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Diff of /pkg/R/Matrix.R

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revision 618, Sat Mar 5 21:20:42 2005 UTC revision 1290, Thu Jun 8 09:30:21 2006 UTC
# Line 1  Line 1 
1  #### Toplevel ``virtual'' class "Matrix"  #### Toplevel ``virtual'' class "Matrix"
2    
3  ## probably not needed eventually:  ## ## probably not needed eventually:
4  setAs(from = "ddenseMatrix", to = "matrix",  ## setAs(from = "ddenseMatrix", to = "matrix",
5        function(from) {  ##       function(from) {
6            if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")  ##        if(length(d <- dim(from)) != 2) stop("dim(.) has not length 2")
7            array(from@x, dim = d, dimnames = dimnames(from))  ##        array(from@x, dim = d, dimnames = dimnames(from))
8    ##       })
9    
10    ## should propagate to all subclasses:
11    setMethod("as.matrix", signature(x = "Matrix"), function(x) as(x, "matrix"))
12    ## for 'Matrix' objects, as.array() should be equivalent:
13    setMethod("as.array",  signature(x = "Matrix"), function(x) as(x, "matrix"))
14    
15    ## slow "fall back" method {subclasses should have faster ones}:
16    setMethod("as.vector", signature(x = "Matrix", mode = "missing"),
17              function(x) as.vector(as(x, "matrix")))
18    
19    
20    ## Note that isSymmetric is *not* exported
21    ## but that "base" has an isSymmetric() S3-generic since R 2.3.0
22    setMethod("isSymmetric", signature(object = "symmetricMatrix"),
23              function(object,tol) TRUE)
24    setMethod("isSymmetric", signature(object = "triangularMatrix"),
25              ## TRUE iff diagonal:
26              function(object,tol) isDiagonal(object))
27    
28    if(paste(R.version$major, R.version$minor, sep=".") < "2.3")
29        ## need a "matrix" method as in R 2.3 and later
30        setMethod("isSymmetric", signature(object = "matrix"),
31                  function(object, tol = 100*.Machine$double.eps, ...)
32              {
33                  ## pretest: is it square?
34                  d <- dim(object)
35                  if(d[1] != d[2]) return(FALSE)
36                  ## for `broken' all.equal in R <= 2.2.x:
37                  dn <- dimnames(object)
38                  if(!identical(dn[1], dn[2])) return(FALSE)
39                  test <-
40                      if(is.complex(object))
41                          all.equal.numeric(object, Conj(t(object)), tol = tol, ...)
42                      else              # numeric, character, ..
43                          all.equal(object, t(object), tol = tol, ...)
44                  isTRUE(test)
45        })        })
46    
47  ## private function to be used as show() method possibly more than once  
48  prMatrix <- function(object) {  setMethod("isTriangular", signature(object = "triangularMatrix"),
49      d <- dim(object)            function(object, ...) TRUE)
50      cl <- class(object)  
51      cat(paste(d, collapse= " x "), " Matrix of class ", sQuote(cl),  setMethod("isTriangular", signature(object = "matrix"), isTriMat)
52          "\n", sep='')  
53      if(cl == "Matrix") { ## have no data slot  setMethod("isDiagonal", signature(object = "matrix"), .is.diagonal)
54          cat("Dim = ", d)  
55          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()  
 }  
   
 setMethod("show", signature(object = "ddenseMatrix"), prMatrix)  
 ## this may go away {since sparse matrices need something better!} :  
 setMethod("show", signature(object = "Matrix"), prMatrix)  
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 58  Line 72 
72  setMethod("dimnames<-", signature(x = "Matrix", value = "list"),  setMethod("dimnames<-", signature(x = "Matrix", value = "list"),
73            dimnamesGets)            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)
81  {  {
82      if (is(data, "Matrix")) return(data)      sparseDefault <- function(m)
83      if (is.matrix(data)) { val <- data }          prod(dim(m)) > 2*sum(as(m, "matrix") != 0)
84      else { ## cut & paste from "base::matrix" :  
85        i.M <- is(data, "Matrix")
86        if(is.null(sparse) && (i.M || is(data, "matrix")))
87            sparse <- sparseDefault(data)
88    
89        if (i.M) {
90            sM <- is(data,"sparseMatrix")
91            if((sparse && sM) || (!sparse && !sM))
92                return(data)
93            ## else : convert  dense <-> sparse -> at end
94        }
95        else if (!is.matrix(data)) { ## cut & paste from "base::matrix" :
96          if (missing(nrow))          if (missing(nrow))
97              nrow <- ceiling(length(data)/ncol)              nrow <- ceiling(length(data)/ncol)
98          else if (missing(ncol))          else if (missing(ncol))
99              ncol <- ceiling(length(data)/nrow)              ncol <- ceiling(length(data)/nrow)
100          val <- .Internal(matrix(data, nrow, ncol, byrow))          data <- .Internal(matrix(data, nrow, ncol, byrow))
101          dimnames(val) <- dimnames          if(is.null(sparse))
102      }              sparse <- sparseDefault(data)
103      as(val, "dgeMatrix")          dimnames(data) <- dimnames
104  }      } else if (!is.null(dimnames))
105            dimnames(data) <- dimnames
106    
107        ## 'data' is now a "matrix" or "Matrix"
108    
109        ## check for symmetric / triangular / diagonal :
110        isSym <- isSymmetric(data)
111        if((isTri <- !isSym))
112            isTri <- isTriangular(data)
113        isDiag <- isSym # cannot be diagonal if it isn't symmetric
114        if(isDiag)
115            isDiag <- isDiagonal(data)
116    
117    ### TODO: Compare with as.Matrix() and its tests in ./dgeMatrix.R
118    
119        ## Find proper matrix class 'cl'
120        cl <-
121            if(isDiag)
122                "diagonalMatrix" # -> will automatically check for type
123            else {
124                ## consider it's type
125                ctype <-
126                    if(is(data,"Matrix")) class(data)
127                    else {
128                        if("complex" == (ctype <- typeof(data)))
129                            "z" else ctype
130                    }
131                ctype <- substr(ctype, 1,1) # "d", "l", "i" or "z"
132                if(ctype == "z")
133                    stop("complex matrices not yet implemented in Matrix package")
134                if(ctype == "i") {
135                    warning("integer matrices not yet implemented in 'Matrix'; ",
136                            "using 'double' ones'")
137                    ctype <- "d"
138                }
139                paste(ctype,
140                      if(sparse) {
141                          if(isSym) "sCMatrix" else
142                          if(isTri) "tCMatrix" else "gCMatrix"
143                      } else { ## dense
144                          if(isSym) "syMatrix" else
145                          if(isTri) "trMatrix" else "geMatrix"
146                      }, sep="")
147            }
148    
149        ## Now coerce and return
150        as(data, cl)
151    }
152    
153    ## Methods for operations where one argument is numeric
154    
155    ## Using as.matrix() and rbind()
156    ## in order to get dimnames from names {at least potentially}:
157    
158    setMethod("%*%", signature(x = "Matrix", y = "numeric"),
159              function(x, y) callGeneric(x, as.matrix(y)))
160    
161    setMethod("%*%", signature(x = "numeric", y = "Matrix"),
162              function(x, y) callGeneric(rbind(x), y))
163    
164    setMethod("crossprod", signature(x = "Matrix", y = "numeric"),
165              function(x, y = NULL) callGeneric(x, as.matrix(y)))
166    
167    setMethod("crossprod", signature(x = "numeric", y = "Matrix"),
168              function(x, y = NULL)  callGeneric(rbind(x), y))
169    
170    setMethod("solve", signature(a = "Matrix", b = "numeric"),
171              function(a, b, ...) callGeneric(a, as.matrix(b)))
172    
173    ## bail-out methods in order to get better error messages
174    setMethod("%*%", signature(x = "Matrix", y = "Matrix"),
175              function (x, y)
176              stop(gettextf('not-yet-implemented method for <%s> %%*%% <%s>',
177                            class(x), class(y))))
178    
179    setMethod("crossprod", signature(x = "Matrix", y = "ANY"),
180              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
181    setMethod("crossprod", signature(x = "ANY", y = "Matrix"),
182              function (x, y = NULL) .bail.out.2(.Generic, class(x), class(y)))
183    
184    ## There are special sparse methods; this is a "fall back":
185    setMethod("kronecker", signature(X = "Matrix", Y = "ANY",
186                                     FUN = "ANY", make.dimnames = "ANY"),
187              function(X, Y, FUN, make.dimnames, ...) {
188                  X <- as(X, "matrix") ; Matrix(callGeneric()) })
189    setMethod("kronecker", signature(X = "ANY", Y = "Matrix",
190                                     FUN = "ANY", make.dimnames = "ANY"),
191              function(X, Y, FUN, make.dimnames, ...) {
192                  Y <- as(Y, "matrix") ; Matrix(callGeneric()) })
193    
194    
195    setMethod("t", signature(x = "Matrix"),
196              function(x) .bail.out.1(.Generic, class(x)))
197    
198    ## Group Methods
199    setMethod("+", signature(e1 = "Matrix", e2 = "missing"), function(e1) e1)
200    ## "fallback":
201    setMethod("-", signature(e1 = "Matrix", e2 = "missing"),
202              function(e1) {
203                  warning("inefficient method used for \"- e1\"")
204                  0-e1
205              })
206    
207    ## bail-outs:
208    setMethod("Compare", signature(e1 = "Matrix", e2 = "Matrix"),
209              function(e1, e2) {
210                  d <- dimCheck(e1,e2)
211                  .bail.out.2(.Generic, class(e1), class(e2))
212              })
213    setMethod("Compare", signature(e1 = "Matrix", e2 = "ANY"),
214              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
215    setMethod("Compare", signature(e1 = "ANY", e2 = "Matrix"),
216              function(e1, e2) .bail.out.2(.Generic, class(e1), class(e2)))
217    
 if(FALSE) { ##--- not-yet used -- {almost same code also in ./dgeMatrix.R }  
218    
 ## 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  
 }  
219    
220  as.Matrix <- function(x, tol = .Machine$double.eps)  ### --------------------------------------------------------------------------
221  {  ###
222      asObject(if (inherits(x, "Matrix")) x else as.matrix(x),  ### Subsetting "["  and
223               Matrix.class(x, tol = tol))  ### SubAssign  "[<-" : The "missing" cases can be dealt with here, "at the top":
224  }  
225    ## Using "index" for indices should allow
226    ## integer (numeric), logical, or character (names!) indices :
227    
228    ## "x[]":
229    setMethod("[", signature(x = "Matrix",
230                             i = "missing", j = "missing", drop = "ANY"),
231              function (x, i, j, drop) x)
232    
233    ## missing 'drop' --> 'drop = TRUE'
234    ##                     -----------
235    ## select rows
236    setMethod("[", signature(x = "Matrix", i = "index", j = "missing",
237                             drop = "missing"),
238              function(x,i,j, drop) callGeneric(x, i=i, drop= TRUE))
239    ## select columns
240    setMethod("[", signature(x = "Matrix", i = "missing", j = "index",
241                             drop = "missing"),
242              function(x,i,j, drop) callGeneric(x, j=j, drop= TRUE))
243    setMethod("[", signature(x = "Matrix", i = "index", j = "index",
244                             drop = "missing"),
245              function(x,i,j, drop) callGeneric(x, i=i, j=j, drop= TRUE))
246    
247    ## bail out if any of (i,j,drop) is "non-sense"
248    setMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY", drop = "ANY"),
249              function(x,i,j, drop)
250              stop("invalid or not-yet-implemented 'Matrix' subsetting"))
251    
252    ##  "logical *vector* indexing, such as  M [ M >= 10 ] :
253    setMethod("[", signature(x = "Matrix", i = "lMatrix", j = "missing",
254                             drop = "ANY"),
255              function (x, i, j, drop) {
256                  as(x, geClass(x))@x[as.vector(i)]
257                                            # -> error when lengths don't match
258              })
259    
260    setMethod("[", signature(x = "Matrix", i = "logical", j = "missing",
261                             drop = "ANY"),
262              function (x, i, j, drop) as(x, geClass(x))@x[i])
263    
264    
265    ## "FIXME:"
266    ## How can we get at   A[ ij ]  where ij is (i,j) 2-column matrix?
267    ##  and                A[ LL ]  where LL is a logical *vector*
268    ## -> [.data.frame uses nargs() - can we do this in the *generic* ?
269    
270    
271  }## not-yet used  ### "[<-" : -----------------
272    
273    ## x[] <- value :
274    setReplaceMethod("[", signature(x = "Matrix", i = "missing", j = "missing",
275                                    value = "ANY"),## double/logical/...
276              function (x, value) {
277                  x@x <- value
278                  validObject(x)# check if type and lengths above match
279                  x
280              })
281    
282    ## Method for all 'Matrix' kinds (rather than incomprehensible error messages);
283    ## (ANY,ANY,ANY) is used when no `real method' is implemented :
284    setReplaceMethod("[", signature(x = "Matrix", i = "ANY", j = "ANY",
285                                    value = "ANY"),
286              function (x, i, j, value) {
287                  if(!is.atomic(value))
288                      stop("RHS 'value' must match matrix class ", class(x))
289                  else stop("not-yet-implemented 'Matrix[<-' method")
290              })
291    
292    
293    ## The trivial methods :
294    setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
295              function(x, y) x)
296    setMethod("cbind2", signature(x = "Matrix", y = "missing"),
297              function(x, y) x)
298    setMethod("cbind2", signature(x = "NULL", y="Matrix"),
299              function(x, y) x)
300    
301    setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
302              function(x, y) x)
303    setMethod("rbind2", signature(x = "Matrix", y = "missing"),
304              function(x, y) x)
305    setMethod("rbind2", signature(x = "NULL", y="Matrix"),
306              function(x, y) x)
307    
308    ## Makes sure one gets x decent error message for the unimplemented cases:
309    setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
310              function(x, y) {
311                  rowCheck(x,y)
312                  stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
313                                class(x), class(y)))
314              })
315    
316    ## Use a working fall back {particularly useful for sparse}:
317    ## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
318    setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
319              function(x, y) {
320                  colCheck(x,y)
321                  t(cbind2(t(x), t(y)))
322              })

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