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Diff of /pkg/R/Matrix.R

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revision 946, Wed Sep 28 08:56:42 2005 UTC revision 2110, Sat Jan 26 20:59:26 2008 UTC
# Line 1  Line 1 
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2    
 ## probably not needed eventually:  
 setAs(from = "ddenseMatrix", to = "matrix",  
       function(from) {  
           if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")  
           array(from@x, dim = d, dimnames = dimnames(from))  
       })  
3    
4  setMethod("show", signature(object = "ddenseMatrix"),  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
           function(object) prMatrix(object))  
5    
6  ##- ## FIXME: The following is only for the "dMatrix" objects that are not  setAs("Matrix", "sparseMatrix", function(from) as(from, "CsparseMatrix"))
7  ##- ##        "dense" nor "sparse" -- i.e. "packed" ones :  setAs("Matrix", "CsparseMatrix", function(from) as_Csparse(from))
8  ##- ## But these could be printed better -- "." for structural zeros.  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
9  ##- setMethod("show", signature(object = "dMatrix"), prMatrix)  
10  ##- ## and improve this as well:  ## Maybe TODO:
11  ##- setMethod("show", signature(object = "pMatrix"), prMatrix)  ## setAs("Matrix", "nMatrix", function(from) ....)
12  ##- ## this should now be superfluous [keep for safety for the moment]:  
13  setMethod("show", signature(object = "Matrix"),  ## Most of these work; this is a last resort:
14            function(object) prMatrix(object))  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:
19    ## setAs(from = "ddenseMatrix", to = "matrix",
20    ##       function(from) {
21    ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
22    ##        array(from@x, dim = d, dimnames = dimnames(from))
23    ##       })
24    
25  ## should propagate to all subclasses:  ## should propagate to all subclasses:
26  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
27    ## for 'Matrix' objects, as.array() should be equivalent:
28    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}:
38    setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
39              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    setMethod("cov2cor", signature(V = "Matrix"),
48              function(V) as(cov2cor(as(V, "matrix")), "dpoMatrix"))
49    
50  ## Note that isSymmetric is *not* exported  ## "base" has an isSymmetric() S3-generic since R 2.3.0
51  setMethod("isSymmetric", signature(object = "symmetricMatrix"),  setMethod("isSymmetric", signature(object = "symmetricMatrix"),
52            function(object) TRUE)            function(object,tol) TRUE)
53  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
54            ## FIXME: 'TRUE' if *diagonal*, i.e. return(isDiagonal(object))            ## TRUE iff diagonal:
55            function(object) FALSE)            function(object,tol) isDiagonal(object))
56  setMethod("isDiagonal", signature(object = "sparseMatrix"),  
57            function(object) {  setMethod("isTriangular", signature(object = "triangularMatrix"),
58                gT <- as(object, "TsparseMatrix")            function(object, ...) TRUE)
59                all(gT@i == gT@j)  
60            })  setMethod("isTriangular", signature(object = "matrix"), isTriMat)
61    
62    setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
63    
64    
65    
66  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
67            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
68    
69    setMethod("length", "Matrix", function(x) prod(dim(x)))
70    
71  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)  setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
72    
73    
74  ## not exported but used more than once for "dimnames<-" method :  ## not exported but used more than once for "dimnames<-" method :
75  ## -- or do only once for all "Matrix" classes ??  ## -- or do only once for all "Matrix" classes ??
76  dimnamesGets <- function (x, value) {  dimnamesGets <- function (x, value) {
# Line 56  Line 89 
89  setMethod("unname", signature("Matrix", force="missing"),  setMethod("unname", signature("Matrix", force="missing"),
90            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
91    
92    setMethod("all", signature(x = "Matrix"),
93              function(x, ..., na.rm)
94              callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
95    
96    setMethod("any", signature(x = "Matrix"),
97              function(x, ..., na.rm)
98              callGeneric(as(x, "lMatrix"), ..., na.rm=na.rm))
99    
100    ## NOTE:  "&" and "|"  are now in group "Logic" c "Ops" --> ./Ops.R
101    ##        "!" is in ./not.R
102    
103    
104  Matrix <-  Matrix <-
105      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
106                  sparse = NULL, forceCheck = FALSE)
107  {  {
108      if (is(data, "Matrix")) return(data)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
109      if (is.matrix(data)) { val <- data }  
110      else { ## cut & paste from "base::matrix" :      i.M <- is(data, "Matrix")
111        if(!i.M && inherits(data, "table")) # special treatment
112            class(data) <- "matrix" # "matrix" first for S4 dispatch
113        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
114            sparse <- sparseDefault(data)
115    
116        doDN <- TRUE
117        if (i.M) {
118            if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
119                warning("'nrow', 'ncol', etc, are disregarded when 'data' is \"Matrix\" already")
120            sM <- is(data,"sparseMatrix")
121            if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
122                return(data)
123            ## else : convert  dense <-> sparse -> at end
124        }
125        else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
126          if (missing(nrow))          if (missing(nrow))
127              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
128          else if (missing(ncol))          else if (missing(ncol))
129              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
130          val <- .Internal(matrix(data, nrow, ncol, byrow))          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
131          dimnames(val) <- dimnames              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
132                if(is.null(sparse)) sparse1 <- sparse <- TRUE
133                i.M <- sM <- TRUE
134                ## will be sparse: do NOT construct full matrix!
135                data <- new(if(is.numeric(data)) "dgTMatrix" else
136                            if(is.logical(data)) "lgTMatrix" else
137                            stop("invalid 'data'"),
138                            Dim = as.integer(c(nrow,ncol)),
139                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
140                            else dimnames)
141            } else { ## normal case - using .Internal() to avoid more copying
142                if(getRversion() >= "2.7.0")
143                    data <- .Internal(matrix(data, nrow, ncol, byrow, dimnames))
144                else {
145                    data <- .Internal(matrix(data, nrow, ncol, byrow))
146                    dimnames(data) <- dimnames
147                }
148                if(is.null(sparse))
149                    sparse <- sparseDefault(data)
150            }
151            doDN <- FALSE
152        } else if(!missing(nrow) || !missing(ncol)|| !missing(byrow))
153            warning("'nrow', 'ncol', etc, are disregarded for matrix 'data'")
154    
155        ## 'data' is now a "matrix" or "Matrix"
156        if (doDN && !is.null(dimnames))
157            dimnames(data) <- dimnames
158    
159        ## check for symmetric / triangular / diagonal :
160        isSym <- isSymmetric(data)
161        if((isTri <- !isSym))
162            isTri <- isTriangular(data)
163        isDiag <- isSym # cannot be diagonal if it isn't symmetric
164        if(isDiag)
165            isDiag <- isDiagonal(data)
166    
167        ## Find proper matrix class 'cl'
168        cl <-
169            if(isDiag && !isTRUE(sparse1))
170                "diagonalMatrix" # -> will automatically check for type
171            else {
172                ## consider it's type
173                ctype <-
174                    if(is(data,"Matrix")) class(data)
175                    else {
176                        if("complex" == (ctype <- typeof(data)))
177                            "z" else ctype
178      }      }
179      as(val, "dgeMatrix")              ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
180                if(ctype == "z")
181                    stop("complex matrices not yet implemented in Matrix package")
182                if(ctype == "i") {
183                    warning("integer matrices not yet implemented in 'Matrix'; ",
184                            "using 'double' ones'")
185                    ctype <- "d"
186                }
187                paste(ctype,
188                      if(sparse) {
189                          if(isSym) "sCMatrix" else
190                          if(isTri) "tCMatrix" else "gCMatrix"
191                      } else { ## dense
192                          if(isSym) "syMatrix" else
193                          if(isTri) "trMatrix" else "geMatrix"
194                      }, sep="")
195            }
196    
197        ## Can we coerce and be done?
198        if(!canCoerce(data,cl)) { ## try to coerce ``via'' virtual classes
199            if(sparse && !sM)
200                data <- as(data, "sparseMatrix")
201            else if(!sparse && !is(data, "denseMatrix"))
202                data <- as(data, "denseMatrix")
203            if(isTri && !is(data, "triangularMatrix"))
204                data <- as(data, "triangularMatrix")
205            else if(isSym && !is(data, "symmetricMatrix"))
206                data <- as(data, "symmetricMatrix")
207        }
208        ## now coerce in any case .. maybe producing sensible error message:
209        as(data, cl)
210  }  }
211    
212  ## Methods for operations where one argument is numeric  ## Methods for operations where one argument is numeric
# Line 79  Line 216 
216    
217  setMethod("%*%", signature(x = "Matrix", y = "numeric"),  setMethod("%*%", signature(x = "Matrix", y = "numeric"),
218            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
   
219  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
220            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
221    
222    setMethod("%*%", signature(x = "Matrix", y = "matrix"),
223              function(x, y) callGeneric(x, Matrix(y)))
224    setMethod("%*%", signature(x = "matrix", y = "Matrix"),
225              function(x, y) callGeneric(Matrix(x), y))
226    
227    
228  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
229            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))
   
230  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
231            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
232    
233    setMethod("crossprod", signature(x = "Matrix", y = "matrix"),
234              function(x, y = NULL) callGeneric(x, Matrix(y)))
235    setMethod("crossprod", signature(x = "matrix", y = "Matrix"),
236              function(x, y = NULL) callGeneric(Matrix(x), y))
237    
238    ## The as.matrix() promotion seems illogical to MM,
239    ## but is according to help(tcrossprod, package = "base") :
240    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
241              function(x, y = NULL) callGeneric(x, as.matrix(y)))
242    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
243              function(x, y = NULL)  callGeneric(as.matrix(x), y))
244    setMethod("tcrossprod", signature(x = "Matrix", y = "matrix"),
245              function(x, y = NULL) callGeneric(x, Matrix(y)))
246    setMethod("tcrossprod", signature(x = "matrix", y = "Matrix"),
247              function(x, y = NULL) callGeneric(Matrix(x), y))
248    
249    ## maybe not 100% optimal, but elegant:
250    setMethod("solve", signature(a = "Matrix", b = "missing"),
251              function(a, b, ...) solve(a, Diagonal(nrow(a))))
252    
253  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
254            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, Matrix(b)))
255    setMethod("solve", signature(a = "Matrix", b = "matrix"),
256              function(a, b, ...) callGeneric(a, Matrix(b)))
257    setMethod("solve", signature(a = "matrix", b = "Matrix"),
258              function(a, b, ...) callGeneric(Matrix(a), b))
259    
260    ## when no sub-class method is found, bail out
261    setMethod("solve", signature(a = "Matrix", b = "Matrix"),
262              function(a, b, ...) .bail.out.2("solve", class(a), class(b)))
263    
264  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
265  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 98  Line 267 
267            stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',            stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
268                          class(x), class(y))))                          class(x), class(y))))
269    
 ## Move this to ./Auxiliaries.R  
 .bail.out.1 <- function(fun, cl) {  
     stop(gettextf('not-yet-implemented method for %s(<%s>)', fun, cl),  
          call. = FALSE)  
 }  
 .bail.out.2 <- function(fun, cl1, cl2) {  
     stop(gettextf('not-yet-implemented method for %s(<%s>, <%s>)',  
                   fun, cl1, cl2), call. = FALSE)  
 }  
   
270  setMethod("crossprod", signature(x = "Matrix", y = "ANY"),  setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
271            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
272    setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
273              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
274    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
275              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
276    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
277              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
278    
279    ## cheap fallbacks
280    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
281              function(x, y = NULL) t(x) %*% y)
282    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
283              function(x, y = NULL) x %*% t(y))
284    
285    ## There are special sparse methods; this is a "fall back":
286    setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
287                                     FUN = "ANY", make.dimnames = "ANY"),
288              function(X, Y, FUN, make.dimnames, ...) {
289                  if(is(X, "sparseMatrix"))
290                      warning("using slow kronecker() method")
291                  X <- as(X, "matrix") ; Matrix(callGeneric()) })
292    
293    setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
294                                     FUN = "ANY", make.dimnames = "ANY"),
295              function(X, Y, FUN, make.dimnames, ...) {
296                  if(is(Y, "sparseMatrix"))
297                      warning("using slow kronecker() method")
298                  Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
299    
300    
301    ## FIXME: All of these should never be called
302    setMethod("chol", signature(x = "Matrix"),
303              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
304    setMethod("determinant", signature(x = "Matrix"),
305              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
306    
307    setMethod("diag", signature(x = "Matrix"),
308              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
309  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
310            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
311    
312  ## Group Methods (bail-out)  setMethod("norm", signature(x = "Matrix", type = "character"),
313  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),            function(x, type, ...) .bail.out.1(.Generic, class(x)))
314            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  setMethod("rcond", signature(x = "Matrix", type = "character"),
315  setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),            function(x, type, ...) .bail.out.1(.Generic, class(x)))
316            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  
317  setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),  
318            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  ## for all :
319    setMethod("norm", signature(x = "ANY", type = "missing"),
320              function(x, type, ...) norm(x, type = "O", ...))
321    setMethod("rcond", signature(x = "ANY", type = "missing"),
322              function(x, type, ...) rcond(x, type = "O", ...))
323    
324    
325    
326    
327    
328    ## MM: More or less "Cut & paste" from
329    ## --- diff.default() from  R/src/library/base/R/diff.R :
330    setMethod("diff", signature(x = "Matrix"),
331              function(x, lag = 1, differences = 1, ...) {
332                  if (length(lag) > 1 || length(differences) > 1 ||
333                      lag < 1 || differences < 1)
334                      stop("'lag' and 'differences' must be integers >= 1")
335                  xlen <- nrow(x)
336                  if (lag * differences >= xlen)
337                      return(x[,FALSE][0])  # empty of proper mode
338    
339                  i1 <- -1:-lag
340                  for (i in 1:differences)
341                      x <- x[i1, , drop = FALSE] -
342                          x[-nrow(x):-(nrow(x)-lag+1), , drop = FALSE]
343                  x
344              })
345    
346    setMethod("image", "Matrix",
347              function(x, ...) { # coercing to sparse is not inefficient,
348                  ##               since we need 'i' and 'j' for levelplot()
349                  x <- as(as(x, "sparseMatrix"), "dMatrix")
350                  callGeneric()
351              })
352    
353    
354    ## Group Methods
355    
356    ##-> see ./Ops.R
357    ##         ~~~~~
358    ## For all  non-dMatrix objects, and note that  "all" and "any" have their own
359    setMethod("Summary", signature(x = "Matrix", na.rm = "ANY"),
360              function(x, ..., na.rm)
361              callGeneric(as(x,"dMatrix"), ..., na.rm = na.rm))
362    
363    
364  ### --------------------------------------------------------------------------  ### --------------------------------------------------------------------------
365  ###  ###
366  ### Subsetting "["  and  ### Subsetting "["  and
# Line 135  Line 372 
372  ## "x[]":  ## "x[]":
373  setMethod("[", signature(x = "Matrix",  setMethod("[", signature(x = "Matrix",
374                           i = "missing", j = "missing", drop = "ANY"),                           i = "missing", j = "missing", drop = "ANY"),
375            function (x, i, j, drop) x)            function (x, i, j, ..., drop) x)
376    
377  ## missing 'drop' --> 'drop = TRUE'  ## missing 'drop' --> 'drop = TRUE'
378  ##                     -----------  ##                     -----------
379  ## select rows  ## select rows
380  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
381                           drop = "missing"),                           drop = "missing"),
382            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, ..., drop) {
383                  if(nargs() == 2) { ## e.g. M[0] , M[TRUE],  M[1:2]
384                      if(any(i) || prod(dim(x)) == 0)
385                          as.vector(x)[i]
386                      else ## save memory
387                          as.vector(x[1,1])[FALSE]
388                  } else {
389                      callGeneric(x, i=i, , drop=TRUE)
390                      ##                  ^^
391                  }
392              })
393    
394  ## select columns  ## select columns
395  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
396                           drop = "missing"),                           drop = "missing"),
397            function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))            function(x,i,j, ..., drop) callGeneric(x, j=j, drop= TRUE))
398  setMethod("[", signature(x = "Matrix", i = "index", j = "index",  setMethod("[", signature(x = "Matrix", i = "index", j = "index",
399                           drop = "missing"),                           drop = "missing"),
400            function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))            function(x,i,j, ..., drop) callGeneric(x, i=i, j=j, drop= TRUE))
401    
402  ## bail out if any of (i,j,drop) is "non-sense"  ## bail out if any of (i,j,drop) is "non-sense"
403  setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),  setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
404            function(x,i,j, drop)            function(x,i,j, ..., drop)
405            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
406    
407  ## "FIXME:"  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
408  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  ## The following is *both* for    M [ <logical>   ]
409  ##  and                A[ LL ]  where LL is a logical *vector*  ##                 and also for   M [ <logical> , ]
410  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?  .M.sub.i.logical <- function (x, i, j, ..., drop)
411    {
412        nA <- nargs()
413        if(nA == 2) { ##  M [ M >= 7 ]
414            ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
415            as(x, geClass(x))@x[as.vector(i)]
416            ## -> error when lengths don't match
417        } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
418            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
419    
420        } else stop("nargs() = ", nA,
421                    ".  Extraneous illegal arguments inside '[ .. ]' (i.logical)?")
422    }
423    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
424                             drop = "ANY"),
425              .M.sub.i.logical)
426    setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
427                             drop = "ANY"),
428              .M.sub.i.logical)
429    
430    
431    ## A[ ij ]  where ij is (i,j) 2-column matrix -- but also when that is logical mat!
432    .M.sub.i.2col <- function (x, i, j, ..., drop)
433    {
434        nA <- nargs()
435        if(nA == 2) { ##  M [ cbind(ii,jj) ] or M [ <logical matrix> ]
436            if(!is.integer(nc <- ncol(i)))
437                stop(".M.sub.i.2col(): 'i' has no integer column number;\n",
438                     "should never happen; please report")
439            if(is.logical(i))
440                return(.M.sub.i.logical(x, i=i)) # call with 2 args!
441            else if(!is.numeric(i) || nc != 2)
442                stop("such indexing must be by logical or 2-column numeric matrix")
443            m <- nrow(i)
444            if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
445            ## else
446            i1 <- i[,1]
447            i2 <- i[,2]
448            ## potentially inefficient -- FIXME --
449            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
450    
451        } else stop("nargs() = ", nA,
452                    ".  Extraneous illegal arguments inside '[ .. ]' (i.2col)?")
453    }
454    setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
455              .M.sub.i.2col)
456    
457    
458  ### "[<-" : -----------------  ### "[<-" : -----------------
459    
460  ## x[] <- value :  ## x[] <- value :
461  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
462                                  value = "index"),##  double/logical/...                                  value = "ANY"),## double/logical/...
463            function (x, value) { x@x <- value ; validObject(x); x })            function (x, value) {
464                  ## Fails for 'nMatrix' ... FIXME : make sure have method there
465                  x@x <- rep(value, length = length(x@x))
466                  validObject(x)# check if type and lengths above match
467                  x
468              })
469    
470  ## Otherwise (value is not "index"): bail out  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
471  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  ## ----------------
472                                  value = "ANY"),  ## The cheap general method --- FIXME: provide special ones; done for Tsparse..
473            function (x, i, j, value)  ## NOTE:  need '...' below such that setMethod() does
474                   if(!is(value,"index"))  ##        not use .local() such that nargs() will work correctly:
475                   stop("RHS 'value' must be of class \"index\"")  .M.repl.i.2col <- function (x, i, j, ..., value)
476                   else stop("not-yet-implemented 'Matrix[<-' method"))  {
477        nA <- nargs()
478        if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value  or M [ Lmat ] <- value
479            if(!is.integer(nc <- ncol(i)))
480                stop(".M.repl.i.2col(): 'i' has no integer column number;\n",
481                     "should never happen; please report")
482            else if(!is.numeric(i) || nc != 2)
483                stop("such indexing must be by logical or 2-column numeric matrix")
484            if(is.logical(i)) {
485                message(".M.repl.i.2col(): drop 'matrix' case ...")
486                ## c(i) : drop "matrix" to logical vector
487                return( callGeneric(x, i=c(i), value=value) )
488            }
489            if(!is.integer(i)) storage.mode(i) <- "integer"
490            if(any(i < 0))
491                stop("negative values are not allowed in a matrix subscript")
492            if(any(is.na(i)))
493                stop("NAs are not allowed in subscripted assignments")
494            if(any(i0 <- (i == 0))) # remove them
495                i <- i[ - which(i0, arr.ind = TRUE)[,"row"], ]
496            ## now have integer i >= 1
497            m <- nrow(i)
498            ## mod.x <- .type.kind[.M.kind(x)]
499            if(length(value) > 0 && m %% length(value) != 0)
500                warning("number of items to replace is not a multiple of replacement length")
501            ## recycle:
502            value <- rep(value, length = m)
503            i1 <- i[,1]
504            i2 <- i[,2]
505            ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
506            for(k in seq_len(m))
507                x[i1[k], i2[k]] <- value[k]
508    
509            x
510        } else stop("nargs() = ", nA,
511                    ".  Extraneous illegal arguments inside '[ .. ]' ?")
512    }
513    
514    setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
515                                    value = "replValue"),
516              .M.repl.i.2col)
517    
518    
519  ## NOTE: the following only works for R 2.2.x (and later) ---  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
520  ## ----  *and* 'Matrix' must have been *installed* by R >= 2.2.x                                  value = "Matrix"),
521                     function (x, i, j, ..., value)
522  if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {                   callGeneric(x=x, , j=j, value = as.vector(value)))
523    
524      ## The trivial methods :  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
525      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),                                  value = "Matrix"),
526                function(x, y) x)                   function (x, i, j, ..., value)
527      setMethod("cbind2", signature(x = "Matrix", y = "missing"),                   callGeneric(x=x, i=i, , value = as.vector(value)))
528                function(x, y) x)  
529      setMethod("cbind2", signature(x = "NULL", y="Matrix"),  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
530                function(x, y) x)                                  value = "Matrix"),
531                     function (x, i, j, ..., value)
532      setMethod("rbind2", signature(x = "Matrix", y = "NULL"),                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))
533                function(x, y) x)  
534      setMethod("rbind2", signature(x = "Matrix", y = "missing"),  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
535                function(x, y) x)                                  value = "matrix"),
536      setMethod("rbind2", signature(x = "NULL", y="Matrix"),                   function (x, i, j, ..., value)
537                function(x, y) x)                   callGeneric(x=x, , j=j, value = c(value)))
538    
539      ## Makes sure one gets x decent error message for the unimplemented cases:  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
540      setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),                                  value = "matrix"),
541                function(x, y) {                   function (x, i, j, ..., value)
542                    rowCheck(x,y)                   callGeneric(x=x, i=i, , value = c(value)))
                   stop(gettextf("cbind2() method for (%s,%s) not-yet defined",  
                                 class(x), class(y)))  
               })  
543    
544      setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
545                function(x, y) {                                  value = "matrix"),
546                    colCheck(x,y)                   function (x, i, j, value)
547                    stop(gettextf("rbind2() method for (%s,%s) not-yet defined",                   callGeneric(x=x, i=i, j=j, value = c(value)))
548                                  class(x), class(y)))  
549    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
550    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
551                                    value = "ANY"),
552              function (x, i, j, value) {
553                  if(!is.atomic(value))
554                      stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
555                                   class(value),class(x)))
556                  else stop("not-yet-implemented 'Matrix[<-' method")
557                })                })
 }## R-2.2.x and newer  

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