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[matrix] Diff of /pkg/R/ddenseMatrix.R
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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 1618, Fri Oct 6 15:44:01 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")))
# Line 46  Line 110 
110            function(x, logarithm, ...)            function(x, logarithm, ...)
111            callGeneric(as(x, "dgeMatrix"), logarithm))            callGeneric(as(x, "dgeMatrix"), logarithm))
112    
113  setMethod("expm", signature(x = "ddenseMatrix"),  ## now done for "dMatrix":
114            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
115    ##           function(x) callGeneric(as(x, "dgeMatrix")))
116    
117  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
118            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
# Line 56  Line 121 
121            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
122    
123    
124    ## Cheap version: work via "dgeMatrix" and use the group methods there:
125    ## FIXME(?): try to preserve "symmetric", "triangular", ...
126    setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
127              signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
128              function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
129                                           as(e2, "dgeMatrix")))
130    setMethod("Arith",
131              signature(e1 = "ddenseMatrix", e2 = "numeric"),
132              function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
133    setMethod("Arith",
134              signature(e1 = "numeric", e2 = "ddenseMatrix"),
135              function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
136    
137    setMethod("Math",
138              signature(x = "ddenseMatrix"),
139              function(x) callGeneric(as(x, "dgeMatrix")))
140    
141    
142    
143    ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
144    
145    ### cbind2
146    setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
147              function(x, y) {
148                  d <- dim(x); nr <- d[1]; nc <- d[2]
149                  y <- rep(y, length.out = nr) # 'silent procrustes'
150                  ## beware of (packed) triangular, symmetric, ...
151                  x <- as(x, "dgeMatrix")
152                  x@x <- c(x@x, as.double(y))
153                  x@Dim[2] <- nc + 1:1
154                  if(is.character(dn <- x@Dimnames[[2]]))
155                      x@Dimnames[[2]] <- c(dn, "")
156                  x
157              })
158    ## the same, (x,y) <-> (y,x):
159    setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
160              function(x, y) {
161                  d <- dim(y); nr <- d[1]; nc <- d[2]
162                  x <- rep(x, length.out = nr)
163                  y <- as(y, "dgeMatrix")
164                  y@x <- c(as.double(x), y@x)
165                  y@Dim[2] <- nc + 1:1
166                  if(is.character(dn <- y@Dimnames[[2]]))
167                      y@Dimnames[[2]] <- c("", dn)
168                  y
169              })
170    
171    setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
172              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
173    setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
174              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
175    
176    setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
177              function(x, y) {
178                  nr <- rowCheck(x,y)
179                  ncx <- x@Dim[2]
180                  ncy <- y@Dim[2]
181                  ## beware of (packed) triangular, symmetric, ...
182                  hasDN <- !is.null(dnx <- dimnames(x)) |
183                  !is.null(dny <- dimnames(y))
184                  x <- as(x, "dgeMatrix")
185                  y <- as(y, "dgeMatrix")
186                  x@x <- c(x@x, y@x)
187                  x@Dim[2] <- ncx + ncy
188                  if(hasDN) {
189                      ## R and S+ are different in which names they take
190                      ## if they differ -- but there's no warning in any case
191                      rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
192                      cx <- dnx[[2]] ; cy <- dny[[2]]
193                      cn <- if(is.null(cx) && is.null(cy)) NULL
194                      else c(if(!is.null(cx)) cx else rep.int("", ncx),
195                             if(!is.null(cy)) cy else rep.int("", ncy))
196                      x@Dimnames <- list(rn, cn)
197                  }
198                  x
199              })
200    
201    ### rbind2 -- analogous to cbind2 --- more to do for @x though:
202    
203    setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
204              function(x, y) {
205                  if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
206                  new("dgeMatrix", Dim = x@Dim + 1:0,
207                      Dimnames = list(dn, x@Dimnames[[2]]),
208                      x = c(rbind2(as(x,"matrix"), y)))
209              })
210    ## the same, (x,y) <-> (y,x):
211    setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
212              function(x, y) {
213                  if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
214                  new("dgeMatrix", Dim = y@Dim + 1:0,
215                      Dimnames = list(dn, y@Dimnames[[2]]),
216                      x = c(rbind2(x, as(y,"matrix"))))
217              })
218    
219    setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
220              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
221    setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
222              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
223    
224    setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
225              function(x, y) {
226                  nc <- colCheck(x,y)
227                  nrx <- x@Dim[1]
228                  nry <- y@Dim[1]
229                  dn <-
230                      if(!is.null(dnx <- dimnames(x)) |
231                         !is.null(dny <- dimnames(y))) {
232                          ## R and S+ are different in which names they take
233                          ## if they differ -- but there's no warning in any case
234                          list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
235                               NULL else
236                               c(if(!is.null(rx)) rx else rep.int("", nrx),
237                                 if(!is.null(ry)) ry else rep.int("", nry)),
238                               if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
239    
240                      } else list(NULL, NULL)
241                  ## beware of (packed) triangular, symmetric, ...
242                  new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
243                      x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
244              })
245    
246    ### FIXME: band() et al should be extended from "ddense" to "dense" !
247    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
248    
249    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
250    ##     for triangular ["dtr" and "dtp"]
251    setMethod("tril", "ddenseMatrix",
252              function(x, k = 0, ...) {
253                  k <- as.integer(k[1])
254                  dd <- dim(x); sqr <- dd[1] == dd[2]
255                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
256                  ## returns "lower triangular" if k <= 0 && sqr
257                  .Call(ddense_band, x, -dd[1], k)
258              })
259    
260    setMethod("triu", "ddenseMatrix",
261              function(x, k = 0, ...) {
262                  k <- as.integer(k[1])
263                  dd <- dim(x); sqr <- dd[1] == dd[2]
264                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
265                  ## returns "upper triangular" if k >= 0
266                  .Call(ddense_band, x, k, dd[2])
267              })
268    
269    setMethod("band", "ddenseMatrix",
270              function(x, k1, k2, ...) {
271                  k1 <- as.integer(k1[1])
272                  k2 <- as.integer(k2[1])
273                  dd <- dim(x); sqr <- dd[1] == dd[2]
274                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
275                  r <- .Call(ddense_band, x, k1, k2)
276                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
277                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
278                  else
279                      r
280              })

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