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Diff of /pkg/R/Matrix.R

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revision 477, Wed Feb 2 14:14:59 2005 UTC revision 1673, Mon Nov 6 20:54:26 2006 UTC
# Line 1  Line 1 
1  setMethod("show", signature(object = "Matrix"),  #### Toplevel ``virtual'' class "Matrix"
2            function(object) print(as(object, "matrix")))  
3    
4    ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
5    
6    setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7    setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8    
9    ## Most of these work; this is a last resort:
10    setAs(from = "Matrix", to = "matrix", # do *not* call base::as.matrix() here:
11          function(from) .bail.out.2("coerce", class(from), class(to)))
12    setAs(from = "matrix", to = "Matrix", function(from) Matrix(from))
13    
14    ## ## probably not needed eventually:
15    ## setAs(from = "ddenseMatrix", to = "matrix",
16    ##       function(from) {
17    ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
18    ##        array(from@x, dim = d, dimnames = dimnames(from))
19    ##       })
20    
21    ## should propagate to all subclasses:
22    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:
27    setMethod("head", signature(x = "Matrix"), utils::head.matrix)
28    setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
29    
30    ## 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"),
43              function(object,tol) TRUE)
44    setMethod("isSymmetric", signature(object = "triangularMatrix"),
45              ## TRUE iff diagonal:
46              function(object,tol) isDiagonal(object))
47    
48    setMethod("isTriangular", signature(object = "triangularMatrix"),
49              function(object, ...) TRUE)
50    
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"),
58              function(x) x@Dim, valueClass = "integer")
59    setMethod("dimnames", signature(x = "Matrix"), function(x) x@Dimnames)
60    ## not exported but used more than once for "dimnames<-" method :
61    ## -- or do only once for all "Matrix" classes ??
62    dimnamesGets <- function (x, value) {
63        d <- dim(x)
64        if (!is.list(value) || length(value) != 2 ||
65            !(is.null(v1 <- value[[1]]) || length(v1) == d[1]) ||
66            !(is.null(v2 <- value[[2]]) || length(v2) == d[2]))
67            stop(sprintf("invalid dimnames given for '%s' object", class(x)))
68        x@Dimnames <- list(if(!is.null(v1)) as.character(v1),
69                           if(!is.null(v2)) as.character(v2))
70        x
71    }
72    setMethod("dimnames<-", signature(x = "Matrix", value = "list"),
73              dimnamesGets)
74    
75    setMethod("unname", signature("Matrix", force="missing"),
76              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 {      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      as(val, "dgeMatrix")              ## 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  Matrix.class <- function(x, tol = 0, symmetry = TRUE, unit.diagonal = TRUE,      ## check for symmetric / triangular / diagonal :
124                           triangularity = c(TRUE, TRUE),      isSym <- isSymmetric(data)
125                           orthogonality = c(TRUE, TRUE), normality = c(TRUE, TRUE))      if((isTri <- !isSym))
126  {          isTri <- isTriangular(data)
127      val <- "Matrix"      isDiag <- isSym # cannot be diagonal if it isn't symmetric
128      x <- as.matrix(x)      if(isDiag)
129      if (symmetry) {          isDiag <- isDiagonal(data)
130          if (is.Hermitian(x, tol)) val <- c("Hermitian", val)  
131      }      ## Find proper matrix class 'cl'
132      if (triangularity[1]) {      cl <-
133          if (is.LowerTriangular(x, tol)) {          if(isDiag && !isTRUE(sparse1))
134              val <- c("LowerTriangular", val)              "diagonalMatrix" # -> will automatically check for type
135              if (unit.diagonal)          else {
136                  if (max(Mod(diag(x) - 1)) <= tol)              ## consider it's type
137                      val <- c("UnitLowerTriangular", val)              ctype <-
138          }                  if(is(data,"Matrix")) class(data)
139      }                  else {
140      if (triangularity[2]) {                      if("complex" == (ctype <- typeof(data)))
141          if (is.UpperTriangular(x, tol)) {                          "z" else ctype
             val <- c("UpperTriangular", val)  
             if (unit.diagonal)  
                 if (max(Mod(diag(x) - 1)) <= tol)  
                     val <- c("UnitUpperTriangular", val)  
         }  
     }  
     if (orthogonality[1]) {  
         if (is.ColOrthonormal(x, tol)) {  
             val <- c("ColOrthoNormal", "ColOrthogonal", val)  
         } else {  
             if (Orthogonal.test(x, normal = FALSE) <= tol)  
                 val <- c("ColOrthogonal", val)  
142          }          }
143                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      if (orthogonality[2]) {  
161          if (normality[2] && is.RowOrthonormal(x, tol)) {      ## Now coerce and return
162              val <- c("RowOrthoNormal", "RowOrthogonal", val)      as(data, cl)
         } else {  
             if (Orthogonal.test(x, byrow = TRUE, normal = FALSE) <= tol)  
                 val <- c("RowOrthogonal", val)  
163          }          }
164    
165    ## Methods for operations where one argument is numeric
166    
167    ## Using as.matrix() and rbind()
168    ## in order to get dimnames from names {at least potentially}:
169    
170    setMethod("%*%", signature(x = "Matrix", y = "numeric"),
171              function(x, y) callGeneric(x, as.matrix(y)))
172    
173    setMethod("%*%", signature(x = "numeric", y = "Matrix"),
174              function(x, y) callGeneric(matrix(x, nrow = 1, byrow=TRUE), y))
175    
176    setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
177              function(x, y = NULL) callGeneric(x, as.matrix(y)))
178    setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
179              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"),
193              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
199    setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
200              function (x, y)
201              stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
202                            class(x), class(y))))
203    
204    setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
205              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"),
239              function(x) .bail.out.1(.Generic, class(x)))
240    
241    ## Group Methods
242    setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
243    ## "fallback":
244    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)))
265    setMethod("Ops", signature(e1 = "ANY", e2 = "Matrix"),
266              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
267    
268    
269    
270    ### --------------------------------------------------------------------------
271    ###
272    ### Subsetting "["  and
273    ### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
274    
275    ## Using "index" for indices should allow
276    ## integer (numeric), logical, or character (names!) indices :
277    
278    ## "x[]":
279    setMethod("[", signature(x = "Matrix",
280                             i = "missing", j = "missing", drop = "ANY"),
281              function (x, i, j, drop) x)
282    
283    ## missing 'drop' --> 'drop = TRUE'
284    ##                     -----------
285    ## select rows
286    setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
287                             drop = "missing"),
288              function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
289    ## select columns
290    setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
291                             drop = "missing"),
292              function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
293    setMethod("[", signature(x = "Matrix", i = "index", j = "index",
294                             drop = "missing"),
295              function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
296    
297    ## bail out if any of (i,j,drop) is "non-sense"
298    setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
299              function(x,i,j, drop)
300              stop("invalid or not-yet-implemented 'Matrix' subsetting"))
301    
302    ## logical indexing, such as M[ M >= 7 ] *BUT* also M[ M[,1] >= 3,],
303    ## The following is *both* for    M [ <logical>   ]
304    ##                 and also for   M [ <logical> , ]
305    .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      val  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  as.Matrix <- function(x, tol = .Machine$double.eps)  ## x[] <- value :
355    setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
356                                    value = "ANY"),## double/logical/...
357              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    ## A[ ij ] <- value,  where ij is (i,j) 2-column matrix :
365    .M.repl.i.2col <- function (x, i, j, value)
366  {  {
367      if (inherits(x, "Matrix")) return(asObject(x, Matrix.class(x, tol = tol)))      nA <- nargs()
368      asObject(as.matrix(x), Matrix.class(x, tol = tol))      if(nA == 3) { ##  M [ cbind(ii,jj) ] <- value
369            if(!is.integer(nc <- ncol(i)))
370                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    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
398                                    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    
416    
417    ## The trivial methods :
418    setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
419              function(x, y) x)
420    setMethod("cbind2", signature(x = "Matrix", y = "missing"),
421              function(x, y) x)
422    setMethod("cbind2", signature(x = "NULL", y="Matrix"),
423              function(x, y) x)
424    
425    setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
426              function(x, y) x)
427    setMethod("rbind2", signature(x = "Matrix", y = "missing"),
428              function(x, y) x)
429    setMethod("rbind2", signature(x = "NULL", y="Matrix"),
430              function(x, y) x)
431    
432    ## Makes sure one gets x decent error message for the unimplemented cases:
433    setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
434              function(x, y) {
435                  rowCheck(x,y)
436                  stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
437                                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"),
443              function(x, y) {
444                  colCheck(x,y)
445                  t(cbind2(t(x), t(y)))
446              })

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