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

# Diff of /pkg/R/Matrix.R

revision 1238, Thu Mar 30 19:56:09 2006 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
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:
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    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
## but that "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,tol) TRUE)            function(object,tol) TRUE)
53  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
54            ## TRUE iff diagonal:            ## TRUE iff diagonal:
55            function(object,tol) isDiagonal(object))            function(object,tol) isDiagonal(object))
56
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)
})

57  setMethod("isTriangular", signature(object = "triangularMatrix"),  setMethod("isTriangular", signature(object = "triangularMatrix"),
58            function(object, ...) TRUE)            function(object, ...) TRUE)
59
# Line 56  Line 65
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 75  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)                sparse = NULL, forceCheck = FALSE)
107  {  {
108      sparseDefault <- function(m)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
109
110      i.M <- is(data, "Matrix")      i.M <- is(data, "Matrix")
111      if(is.null(sparse) && (i.M || is(data, "matrix")))      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)          sparse <- sparseDefault(data)
115
116        doDN <- TRUE
117      if (i.M) {      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")          sM <- is(data,"sparseMatrix")
121          if((sparse && sM) || (!sparse && !sM))          if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
122              return(data)              return(data)
123          ## else : convert  dense <-> sparse -> at end          ## else : convert  dense <-> sparse -> at end
124      }      }
# Line 97  Line 127
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            if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
131                ## 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))          data <- .Internal(matrix(data, nrow, ncol, byrow))
146                    dimnames(data) <- dimnames
147                }
148          if(is.null(sparse))          if(is.null(sparse))
149              sparse <- sparseDefault(data)              sparse <- sparseDefault(data)
150          dimnames(data) <- dimnames          }
151      } else if (!is.null(dimnames))          doDN <- FALSE
152          dimnames(data) <- dimnames      } 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"      ## 'data' is now a "matrix" or "Matrix"
156        if (doDN && !is.null(dimnames))
157            dimnames(data) <- dimnames
158
159      ## check for symmetric / triangular / diagonal :      ## check for symmetric / triangular / diagonal :
160      isSym <- isSymmetric(data)      isSym <- isSymmetric(data)
# Line 114  Line 164
164      if(isDiag)      if(isDiag)
165          isDiag <- isDiagonal(data)          isDiag <- isDiagonal(data)
166
### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R

167      ## Find proper matrix class 'cl'      ## Find proper matrix class 'cl'
168      cl <-      cl <-
169          if(isDiag)          if(isDiag && !isTRUE(sparse1))
170              "diagonalMatrix" # -> will automatically check for type              "diagonalMatrix" # -> will automatically check for type
171          else {          else {
172              ## consider it's type              ## consider it's type
# Line 146  Line 194
194                    }, sep="")                    }, sep="")
195          }          }
196
197      ## Now coerce and return      ## 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)      as(data, cl)
210  }  }
211
# Line 157  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 180  Line 271
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"),  setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
273            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            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":  ## There are special sparse methods; this is a "fall back":
286  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",  setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
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(X, "sparseMatrix"))
290                      warning("using slow kronecker() method")
291                X <- as(X, "matrix") ; Matrix(callGeneric()) })                X <- as(X, "matrix") ; Matrix(callGeneric()) })
292
293  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",  setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
294                                   FUN = "ANY", make.dimnames = "ANY"),                                   FUN = "ANY", make.dimnames = "ANY"),
295            function(X, Y, FUN, make.dimnames, ...) {            function(X, Y, FUN, make.dimnames, ...) {
296                  if(is(Y, "sparseMatrix"))
297                      warning("using slow kronecker() method")
298                Y <- as(Y, "matrix") ; Matrix(callGeneric()) })                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  setMethod("norm", signature(x = "Matrix", type = "character"),
313  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)            function(x, type, ...) .bail.out.1(.Generic, class(x)))
314  ## "fallback":  setMethod("rcond", signature(x = "Matrix", type = "character"),
315  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),            function(x, type, ...) .bail.out.1(.Generic, class(x)))
316            function(e1) {
317                warning("inefficient method used for \"- e1\"")
318                0-e1  ## 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  ## bail-outs:  setMethod("image", "Matrix",
347  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),            function(x, ...) { # coercing to sparse is not inefficient,
348            function(e1, e2) {                ##               since we need 'i' and 'j' for levelplot()
349                d <- dimCheck(e1,e2)                x <- as(as(x, "sparseMatrix"), "dMatrix")
350                .bail.out.2(.Generic, class(e1), class(e2))                callGeneric()
351            })            })
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)))
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  ###  ###
# Line 228  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  ##  "logical *vector* indexing, such as  M [ M >= 10 ] :  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
408  setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",  ## The following is *both* for    M [ <logical>   ]
409                           drop = "ANY"),  ##                 and also for   M [ <logical> , ]
410            function (x, i, j, drop) {  .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)]                as(x, geClass(x))@x[as.vector(i)]
416                                          # -> error when lengths don't match          ## -> 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",  setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
427                           drop = "ANY"),                           drop = "ANY"),
428            function (x, i, j, drop) as(x, geClass(x))@x[i])            .M.sub.i.logical)
429
430
431  ## "FIXME:"  ## A[ ij ]  where ij is (i,j) 2-column matrix -- but also when that is logical mat!
432  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  .M.sub.i.2col <- function (x, i, j, ..., drop)
433  ##  and                A[ LL ]  where LL is a logical *vector*  {
434  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?      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  ### "[<-" : -----------------  ### "[<-" : -----------------
# Line 274  Line 461
461  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
462                                  value = "ANY"),## double/logical/...                                  value = "ANY"),## double/logical/...
463            function (x, value) {            function (x, value) {
464                x@x <- value                ## 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                validObject(x)# check if type and lengths above match
467                x                x
468            })            })
469
470  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
471  ## (ANY,ANY,ANY) is used when no `real method' is implemented :  ## ----------------
472  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  ## The cheap general method --- FIXME: provide special ones; done for Tsparse..
473                                  value = "ANY"),  ## NOTE:  need '...' below such that setMethod() does
474            function (x, i, j, value) {  ##        not use .local() such that nargs() will work correctly:
475                if(!is.atomic(value))  .M.repl.i.2col <- function (x, i, j, ..., value)
476                    stop("RHS 'value' must match matrix class ", class(x))  {
477                else stop("not-yet-implemented 'Matrix[<-' method")      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
## NOTE: the following only works for R 2.2.x (and later) ---
## ----  *and* 'Matrix' must have been *installed* by R >= 2.2.x
518
519  if(paste(R.version\$major, R.version\$minor, sep=".") >= "2.2") {  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
520                                    value = "Matrix"),
521                     function (x, i, j, ..., value)
522                     callGeneric(x=x, , j=j, value = as.vector(value)))
523
524    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
525                                    value = "Matrix"),
526                     function (x, i, j, ..., value)
527                     callGeneric(x=x, i=i, , value = as.vector(value)))
528
529      ## The trivial methods :  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
530      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),                                  value = "Matrix"),
531                function(x, y) x)                   function (x, i, j, ..., value)
532      setMethod("cbind2", signature(x = "Matrix", y = "missing"),                   callGeneric(x=x, i=i, j=j, value = as.vector(value)))
533                function(x, y) x)
534      setMethod("cbind2", signature(x = "NULL", y="Matrix"),  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "ANY",
535                function(x, y) x)                                  value = "matrix"),
536                     function (x, i, j, ..., value)
537      setMethod("rbind2", signature(x = "Matrix", y = "NULL"),                   callGeneric(x=x, , j=j, value = c(value)))
538                function(x, y) x)
539      setMethod("rbind2", signature(x = "Matrix", y = "missing"),  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "missing",
540                function(x, y) x)                                  value = "matrix"),
541      setMethod("rbind2", signature(x = "NULL", y="Matrix"),                   function (x, i, j, ..., value)
542                function(x, y) x)                   callGeneric(x=x, i=i, , value = c(value)))

## 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)))
})
543
544      ## Use a working fall back {particularly useful for sparse}:  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
545      ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones                                  value = "matrix"),
546      setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),                   function (x, i, j, value)
547                function(x, y) {                   callGeneric(x=x, i=i, j=j, value = c(value)))
colCheck(x,y)
t(cbind2(t(x), t(y)))
})
548
549  }## R-2.2.x and newer  ## (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              })

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