# SCM Repository

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

# Diff of /pkg/R/Matrix.R

revision 949, Wed Sep 28 09:17:08 2005 UTC revision 1673, Mon Nov 6 20:54:26 2006 UTC
# Line 1  Line 1
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2
3  ## probably not needed eventually:
4  setAs(from = "ddenseMatrix", to = "matrix",  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5        function(from) {
6            if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7            array(from@x, dim = d, dimnames = dimnames(from))  setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8        })
9    ## Most of these work; this is a last resort:
10  setMethod("show", signature(object = "ddenseMatrix"),  setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
11            function(object) prMatrix(object))        function(from) .bail.out.2("coerce", class(from), class(to)))
12    setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
13  ##- ## FIXME: The following is only for the "dMatrix" objects that are not
14  ##- ##        "dense" nor "sparse" -- i.e. "packed" ones :  ## ## probably not needed eventually:
15  ##- ## But these could be printed better -- "." for structural zeros.  ## setAs(from = "ddenseMatrix", to = "matrix",
16  ##- setMethod("show", signature(object = "dMatrix"), prMatrix)  ##       function(from) {
17  ##- ## and improve this as well:  ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
18  ##- setMethod("show", signature(object = "pMatrix"), prMatrix)  ##        array(from@x, dim = d, dimnames = dimnames(from))
19  ##- ## this should now be superfluous [keep for safety for the moment]:  ##       })
setMethod("show", signature(object = "Matrix"),
function(object) prMatrix(object))
20
21  ## should propagate to all subclasses:  ## should propagate to all subclasses:
22  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
23    ## for 'Matrix' objects, as.array() should be equivalent:
24    setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
25
26    ## head and tail apply to all Matrix objects for which subscripting is allowed:
28    setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
29
30  ## Note that isSymmetric is *not* exported  ## slow "fall back" method {subclasses should have faster ones}:
31    setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
32              function(x) as.vector(as(x, "matrix")))
33
34    ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
35    setMethod("as.numeric", signature(x = "Matrix"),
36              function(x, ...) as.numeric(as.vector(x)))
37    setMethod("as.logical", signature(x = "Matrix"),
38              function(x, ...) as.logical(as.vector(x)))
39
40
41    ## "base" has an isSymmetric() S3-generic since R 2.3.0
42  setMethod("isSymmetric", signature(object = "symmetricMatrix"),  setMethod("isSymmetric", signature(object = "symmetricMatrix"),
43            function(object) TRUE)            function(object,tol) TRUE)
44  setMethod("isSymmetric", signature(object = "triangularMatrix"),  setMethod("isSymmetric", signature(object = "triangularMatrix"),
45            ## FIXME: 'TRUE' if *diagonal*, i.e. return(isDiagonal(object))            ## TRUE iff diagonal:
46            function(object) FALSE)            function(object,tol) isDiagonal(object))
47  setMethod("isDiagonal", signature(object = "sparseMatrix"),
48            function(object) {  setMethod("isTriangular", signature(object = "triangularMatrix"),
49                gT <- as(object, "TsparseMatrix")            function(object, ...) TRUE)
50                all(gT@i == gT@j)
51            })  setMethod("isTriangular", signature(object = "matrix"), isTriMat)
52
53    setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
54
55
56
57  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
58            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
# Line 57  Line 76
76            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
77
78  Matrix <-  Matrix <-
79      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
80                  sparse = NULL, forceCheck = FALSE)
81  {  {
82      if (is(data, "Matrix")) return(data)      sparseDefault <- function(m) prod(dim(m)) > 2*sum(isN0(as(m, "matrix")))
83      if (is.matrix(data)) { val <- data }
84      else { ## cut & paste from "base::matrix" :      i.M <- is(data, "Matrix")
85
86        if(is.null(sparse1 <- sparse) && (i.M || is(data, "matrix")))
87            sparse <- sparseDefault(data)
88
89        doDN <- TRUE
90        if (i.M) {
91            sM <- is(data,"sparseMatrix")
92            if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
93                return(data)
94            ## else : convert  dense <-> sparse -> at end
95        }
96        else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
97          if (missing(nrow))          if (missing(nrow))
98              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
99          else if (missing(ncol))          else if (missing(ncol))
100              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
101          val <- .Internal(matrix(data, nrow, ncol, byrow))          if(length(data) == 1 && is0(data) && !identical(sparse, FALSE)) {
102          dimnames(val) <- dimnames              ## Matrix(0, ...) : always sparse unless "sparse = FALSE":
103                if(is.null(sparse)) sparse1 <- sparse <- TRUE
104                ## will be sparse: do NOT construct full matrix!
105                data <- new(if(is.numeric(data)) "dgTMatrix" else
106                            if(is.logical(data)) "lgTMatrix" else
107                            stop("invalid 'data'"),
108                            Dim = as.integer(c(nrow,ncol)),
109                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
110                            else dimnames)
111            } else { ## normal case
112                data <- .Internal(matrix(data, nrow, ncol, byrow))
113                if(is.null(sparse))
114                    sparse <- sparseDefault(data)
115                dimnames(data) <- dimnames
116            }
117            doDN <- FALSE
118        }
119        ## 'data' is now a "matrix" or "Matrix"
120        if (doDN && !is.null(dimnames))
121            dimnames(data) <- dimnames
122
123        ## check for symmetric / triangular / diagonal :
124        isSym <- isSymmetric(data)
125        if((isTri <- !isSym))
126            isTri <- isTriangular(data)
127        isDiag <- isSym # cannot be diagonal if it isn't symmetric
128        if(isDiag)
129            isDiag <- isDiagonal(data)
130
131        ## Find proper matrix class 'cl'
132        cl <-
133            if(isDiag && !isTRUE(sparse1))
134                "diagonalMatrix" # -> will automatically check for type
135            else {
136                ## consider it's type
137                ctype <-
138                    if(is(data,"Matrix")) class(data)
139                    else {
140                        if("complex" == (ctype <- typeof(data)))
141                            "z" else ctype
142      }      }
143      as(val, "dgeMatrix")              ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
144                if(ctype == "z")
145                    stop("complex matrices not yet implemented in Matrix package")
146                if(ctype == "i") {
147                    warning("integer matrices not yet implemented in 'Matrix'; ",
148                            "using 'double' ones'")
149                    ctype <- "d"
150                }
151                paste(ctype,
152                      if(sparse) {
153                          if(isSym) "sCMatrix" else
154                          if(isTri) "tCMatrix" else "gCMatrix"
155                      } else { ## dense
156                          if(isSym) "syMatrix" else
157                          if(isTri) "trMatrix" else "geMatrix"
158                      }, sep="")
159            }
160
161        ## Now coerce and return
162        as(data, cl)
163  }  }
164
165  ## Methods for operations where one argument is numeric  ## Methods for operations where one argument is numeric
# Line 81  Line 171
171            function(x, y) callGeneric(x, as.matrix(y)))            function(x, y) callGeneric(x, as.matrix(y)))
172
173  setMethod("%*%", signature(x = "numeric", y = "Matrix"),  setMethod("%*%", signature(x = "numeric", y = "Matrix"),
174            function(x, y) callGeneric(rbind(x), y))            function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
175
176  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
177            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))

178  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
179            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
180
181    ## The as.matrix() promotion seems illogical to MM,
182    ## but is according to help(tcrossprod, package = "base") :
183    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
184              function(x, y = NULL) callGeneric(x, as.matrix(y)))
185    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
186              function(x, y = NULL)  callGeneric(as.matrix(x), y))
187
188    ## maybe not optimal
189    setMethod("solve", signature(a = "Matrix", b = "missing"),
190              function(a, b, ...) solve(a, Diagonal(nrow(a))))
191
192  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
193            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
194    ## when no sub-class method is found, bail out
195    setMethod("solve", signature(a = "Matrix", b = "matrix"),
196              function(a, b, ...) .bail.out.2("solve", class(a), "matrix"))
197
198  ## bail-out methods in order to get better error messages  ## bail-out methods in order to get better error messages
199  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),  setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
# Line 100  Line 203
203
204  setMethod("crossprod", signature(x = "Matrix", y = "ANY"),  setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
205            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))            function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
206    setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
207              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
208    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
209              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
210    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
211              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
212
213    ## cheap fallbacks
214    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
215              function(x, y = NULL) t(x) %*% y)
216    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
217              function(x, y = NULL) x %*% t(y))
218
219    ## There are special sparse methods; this is a "fall back":
220    setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
221                                     FUN = "ANY", make.dimnames = "ANY"),
222              function(X, Y, FUN, make.dimnames, ...) {
223                  X <- as(X, "matrix") ; Matrix(callGeneric()) })
224    setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
225                                     FUN = "ANY", make.dimnames = "ANY"),
226              function(X, Y, FUN, make.dimnames, ...) {
227                  Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
228
229
230    ## FIXME: All of these should never be called
231    setMethod("chol", signature(x = "Matrix"),
232              function(x, pivot = FALSE) .bail.out.1(.Generic, class(x)))
233    setMethod("determinant", signature(x = "Matrix"),
234              function(x, logarithm = TRUE) .bail.out.1(.Generic, class(x)))
235
236    setMethod("diag", signature(x = "Matrix"),
237              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
238  setMethod("t", signature(x = "Matrix"),  setMethod("t", signature(x = "Matrix"),
239            function(x) .bail.out.1(.Generic, class(x)))            function(x) .bail.out.1(.Generic, class(x)))
240
241  ## Group Methods (bail-out)  ## Group Methods
242  setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),  setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
243            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))  ## "fallback":
244  setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),  setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
245              function(e1) {
246                  warning("inefficient method used for \"- e1\"")
247                  0-e1
248              })
249
250    ## old-style matrices are made into new ones
251    setMethod("Ops", signature(e1 = "Matrix", e2 = "matrix"),
252              function(e1, e2) callGeneric(e1, Matrix(e2)))
253    ##          callGeneric(e1, Matrix(e2, sparse=is(e1,"sparseMatrix"))))
254    setMethod("Ops", signature(e1 = "matrix", e2 = "Matrix"),
255              function(e1, e2) callGeneric(Matrix(e1), e2))
256
257    ## bail-outs -- on highest possible level, hence "Ops", not "Compare"/"Arith" :
258    setMethod("Ops", signature(e1 = "Matrix", e2 = "Matrix"),
259              function(e1, e2) {
260                  d <- dimCheck(e1,e2)
261                  .bail.out.2(.Generic, class(e1), class(e2))
262              })
263    setMethod("Ops", signature(e1 = "Matrix", e2 = "ANY"),
264            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
265  setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),  setMethod("Ops", signature(e1 = "ANY", e2 = "Matrix"),
266            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))            function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
267
268
# Line 126  Line 279
279  setMethod("[", signature(x = "Matrix",  setMethod("[", signature(x = "Matrix",
280                           i = "missing", j = "missing", drop = "ANY"),                           i = "missing", j = "missing", drop = "ANY"),
281            function (x, i, j, drop) x)            function (x, i, j, drop) x)
282
283  ## missing 'drop' --> 'drop = TRUE'  ## missing 'drop' --> 'drop = TRUE'
284  ##                     -----------  ##                     -----------
285  ## select rows  ## select rows
# Line 145  Line 299
299            function(x,i,j, drop)            function(x,i,j, drop)
300            stop("invalid or not-yet-implemented 'Matrix' subsetting"))            stop("invalid or not-yet-implemented 'Matrix' subsetting"))
301
302  ## "FIXME:"  ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
303  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  ## The following is *both* for    M [ <logical>   ]
304  ##  and                A[ LL ]  where LL is a logical *vector*  ##                 and also for   M [ <logical> , ]
305  ## -> [.data.frame uses nargs() - can we do this in the *generic* ?  .M.sub.i.logical <- function (x, i, j, drop)
306    {
307        nA <- nargs()
308        if(nA == 2) { ##  M [ M >= 7 ]
309            ## FIXME: when both 'x' and 'i' are sparse, this can be very inefficient
310            as(x, geClass(x))@x[as.vector(i)]
311            ## -> error when lengths don't match
312        } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
313            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
314
315        } else stop("nargs() = ", nA,
316                    " should never happen; please report.")
317    }
318    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
319                             drop = "ANY"),
320              .M.sub.i.logical)
321    setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
322                             drop = "ANY"),
323              .M.sub.i.logical)
324
325
326    ## A[ ij ]  where ij is (i,j) 2-column matrix :
327    .M.sub.i.2col <- function (x, i, j, drop)
328    {
329        nA <- nargs()
330        if(nA == 2) { ##  M [ cbind(ii,jj) ]
331            if(!is.integer(nc <- ncol(i)))
332                stop("'i' has no integer column number",
333                     " should never happen; please report")
334            if(is.logical(i))
335                return(.M.sub.i.logical(x,i,j,drop))
336            else if(!is.numeric(i) || nc != 2)
337                stop("such indexing must be by logical or 2-column numeric matrix")
338            m <- nrow(i)
339            if(m == 0) return(vector(mode = .type.kind[.M.kind(x)]))
340            ## else
341            i1 <- i[,1]
342            i2 <- i[,2]
343            ## potentially inefficient -- FIXME --
344            unlist(lapply(seq_len(m), function(j) x[i1[j], i2[j]]))
345
346        } else stop("nargs() = ", nA, " should never happen; please report.")
347    }
348    setMethod("[", signature(x = "Matrix", i = "matrix", j = "missing"),# drop="ANY"
349              .M.sub.i.2col)
350
351
352  ### "[<-" : -----------------  ### "[<-" : -----------------
353
354  ## x[] <- value :  ## x[] <- value :
355  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
356                                  value = "index"),##  double/logical/...                                  value = "ANY"),## double/logical/...
357            function (x, value) { x@x <- value ; validObject(x); x })            function (x, value) {
358                  ## Fails for 'nMatrix' ... FIXME : make sure have method there
359                  x@x <- value
360                  validObject(x)# check if type and lengths above match
361                  x
362              })
363
364  ## Otherwise (value is not "index"): bail out  ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
365  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",  .M.repl.i.2col <- function (x, i, j, value)
366                                  value = "ANY"),  {
367            function (x, i, j, value)      nA <- nargs()
368                   if(!is(value,"index"))      if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value
369                   stop("RHS 'value' must be of class \"index\"")          if(!is.integer(nc <- ncol(i)))
370                   else stop("not-yet-implemented 'Matrix[<-' method"))              stop("'i' has no integer column number",
371                     " should never happen; please report")
372            if(is.logical(i)) {
373                i <- c(i) # drop "matrix"
374                return( callNextMethod() )
375            } else if(!is.numeric(i) || nc != 2)
376                stop("such indexing must be by logical or 2-column numeric matrix")
377            m <- nrow(i)
378            mod.x <- .type.kind[.M.kind(x)]
379            if(length(value) > 0 && m %% length(value) != 0)
380                warning("number of items to replace is not a multiple of replacement length")
381            ## recycle:
382            value <- rep(value, length = m)
383            i1 <- i[,1]
384            i2 <- i[,2]
385            ## inefficient -- FIXME -- (also loses "symmetry" unnecessarily)
386            for(k in seq_len(m))
387                x[i1[k], i2[k]] <- value[k]
388            x
389
390        } else stop("nargs() = ", nA, " should never happen; please report.")
391    }
392    setReplaceMethod("[", signature(x = "Matrix", i = "matrix", j = "missing",
393                                    value = "replValue"),
394              .M.repl.i.2col)
395
396
397  ## NOTE: the following only works for R 2.2.x (and later) ---  setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
398  ## ----  *and* 'Matrix' must have been *installed* by R >= 2.2.x                                  value = "Matrix"),
399                     function (x, i, j, value)
400                     callGeneric(x=x, i=i, j=j, value = as.vector(value)))
401    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
402                                    value = "matrix"),
403                     function (x, i, j, value)
404                     callGeneric(x=x, i=i, j=j, value = c(value)))
405
406    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
407    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
408                                    value = "ANY"),
409              function (x, i, j, value) {
410                  if(!is.atomic(value))
411                      stop(sprintf("RHS 'value' (class %s) matches 'ANY', but must match matrix class %s",
412                                   class(value),class(x)))
413                  else stop("not-yet-implemented 'Matrix[<-' method")
414              })
415
if(paste(R.version\$major, R.version\$minor, sep=".") >= "2.2") {
416
417      ## The trivial methods :      ## The trivial methods :
418      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),      setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
# Line 196  Line 437
437                                  class(x), class(y)))                                  class(x), class(y)))
438                })                })
439
440    ## Use a working fall back {particularly useful for sparse}:
441    ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
442      setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),      setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
443                function(x, y) {                function(x, y) {
444                    colCheck(x,y)                    colCheck(x,y)
445                    stop(gettextf("rbind2() method for (%s,%s) not-yet defined",                t(cbind2(t(x), t(y)))
class(x), class(y)))
446                })                })