ANY"),
414            function (x, i, j, drop) {            .M.sub.i.logical)
               ## DEBUG  
               cat("[(Matrix,i,..): nargs=", nargs(),"\n")  
               as(x, geClass(x))@x[i] })  
415    
416    
417  ## "FIXME:"  ## A[ ij ]  where ij is (i,j) 2-column matrix :
418  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  .M.sub.i.2col <- function (x, i, j, drop)
419  ##  and                A[ LL ]  where LL is a logical *vector*  {
420  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?      nA <- nargs()
421        if(nA == 2) { ##  M [ cbind(ii,jj) ]
422            if(!is.integer(nc <- ncol(i)))
423                stop("'i' has no integer column number",
424                     " should never happen; please report")
425            if(is.logical(i))
426                return(.M.sub.i.logical(x,i,j,drop))
427            else if(!is.numeric(i) || nc != 2)
428                stop("such indexing must be by logical or 2-column numeric matrix")
429            m <- nrow(i)
430            if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
431            ## else
432            i1 <- i[,1]
433            i2 <- i[,2]
434            ## potentially inefficient -- FIXME --
435            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
436    
437        } else stop("nargs() = ", nA,
438                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
439    }
440    setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
441              .M.sub.i.2col)
442    
443    
444  ### "[<-" : -----------------  ### "[<-" : -----------------
# Line 333  Line 447 
447  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
448                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
449            function (x, value) {            function (x, value) {
450                x@x <- value                ## Fails for 'nMatrix' ... FIXME : make sure have method there
451                  x@x <- rep(value, length = length(x@x))
452                validObject(x)# check if type and lengths above match                validObject(x)# check if type and lengths above match
453                x                x
454            })            })
455    
456  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
457    ## ----------------   The cheap general method --- FIXME: provide special ones
458    .M.repl.i.2col <- function (x, i, j, value)
459    {
460        nA <- nargs()
461        if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value
462            if(!is.integer(nc <- ncol(i)))
463                stop("'i' has no integer column number",
464                     " should never happen; please report")
465            else if(!is.numeric(i) || nc != 2)
466                stop("such indexing must be by logical or 2-column numeric matrix")
467            if(is.logical(i)) {
468                message(".M.repl.i.2col(): drop 'matrix' case ...")
469                i <- c(i) # drop "matrix"
470                return( callNextMethod() )
471            }
472            if(!is.integer(i)) storage.mode(i) <- "integer"
473            if(any(i < 0))
474                stop("negative values are not allowed in a matrix subscript")
475            if(any(is.na(i)))
476                stop("NAs are not allowed in subscripted assignments")
477            if(any(i0 <- (i == 0))) # remove them
478                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
479            ## now have integer i >= 1
480            m <- nrow(i)
481            ## mod.x <- .type.kind[.M.kind(x)]
482            if(length(value) > 0 && m %% length(value) != 0)
483                warning("number of items to replace is not a multiple of replacement length")
484            ## recycle:
485            value <- rep(value, length = m)
486            i1 <- i[,1]
487            i2 <- i[,2]
488            ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
489            for(k in seq_len(m))
490                x[i1[k], i2[k]] <- value[k]
491    
492            x
493        } else stop("nargs() = ", nA,
494                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
495    }
496    
497    setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
498                                    value = "replValue"),
499              .M.repl.i.2col)
500    
501    
502    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
503                                    value = "Matrix"),
504                     function (x, i, j, value) {
505    ### *TEMPORARY* diagnostic output:
506    ##                  cat("<Matrix1>[i,j] <- <Matrix1>:\n<Matrix1> = x :")
507    ##                  str(x)
508    ##                  cat("<Matrix2> = value :")
509    ##                  str(value)
510    ##                  cat("i :"); if(!missing(i)) str(i) else cat("<missing>\n")
511    ##                  cat("j :"); if(!missing(j)) str(j) else cat("<missing>\n")
512    
513                         callGeneric(x=x, i=i, j=j, value = as.vector(value))
514                     })
515    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
516                                    value = "Matrix"),
517                     function (x, i, j, value)
518                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
519    
520    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
521                                    value = "matrix"),
522                     function (x, i, j, value)
523                     callGeneric(x=x, i=i, j=j, value = c(value)))
524    
525  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## (ANY,ANY,ANY) is used when no `real method' is implemented :
526  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
527                                  value = "ANY"),                                  value = "ANY"),
528            function (x, i, j, value) {            function (x, i, j, value) {
529                if(!is.atomic(value))                if(!is.atomic(value))
530                    stop("RHS 'value' must match matrix class ", class(x))                    stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
531                                   class(value),class(x)))
532                else stop("not-yet-implemented 'Matrix[<-' method")                else stop("not-yet-implemented 'Matrix[<-' method")
533            })            })
   
   
 ## 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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