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Diff of /pkg/R/ddenseMatrix.R

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revision 856, Tue Aug 16 20:20:13 2005 UTC revision 1654, Fri Oct 27 16:58:15 2006 UTC
# Line 1  Line 1 
1  ### Define Methods that can be inherited for all subclasses  ### Define Methods that can be inherited for all subclasses
2    
3    ## This replaces many "d..Matrix" -> "dgeMatrix" ones
4    ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5    ##   -----  in  ../src/Mutils.c
6    
7    ## Should this method return 'from' without duplication when it has
8    ## class dgeMatrix?
9    setAs("ddenseMatrix", "dgeMatrix",
10          function(from) {
11              if (class(from) != "dgeMatrix")
12                  from <- .Call(dup_mMatrix_as_dgeMatrix, from)
13              from
14          })
15    
16    ## d(ouble) to l(ogical):
17    setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)
18    setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)
19    setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)
20    setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
21    setAs("dspMatrix", "lspMatrix", d2l_Matrix)
22    
23    setAs("ddenseMatrix", "CsparseMatrix",
24          function(from) {
25              if (class(from) != "dgeMatrix")
26                  from <- .Call(dup_mMatrix_as_dgeMatrix, from)
27              .Call(dense_to_Csparse, from)
28          })
29    
30    ## special case
31    setAs("dgeMatrix", "dgCMatrix",
32          function(from) .Call(dense_to_Csparse, from))
33    
34    setAs("matrix", "CsparseMatrix",
35          function(from) {
36                if(is.numeric(from))
37                    .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
38                else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
39                    as(Matrix(from, sparse=TRUE), "CsparseMatrix")
40                else stop('not-yet-implemented coercion to "CsparseMatrix"')
41          })
42    
43    
44    ## special case needed in the Matrix function
45    setAs("matrix", "dgCMatrix",
46          function(from) {
47              storage.mode(from) <- "double"
48              .Call(dense_to_Csparse, from)
49          })
50    
51    setAs("numeric", "CsparseMatrix",
52          function(from)
53          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
54    
55    setMethod("as.numeric", signature(x = "ddenseMatrix"),
56              function(x, ...) as(x, "dgeMatrix")@x)
57    
58  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
59    
60  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 18  Line 73 
73  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
74            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
75    
76  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
77            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
78    ##        function(x) callGeneric(as(x, "dgeMatrix")))
79    
80  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
82    
83  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
84            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
# Line 30  Line 86 
86  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
87            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
88    
89  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  ## These methods cause an infinite loop in pre-2.4.0
90            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
91    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
92  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
93            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
94    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
95    
96    ## General method for dense matrix multiplication in case specific methods
97    ## have not been defined.
98    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
99              function(x, y) .Call(dgeMatrix_matrix_mm,
100                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
101              valueClass = "dgeMatrix")
102    
103  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
104            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) callGeneric(as(x, "dgeMatrix")))
105    
106    setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
107    
108  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
109            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
110    
# Line 46  Line 112 
112            function(x, logarithm, ...)            function(x, logarithm, ...)
113            callGeneric(as(x, "dgeMatrix"), logarithm))            callGeneric(as(x, "dgeMatrix"), logarithm))
114    
115  setMethod("expm", signature(x = "ddenseMatrix"),  ## now done for "dMatrix":
116            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
117    ##           function(x) callGeneric(as(x, "dgeMatrix")))
118    
119  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
120            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
# Line 56  Line 123 
123            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
124    
125    
126    ## Cheap version: work via "dgeMatrix" and use the group methods there:
127    ## FIXME(?): try to preserve "symmetric", "triangular", ...
128    setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
129              signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
130              function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
131                                           as(e2, "dgeMatrix")))
132    setMethod("Arith",
133              signature(e1 = "ddenseMatrix", e2 = "numeric"),
134              function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
135    setMethod("Arith",
136              signature(e1 = "numeric", e2 = "ddenseMatrix"),
137              function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
138    
139    setMethod("Math",
140              signature(x = "ddenseMatrix"),
141              function(x) callGeneric(as(x, "dgeMatrix")))
142    
143    
144    
145    ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
146    
147    ### cbind2
148    setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
149              function(x, y) {
150                  d <- dim(x); nr <- d[1]; nc <- d[2]
151                  y <- rep(y, length.out = nr) # 'silent procrustes'
152                  ## beware of (packed) triangular, symmetric, ...
153                  x <- as(x, "dgeMatrix")
154                  x@x <- c(x@x, as.double(y))
155                  x@Dim[2] <- nc + 1:1
156                  if(is.character(dn <- x@Dimnames[[2]]))
157                      x@Dimnames[[2]] <- c(dn, "")
158                  x
159              })
160    ## the same, (x,y) <-> (y,x):
161    setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
162              function(x, y) {
163                  d <- dim(y); nr <- d[1]; nc <- d[2]
164                  x <- rep(x, length.out = nr)
165                  y <- as(y, "dgeMatrix")
166                  y@x <- c(as.double(x), y@x)
167                  y@Dim[2] <- nc + 1:1
168                  if(is.character(dn <- y@Dimnames[[2]]))
169                      y@Dimnames[[2]] <- c("", dn)
170                  y
171              })
172    
173    setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
174              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
175    setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
176              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
177    
178    setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
179              function(x, y) {
180                  nr <- rowCheck(x,y)
181                  ncx <- x@Dim[2]
182                  ncy <- y@Dim[2]
183                  ## beware of (packed) triangular, symmetric, ...
184                  hasDN <- !is.null(dnx <- dimnames(x)) |
185                  !is.null(dny <- dimnames(y))
186                  x <- as(x, "dgeMatrix")
187                  y <- as(y, "dgeMatrix")
188                  x@x <- c(x@x, y@x)
189                  x@Dim[2] <- ncx + ncy
190                  if(hasDN) {
191                      ## R and S+ are different in which names they take
192                      ## if they differ -- but there's no warning in any case
193                      rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
194                      cx <- dnx[[2]] ; cy <- dny[[2]]
195                      cn <- if(is.null(cx) && is.null(cy)) NULL
196                      else c(if(!is.null(cx)) cx else rep.int("", ncx),
197                             if(!is.null(cy)) cy else rep.int("", ncy))
198                      x@Dimnames <- list(rn, cn)
199                  }
200                  x
201              })
202    
203    ### rbind2 -- analogous to cbind2 --- more to do for @x though:
204    
205    setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
206              function(x, y) {
207                  if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
208                  new("dgeMatrix", Dim = x@Dim + 1:0,
209                      Dimnames = list(dn, x@Dimnames[[2]]),
210                      x = c(rbind2(as(x,"matrix"), y)))
211              })
212    ## the same, (x,y) <-> (y,x):
213    setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
214              function(x, y) {
215                  if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
216                  new("dgeMatrix", Dim = y@Dim + 1:0,
217                      Dimnames = list(dn, y@Dimnames[[2]]),
218                      x = c(rbind2(x, as(y,"matrix"))))
219              })
220    
221    setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
222              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
223    setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
224              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
225    
226    setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
227              function(x, y) {
228                  nc <- colCheck(x,y)
229                  nrx <- x@Dim[1]
230                  nry <- y@Dim[1]
231                  dn <-
232                      if(!is.null(dnx <- dimnames(x)) |
233                         !is.null(dny <- dimnames(y))) {
234                          ## R and S+ are different in which names they take
235                          ## if they differ -- but there's no warning in any case
236                          list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
237                               NULL else
238                               c(if(!is.null(rx)) rx else rep.int("", nrx),
239                                 if(!is.null(ry)) ry else rep.int("", nry)),
240                               if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
241    
242                      } else list(NULL, NULL)
243                  ## beware of (packed) triangular, symmetric, ...
244                  new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
245                      x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
246              })
247    
248    ### FIXME: band() et al should be extended from "ddense" to "dense" !
249    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
250    
251    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
252    ##     for triangular ["dtr" and "dtp"]
253    setMethod("tril", "ddenseMatrix",
254              function(x, k = 0, ...) {
255                  k <- as.integer(k[1])
256                  dd <- dim(x); sqr <- dd[1] == dd[2]
257                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
258                  ## returns "lower triangular" if k <= 0 && sqr
259                  .Call(ddense_band, x, -dd[1], k)
260              })
261    
262    setMethod("triu", "ddenseMatrix",
263              function(x, k = 0, ...) {
264                  k <- as.integer(k[1])
265                  dd <- dim(x); sqr <- dd[1] == dd[2]
266                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
267                  ## returns "upper triangular" if k >= 0
268                  .Call(ddense_band, x, k, dd[2])
269              })
270    
271    setMethod("band", "ddenseMatrix",
272              function(x, k1, k2, ...) {
273                  k1 <- as.integer(k1[1])
274                  k2 <- as.integer(k2[1])
275                  dd <- dim(x); sqr <- dd[1] == dd[2]
276                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
277                  r <- .Call(ddense_band, x, k1, k2)
278                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
279                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
280                  else
281                      r
282              })

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