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

Diff of /pkg/R/Matrix.R

revision 868, Fri Aug 19 17:01:11 2005 UTC revision 1551, Tue Sep 12 16:39:13 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    setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
10  ## private function to be used as show() method possibly more than once        function(from) .bail.out.2("coerce", class(from), class(to)))
11  prMatrix <- function(object) {
12      d <- dim(object)  ## ## probably not needed eventually:
13      cl <- class(object)  ## setAs(from = "ddenseMatrix", to = "matrix",
14      cat(sprintf('%d x %d Matrix of class "%s"\n', d[1], d[2], cl))  ##       function(from) {
15      m <- as(object, "matrix")  ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
16      maxp <- getOption("max.print")  ##        array(from@x, dim = d, dimnames = dimnames(from))
17      if(prod(d) <= maxp) print(m)  ##       })
else { ## d[1] > maxp / d[2] >= nr :
nr <- maxp %/% d[2]
n2 <- ceiling(nr / 2)
cat("\n ..........\n\n")
print(tail(m, max(1, nr - n2)))
}
## DEBUG: cat("str(.):\n") ; str(object)
invisible(object)# as print() S3 methods do
}

setMethod("show", signature(object = "ddenseMatrix"), prMatrix)

##- ## FIXME: The following is only for the "dMatrix" objects that are not
##- ##        "dense" nor "sparse" -- i.e. "packed" ones :
##- ## But these could be printed better -- "." for structural zeros.
##- setMethod("show", signature(object = "dMatrix"), prMatrix)
##- ## and improve this as well:
##- setMethod("show", signature(object = "pMatrix"), prMatrix)
##- ## this should now be superfluous [keep for safety for the moment]:
setMethod("show", signature(object = "Matrix"), prMatrix)
18
19  ## should propagate to all subclasses:  ## should propagate to all subclasses:
20  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
21    ## for 'Matrix' objects, as.array() should be equivalent:
22    setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
23
24    ## head and tail apply to all Matrix objects for which subscripting is allowed:
26    setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
27
28    ## slow "fall back" method {subclasses should have faster ones}:
29    setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
30              function(x) as.vector(as(x, "matrix")))
31
32    ## mainly need these for "dMatrix" or "lMatrix" respectively, but why not general:
33    setMethod("as.numeric", signature(x = "Matrix"),
34              function(x, ...) as.numeric(as.vector(x)))
35    setMethod("as.logical", signature(x = "Matrix"),
36              function(x, ...) as.logical(as.vector(x)))
37
38
39    ## "base" has an isSymmetric() S3-generic since R 2.3.0
40    setMethod("isSymmetric", signature(object = "symmetricMatrix"),
41              function(object,tol) TRUE)
42    setMethod("isSymmetric", signature(object = "triangularMatrix"),
43              ## TRUE iff diagonal:
44              function(object,tol) isDiagonal(object))
45
46    setMethod("isTriangular", signature(object = "triangularMatrix"),
47              function(object, ...) TRUE)
48
49    setMethod("isTriangular", signature(object = "matrix"), isTriMat)
50
51    setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
52
53
54
55  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
56            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
# Line 62  Line 74
74            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
75
76  Matrix <-  Matrix <-
77      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
78                  sparse = NULL, forceCheck = FALSE)
79  {  {
80      if (is(data, "Matrix")) return(data)      sparseDefault <- function(m)
81      if (is.matrix(data)) { val <- data }          prod(dim(m)) > 2*sum(is.na(m <- as(m, "matrix")) | m != 0)
82      else { ## cut & paste from "base::matrix" :
83        i.M <- is(data, "Matrix")
84        if(is.null(sparse) && (i.M || is(data, "matrix")))
85            sparse <- sparseDefault(data)
86
87        doDN <- TRUE
88        if (i.M) {
89            sM <- is(data,"sparseMatrix")
90            if(!forceCheck && ((sparse && sM) || (!sparse && !sM)))
91                return(data)
92            ## else : convert  dense <-> sparse -> at end
93        }
94        else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
95          if (missing(nrow))          if (missing(nrow))
96              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
97          else if (missing(ncol))          else if (missing(ncol))
98              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
99          val <- .Internal(matrix(data, nrow, ncol, byrow))          if(length(data) == 1 && !is.na(data) && data == 0 &&
100          dimnames(val) <- dimnames             !identical(sparse, FALSE)) {
101
102                if(is.null(sparse)) sparse <- TRUE
103                ## will be sparse: do NOT construct full matrix!
104                data <- new(if(is.numeric(data)) "dgTMatrix" else
105                            if(is.logical(data)) "lgTMatrix" else
106                            stop("invalid 'data'"),
107                            Dim = as.integer(c(nrow,ncol)),
108                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
109                            else dimnames)
110            } else { ## normal case
111                data <- .Internal(matrix(data, nrow, ncol, byrow))
112                if(is.null(sparse))
113                    sparse <- sparseDefault(data)
114                dimnames(data) <- dimnames
115            }
116            doDN <- FALSE
117        }
118        ## 'data' is now a "matrix" or "Matrix"
119        if (doDN && !is.null(dimnames))
120            dimnames(data) <- dimnames
121
122        ## check for symmetric / triangular / diagonal :
123        isSym <- isSymmetric(data)
124        if((isTri <- !isSym))
125            isTri <- isTriangular(data)
126        isDiag <- isSym # cannot be diagonal if it isn't symmetric
127        if(isDiag)
128            isDiag <- isDiagonal(data)
129
130    ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
131
132        ## Find proper matrix class 'cl'
133        cl <-
134            if(isDiag)
135                "diagonalMatrix" # -> will automatically check for type
136            else {
137                ## consider it's type
138                ctype <-
139                    if(is(data,"Matrix")) class(data)
140                    else {
141                        if("complex" == (ctype <- typeof(data)))
142                            "z" else ctype
143      }      }
144      as(val, "dgeMatrix")              ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
145                if(ctype == "z")
146                    stop("complex matrices not yet implemented in Matrix package")
147                if(ctype == "i") {
148                    warning("integer matrices not yet implemented in 'Matrix'; ",
149                            "using 'double' ones'")
150                    ctype <- "d"
151                }
152                paste(ctype,
153                      if(sparse) {
154                          if(isSym) "sCMatrix" else
155                          if(isTri) "tCMatrix" else "gCMatrix"
156                      } else { ## dense
157                          if(isSym) "syMatrix" else
158                          if(isTri) "trMatrix" else "geMatrix"
159                      }, sep="")
160            }
161
162        ## Now coerce and return
163        as(data, cl)
164  }  }
165
166  ## Methods for operations where one argument is numeric  ## Methods for operations where one argument is numeric
# Line 90  Line 176
176
177  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),  setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
178            function(x, y = NULL) callGeneric(x, as.matrix(y)))            function(x, y = NULL) callGeneric(x, as.matrix(y)))

179  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),  setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
180            function(x, y = NULL)  callGeneric(rbind(x), y))            function(x, y = NULL)  callGeneric(as.matrix(x), y))
181
182    ## The as.matrix() promotion seems illogical to MM,
183    ## but is according to help(tcrossprod, package = "base") :
184    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
185              function(x, y = NULL) callGeneric(x, as.matrix(y)))
186    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
187              function(x, y = NULL)  callGeneric(as.matrix(x), y))
188
189  setMethod("solve", signature(a = "Matrix", b = "numeric"),  setMethod("solve", signature(a = "Matrix", b = "numeric"),
190            function(a, b, ...) callGeneric(a, as.matrix(b)))            function(a, b, ...) callGeneric(a, as.matrix(b)))
191
192  ## Subsetting : The "missing" cases can be dealt with here, "at the top":  ## bail-out methods in order to get better error messages
193    setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
194              function (x, y)
195              stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
196                            class(x), class(y))))
197
198    setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
199              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
200    setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
201              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
202    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
203              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
204    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
205              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
206
207    ## cheap fallbacks
208    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
209              function(x, y = NULL) t(x) %*% y)
210    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
211              function(x, y = NULL) x %*% t(y))
212
213    ## There are special sparse methods; this is a "fall back":
214    setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
215                                     FUN = "ANY", make.dimnames = "ANY"),
216              function(X, Y, FUN, make.dimnames, ...) {
217                  X <- as(X, "matrix") ; Matrix(callGeneric()) })
218    setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
219                                     FUN = "ANY", make.dimnames = "ANY"),
220              function(X, Y, FUN, make.dimnames, ...) {
221                  Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
222
223
224    setMethod("diag", signature(x = "Matrix"),
225              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
226    setMethod("t", signature(x = "Matrix"),
227              function(x) .bail.out.1(.Generic, class(x)))
228
229    ## Group Methods
230    setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
231    ## "fallback":
232    setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
233              function(e1) {
234                  warning("inefficient method used for \"- e1\"")
235                  0-e1
236              })
237
238    ## bail-outs:
239    setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
240              function(e1, e2) {
241                  d <- dimCheck(e1,e2)
242                  .bail.out.2(.Generic, class(e1), class(e2))
243              })
244    setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
245              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
246    setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
247              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
248
249
250
251    ### --------------------------------------------------------------------------
252    ###
253    ### Subsetting "["  and
254    ### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
255
256    ## Using "index" for indices should allow
257    ## integer (numeric), logical, or character (names!) indices :
258
259  ## "x[]":  ## "x[]":
260  setMethod("[", signature(x = "Matrix",  setMethod("[", signature(x = "Matrix",
# Line 107  Line 264
264  ## missing 'drop' --> 'drop = TRUE'  ## missing 'drop' --> 'drop = TRUE'
265  ##                     -----------  ##                     -----------
266  ## select rows  ## select rows
267  setMethod("[", signature(x = "Matrix", i = "numeric", j = "missing",  setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
268                           drop = "missing"),                           drop = "missing"),
269            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))            function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
270  ## select columns  ## select columns
271  setMethod("[", signature(x = "Matrix", i = "missing", j = "numeric",  setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
272                           drop = "missing"),                           drop = "missing"),
273            function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))            function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
274  setMethod("[", signature(x = "Matrix", i = "numeric", j = "numeric",  setMethod("[", signature(x = "Matrix", i = "index", j = "index",
275                           drop = "missing"),                           drop = "missing"),
276            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))
277
278    ## bail out if any of (i,j,drop) is "non-sense"
279    setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
280              function(x,i,j, drop)
281              stop("invalid or not-yet-implemented 'Matrix' subsetting"))
282
283    ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
284    ## The following is *both* for    M [ <logical>   ]
285    ##                 and also for   M [ <logical> , ]
286    .M.sub.i.logical <- function (x, i, j, drop)
287    {
288        nA <- nargs()
289        if(nA == 2) { ##  M [ M >= 7 ]
290            as(x, geClass(x))@x[as.vector(i)]
291            ## -> error when lengths don't match
292        } else if(nA == 3) { ##  M [ M[,1, drop=FALSE] >= 7, ]
293            stop("not-yet-implemented 'Matrix' subsetting") ## FIXME
294
295        } else stop("nargs() = ", nA,
296                    " should never happen; please report.")
297    }
298    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
299                             drop = "ANY"),
300              .M.sub.i.logical)
301    setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
302                             drop = "ANY"),
303              .M.sub.i.logical)
304
305
306  ## "FIXME:"  ## "FIXME:"
307  ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?  ## ------ get at  A[ ij ]  where ij is (i,j) 2-column matrix?
##  and                A[ LL ]  where LL is a logical *vector*
308
309
310
311    ### "[<-" : -----------------
312
313  if(FALSE) ## The following can't work as long as cbind is function(..., *)  ## x[] <- value :
314  setMethod("cbind", signature(a = "Matrix", b = "Matrix"),  setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
315            function(a, b, ...) {                                  value = "ANY"),## double/logical/...
316                da <- Dim(a)            function (x, value) {
317                db <- Dim(b)                x@x <- value
318                if(da[1] != db[1])                validObject(x)# check if type and lengths above match
319                    stop("Matrices must have same number of rows for cbind()ing")                x
320            })            })
321
322    ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
323    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
324    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
325                                    value = "ANY"),
326              function (x, i, j, value) {
327                  if(!is.atomic(value))
328                      stop("RHS 'value' must match matrix class ", class(x))
329                  else stop("not-yet-implemented 'Matrix[<-' method")
330              })
331
332
333    ## The trivial methods :
334    setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
335              function(x, y) x)
336    setMethod("cbind2", signature(x = "Matrix", y = "missing"),
337              function(x, y) x)
338    setMethod("cbind2", signature(x = "NULL", y="Matrix"),
339              function(x, y) x)
340
341    setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
342              function(x, y) x)
343    setMethod("rbind2", signature(x = "Matrix", y = "missing"),
344              function(x, y) x)
345    setMethod("rbind2", signature(x = "NULL", y="Matrix"),
346              function(x, y) x)
347
348    ## Makes sure one gets x decent error message for the unimplemented cases:
349    setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
350              function(x, y) {
351                  rowCheck(x,y)
352                  stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
353                                class(x), class(y)))
354              })
355
356    ## Use a working fall back {particularly useful for sparse}:
357    ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
358    setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
359              function(x, y) {
360                  colCheck(x,y)
361                  t(cbind2(t(x), t(y)))
362              })

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