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Diff of /pkg/R/Matrix.R

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revision 676, Sat Mar 26 15:59:18 2005 UTC revision 1455, Mon Aug 28 15:35:44 2006 UTC
# Line 1  Line 1 
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2    
 ## probably not needed eventually:  
 setAs(from = "ddenseMatrix", to = "matrix",  
       function(from) {  
           if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")  
           array(from@x, dim = d, dimnames = dimnames(from))  
       })  
3    
4  ## private function to be used as show() method possibly more than once  ### Virtual coercions -- via smart "helpers" (-> ./Auxiliaries.R)
 prMatrix <- function(object) {  
     d <- dim(object)  
     cl <- class(object)  
     cat(sprintf('%d x %d Matrix of class "%s"\n', d[1], d[2], cl))  
 ##- no longer needed: have no objects of virtual classes:  
 ##     if(cl == "Matrix") { ## have no data slot  
 ##         cat("Dim = ", d)  
 ##         if(any(sapply(object@Dimnames,length) > 0)) {  
 ##             cat("; Dimnames = ")  
 ##             str(object@Dimnames)  
 ##         }  
 ##         cat("\n")  
 ##     } else { # not "Matrix", hence have data 'x' slot  
         m <- as(object, "matrix")  
         maxp <- getOption("max.print")  
         if(prod(d) <= maxp) print(m)  
         else { ## d[1] > maxp / d[2] >= nr :  
             nr <- maxp %/% d[2]  
             n2 <- ceiling(nr / 2)  
             print(head(m, max(1, n2)))  
             cat("\n ..........\n\n")  
             print(tail(m, max(1, nr - n2)))  
         }  
         ## DEBUG: cat("str(.):\n") ; str(object)  
 ##    }  
     invisible(object)# as print() S3 methods do  
 }  
5    
6  setMethod("show", signature(object = "ddenseMatrix"), prMatrix)  setAs("Matrix", "sparseMatrix", function(from) as_Csparse(from))
7    setAs("Matrix", "denseMatrix",  function(from) as_dense(from))
8    
9  setMethod("show", signature(object = "sparseMatrix"),  ## ## probably not needed eventually:
10     function(object) {  ## setAs(from = "ddenseMatrix", to = "matrix",
11         d <- dim(object)  ##       function(from) {
12         cl <- class(object)  ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
13         cat(sprintf('%d x %d sparse Matrix of class "%s"\n', d[1], d[2], cl))  ##        array(from@x, dim = d, dimnames = dimnames(from))
14    ##       })
15    
16         maxp <- getOption("max.print")  ## should propagate to all subclasses:
17         if(prod(d) <= maxp) print(as(object, "matrix"))  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
18         else { ## d[1] > maxp / d[2] >= nr :  ## for 'Matrix' objects, as.array() should be equivalent:
19             cat("\n Not printing large sparse matrix -- maybe increase options(max.print)\n")  setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
20             if(FALSE) { ### need storage economic "[,]" method for sparse!!  
21                 nr <- maxp %/% d[2]  ## head and tail apply to all Matrix objects for which subscripting is allowed:
22                 n2 <- ceiling(nr / 2)  ## if(paste(R.version$major, R.version$minor, sep=".") < "2.4") {
23                 print(head(m, max(1, n2)))      setMethod("head", signature(x = "Matrix"), utils:::head.matrix)
24                 cat("\n ..........\n\n")      setMethod("tail", signature(x = "Matrix"), utils:::tail.matrix)
25                 print(tail(m, max(1, nr - n2)))  ## } else { # R 2.4.0 and newer
26             }  ##     setMethod("head", signature(x = "Matrix"), utils::head.matrix)
27         }  ##     setMethod("tail", signature(x = "Matrix"), utils::tail.matrix)
28          ## DEBUG: cat("str(.):\n") ; str(object)  ## }
29         invisible(object)  
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    ## Note that isSymmetric is *not* exported
42    ## but that "base" has an isSymmetric() S3-generic since R 2.3.0
43    setMethod("isSymmetric", signature(object = "symmetricMatrix"),
44              function(object,tol) TRUE)
45    setMethod("isSymmetric", signature(object = "triangularMatrix"),
46              ## TRUE iff diagonal:
47              function(object,tol) isDiagonal(object))
48    
49    if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
50        ## need a "matrix" method as in R 2.3 and later
51        setMethod("isSymmetric", signature(object = "matrix"),
52                  function(object, tol = 100*.Machine$double.eps, ...)
53              {
54                  ## pretest: is it square?
55                  d <- dim(object)
56                  if(d[1] != d[2]) return(FALSE)
57                  ## for `broken' all.equal in R <= 2.2.x:
58                  dn <- dimnames(object)
59                  if(!identical(dn[1], dn[2])) return(FALSE)
60                  test <-
61                      if(is.complex(object))
62                          all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
63                      else              # numeric, character, ..
64                          all.equal(object, t(object), tol = tol, ...)
65                  isTRUE(test)
66     })     })
67    
 ## this may go away {since sparse matrices need something better!} :  
 setMethod("show", signature(object = "Matrix"), prMatrix)  
68    
69  ## should propagate to all subclasses:  setMethod("isTriangular", signature(object = "triangularMatrix"),
70  setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))            function(object, ...) TRUE)
71    
72    setMethod("isTriangular", signature(object = "matrix"), isTriMat)
73    
74    setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
75    
76    
77    
78  setMethod("dim", signature(x = "Matrix"),  setMethod("dim", signature(x = "Matrix"),
79            function(x) x@Dim, valueClass = "integer")            function(x) x@Dim, valueClass = "integer")
# Line 88  Line 97 
97            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})            function(obj) { obj@Dimnames <- list(NULL,NULL); obj})
98    
99  Matrix <-  Matrix <-
100      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL)      function (data = NA, nrow = 1, ncol = 1, byrow = FALSE, dimnames = NULL,
101                  sparse = NULL, forceCheck = FALSE)
102  {  {
103      if (is(data, "Matrix")) return(data)      sparseDefault <- function(m)
104      if (is.matrix(data)) { val <- data }          prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
105      else { ## cut & paste from "base::matrix" :  
106        i.M <- is(data, "Matrix")
107        if(is.null(sparse) && (i.M || is(data, "matrix")))
108            sparse <- sparseDefault(data)
109    
110        doDN <- TRUE
111        if (i.M && !forceCheck) {
112            sM <- is(data,"sparseMatrix")
113            if((sparse && sM) || (!sparse && !sM))
114                return(data)
115            ## else : convert  dense <-> sparse -> at end
116        }
117        else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
118          if (missing(nrow))          if (missing(nrow))
119              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
120          else if (missing(ncol))          else if (missing(ncol))
121              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
122          val <- .Internal(matrix(data, nrow, ncol, byrow))          if(length(data) == 1 && data == 0 && !identical(sparse,FALSE)) {
123          dimnames(val) <- dimnames              if(is.null(sparse)) sparse <- TRUE
124      }              ## will be sparse: do NOT construct full matrix!
125      as(val, "dgeMatrix")              data <- new(if(is.numeric(data)) "dgTMatrix" else
126  }                          if(is.logical(data)) "lgTMatrix" else
127                            stop("invalid 'data'"),
128                            Dim = as.integer(c(nrow,ncol)),
129                            Dimnames = if(is.null(dimnames)) list(NULL,NULL)
130                            else dimnames)
131            } else { ## normal case
132                data <- .Internal(matrix(data, nrow, ncol, byrow))
133                if(is.null(sparse))
134                    sparse <- sparseDefault(data)
135                dimnames(data) <- dimnames
136            }
137            doDN <- FALSE
138        }
139        ## 'data' is now a "matrix" or "Matrix"
140        if (doDN && !is.null(dimnames))
141            dimnames(data) <- dimnames
142    
143        ## check for symmetric / triangular / diagonal :
144        isSym <- isSymmetric(data)
145        if((isTri <- !isSym))
146            isTri <- isTriangular(data)
147        isDiag <- isSym # cannot be diagonal if it isn't symmetric
148        if(isDiag)
149            isDiag <- isDiagonal(data)
150    
151    ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
152    
153        ## Find proper matrix class 'cl'
154        cl <-
155            if(isDiag)
156                "diagonalMatrix" # -> will automatically check for type
157            else {
158                ## consider it's type
159                ctype <-
160                    if(is(data,"Matrix")) class(data)
161                    else {
162                        if("complex" == (ctype <- typeof(data)))
163                            "z" else ctype
164                    }
165                ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
166                if(ctype == "z")
167                    stop("complex matrices not yet implemented in Matrix package")
168                if(ctype == "i") {
169                    warning("integer matrices not yet implemented in 'Matrix'; ",
170                            "using 'double' ones'")
171                    ctype <- "d"
172                }
173                paste(ctype,
174                      if(sparse) {
175                          if(isSym) "sCMatrix" else
176                          if(isTri) "tCMatrix" else "gCMatrix"
177                      } else { ## dense
178                          if(isSym) "syMatrix" else
179                          if(isTri) "trMatrix" else "geMatrix"
180                      }, sep="")
181            }
182    
183        ## Now coerce and return
184        as(data, cl)
185    }
186    
187    ## Methods for operations where one argument is numeric
188    
189    ## Using as.matrix() and rbind()
190    ## in order to get dimnames from names {at least potentially}:
191    
192    setMethod("%*%", signature(x = "Matrix", y = "numeric"),
193              function(x, y) callGeneric(x, as.matrix(y)))
194    
195    setMethod("%*%", signature(x = "numeric", y = "Matrix"),
196              function(x, y) callGeneric(rbind(x), y))
197    
198    setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
199              function(x, y = NULL) callGeneric(x, as.matrix(y)))
200    setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
201              function(x, y = NULL)  callGeneric(as.matrix(x), y))
202    
203    ## The as.matrix() promotion seems illogical to MM,
204    ## but is according to help(tcrossprod, package = "base") :
205    setMethod("tcrossprod", signature(x = "Matrix", y = "numeric"),
206              function(x, y = NULL) callGeneric(x, as.matrix(y)))
207    setMethod("tcrossprod", signature(x = "numeric", y = "Matrix"),
208              function(x, y = NULL)  callGeneric(as.matrix(x), y))
209    
210    setMethod("solve", signature(a = "Matrix", b = "numeric"),
211              function(a, b, ...) callGeneric(a, as.matrix(b)))
212    
213    ## bail-out methods in order to get better error messages
214    setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
215              function (x, y)
216              stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
217                            class(x), class(y))))
218    
219    setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
220              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
221    setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
222              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
223    setMethod("tcrossprod", signature(x = "Matrix", y = "ANY"),
224              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
225    setMethod("tcrossprod", signature(x = "ANY", y = "Matrix"),
226              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
227    
228    ## cheap fallbacks
229    setMethod("crossprod", signature(x = "Matrix", y = "Matrix"),
230              function(x, y = NULL) t(x) %*% y)
231    setMethod("tcrossprod", signature(x = "Matrix", y = "Matrix"),
232              function(x, y = NULL) x %*% t(y))
233    
234    ## There are special sparse methods; this is a "fall back":
235    setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
236                                     FUN = "ANY", make.dimnames = "ANY"),
237              function(X, Y, FUN, make.dimnames, ...) {
238                  X <- as(X, "matrix") ; Matrix(callGeneric()) })
239    setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
240                                     FUN = "ANY", make.dimnames = "ANY"),
241              function(X, Y, FUN, make.dimnames, ...) {
242                  Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
243    
244    
245    setMethod("diag", signature(x = "Matrix"),
246              function(x, nrow, ncol) .bail.out.1(.Generic, class(x)))
247    setMethod("t", signature(x = "Matrix"),
248              function(x) .bail.out.1(.Generic, class(x)))
249    
250    ## Group Methods
251    setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
252    ## "fallback":
253    setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
254              function(e1) {
255                  warning("inefficient method used for \"- e1\"")
256                  0-e1
257              })
258    
259    ## bail-outs:
260    setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
261              function(e1, e2) {
262                  d <- dimCheck(e1,e2)
263                  .bail.out.2(.Generic, class(e1), class(e2))
264              })
265    setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
266              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
267    setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
268              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
269    
 if(FALSE) { ##--- not-yet used -- {almost same code also in ./dgeMatrix.R }  
270    
 ## utility for as.Matrix() {which is currently invalid }  
 Matrix.class <- function(x, tol = 0, symmetry = TRUE, unit.diagonal = TRUE,  
                          triangularity = c(TRUE, TRUE),  
                          orthogonality = c(TRUE, TRUE),  
                          normality = c(TRUE, TRUE))  
 {  
     val <- "Matrix"  
     x <- as.matrix(x)  
     if (symmetry) {  
         if (is.Hermitian(x, tol)) val <- c("Hermitian", val)  
     }  
     if (triangularity[1]) {  
         if (is.LowerTriangular(x, tol)) {  
             val <- c("LowerTriangular", val)  
             if (unit.diagonal)  
                 if (max(Mod(diag(x) - 1)) <= tol)  
                     val <- c("UnitLowerTriangular", val)  
         }  
     }  
     if (triangularity[2]) {  
         if (is.UpperTriangular(x, tol)) {  
             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)  
         }  
     }  
     if (orthogonality[2]) {  
         if (normality[2] && is.RowOrthonormal(x, tol)) {  
             val <- c("RowOrthoNormal", "RowOrthogonal", val)  
         } else {  
             if (Orthogonal.test(x, byrow = TRUE, normal = FALSE) <= tol)  
                 val <- c("RowOrthogonal", val)  
         }  
     }  
     val  
 }  
271    
272  as.Matrix <- function(x, tol = .Machine$double.eps)  ### --------------------------------------------------------------------------
273  {  ###
274      asObject(if (inherits(x, "Matrix")) x else as.matrix(x),  ### Subsetting "["  and
275               Matrix.class(x, tol = tol))  ### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
276  }  
277    ## Using "index" for indices should allow
278    ## integer (numeric), logical, or character (names!) indices :
279    
280    ## "x[]":
281    setMethod("[", signature(x = "Matrix",
282                             i = "missing", j = "missing", drop = "ANY"),
283              function (x, i, j, drop) x)
284    
285    ## missing 'drop' --> 'drop = TRUE'
286    ##                     -----------
287    ## select rows
288    setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
289                             drop = "missing"),
290              function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
291    ## select columns
292    setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
293                             drop = "missing"),
294              function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
295    setMethod("[", signature(x = "Matrix", i = "index", j = "index",
296                             drop = "missing"),
297              function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
298    
299    ## bail out if any of (i,j,drop) is "non-sense"
300    setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
301              function(x,i,j, drop)
302              stop("invalid or not-yet-implemented 'Matrix' subsetting"))
303    
304    ##  "logical *vector* indexing, such as  M [ M >= 10 ] :
305    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
306                             drop = "ANY"),
307              function (x, i, j, drop) {
308                  as(x, geClass(x))@x[as.vector(i)]
309                  ## -> error when lengths don't match
310              })
311    
312    ## FIXME: The following is good for    M [ <logical>   ]
313    ##        *BUT* it also triggers for   M [ <logical> , ] where it is *WRONG*
314    ##       using nargs() does not help: it gives '3' for both cases
315    if(FALSE)
316    setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
317                             drop = "ANY"),
318              function (x, i, j, drop) {
319                  ## DEBUG
320                  cat("[(Matrix,i,..): nargs=", nargs(),"\n")
321                  as(x, geClass(x))@x[i] })
322    
323    
324    ## "FIXME:"
325    ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?
326    ##  and                A[ LL ]  where LL is a logical *vector*
327    ## -> [.data.frame uses nargs() - can we do this in the *generic* ?
328    
329    
330    ### "[<-" : -----------------
331    
332    ## x[] <- value :
333    setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
334                                    value = "ANY"),## double/logical/...
335              function (x, value) {
336                  x@x <- value
337                  validObject(x)# check if type and lengths above match
338                  x
339              })
340    
341  }## not-yet used  ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
342    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
343    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
344                                    value = "ANY"),
345              function (x, i, j, value) {
346                  if(!is.atomic(value))
347                      stop("RHS 'value' must match matrix class ", class(x))
348                  else stop("not-yet-implemented 'Matrix[<-' method")
349              })
350    
351    
352    ## The trivial methods :
353    setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
354              function(x, y) x)
355    setMethod("cbind2", signature(x = "Matrix", y = "missing"),
356              function(x, y) x)
357    setMethod("cbind2", signature(x = "NULL", y="Matrix"),
358              function(x, y) x)
359    
360    setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
361              function(x, y) x)
362    setMethod("rbind2", signature(x = "Matrix", y = "missing"),
363              function(x, y) x)
364    setMethod("rbind2", signature(x = "NULL", y="Matrix"),
365              function(x, y) x)
366    
367    ## Makes sure one gets x decent error message for the unimplemented cases:
368    setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
369              function(x, y) {
370                  rowCheck(x,y)
371                  stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
372                                class(x), class(y)))
373              })
374    
375    ## Use a working fall back {particularly useful for sparse}:
376    ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
377    setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
378              function(x, y) {
379                  colCheck(x,y)
380                  t(cbind2(t(x), t(y)))
381              })

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