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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 1463, Tue Aug 29 22:30:57 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          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
37    
38    ## special case needed in the Matrix function
39    setAs("matrix", "dgCMatrix",
40          function(from) {
41              storage.mode(from) <- "double"
42              .Call(dense_to_Csparse, from)
43          })
44    
45    setAs("numeric", "CsparseMatrix",
46          function(from)
47          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
48    
49    setMethod("as.numeric", signature(x = "ddenseMatrix"),
50              function(x, ...) as(x, "dgeMatrix")@x)
51    
52  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
53    
54  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 18  Line 67 
67  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
68            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
69    
70  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
71            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
72    ##        function(x) callGeneric(as(x, "dgeMatrix")))
73    
74  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
75            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
76    
77  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
78            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
# Line 30  Line 80 
80  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
81            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
82    
83  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  ## These methods cause an infinite loop in pre-2.4.0
84            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
85    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
86  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
87            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
88    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
89    
90    ## General method for dense matrix multiplication in case specific methods
91    ## have not been defined.
92    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
93              function(x, y) .Call(dgeMatrix_matrix_mm,
94                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
95              valueClass = "dgeMatrix")
96    
97  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
98            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) callGeneric(as(x, "dgeMatrix")))
# Line 46  Line 104 
104            function(x, logarithm, ...)            function(x, logarithm, ...)
105            callGeneric(as(x, "dgeMatrix"), logarithm))            callGeneric(as(x, "dgeMatrix"), logarithm))
106    
107  setMethod("expm", signature(x = "ddenseMatrix"),  ## now done for "dMatrix":
108            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
109    ##           function(x) callGeneric(as(x, "dgeMatrix")))
110    
111  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
112            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
# Line 56  Line 115 
115            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
116    
117    
118    ## Cheap version: work via "dgeMatrix" and use the group methods there:
119    ## FIXME(?): try to preserve "symmetric", "triangular", ...
120    setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
121              signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
122              function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
123                                           as(e2, "dgeMatrix")))
124    setMethod("Arith",
125              signature(e1 = "ddenseMatrix", e2 = "numeric"),
126              function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
127    setMethod("Arith",
128              signature(e1 = "numeric", e2 = "ddenseMatrix"),
129              function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
130    
131    setMethod("Math",
132              signature(x = "ddenseMatrix"),
133              function(x) callGeneric(as(x, "dgeMatrix")))
134    
135    
136    
137    ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
138    
139    ### cbind2
140    setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
141              function(x, y) {
142                  d <- dim(x); nr <- d[1]; nc <- d[2]
143                  y <- rep(y, length.out = nr) # 'silent procrustes'
144                  ## beware of (packed) triangular, symmetric, ...
145                  x <- as(x, "dgeMatrix")
146                  x@x <- c(x@x, as.double(y))
147                  x@Dim[2] <- nc + 1:1
148                  if(is.character(dn <- x@Dimnames[[2]]))
149                      x@Dimnames[[2]] <- c(dn, "")
150                  x
151              })
152    ## the same, (x,y) <-> (y,x):
153    setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
154              function(x, y) {
155                  d <- dim(y); nr <- d[1]; nc <- d[2]
156                  x <- rep(x, length.out = nr)
157                  y <- as(y, "dgeMatrix")
158                  y@x <- c(as.double(x), y@x)
159                  y@Dim[2] <- nc + 1:1
160                  if(is.character(dn <- y@Dimnames[[2]]))
161                      y@Dimnames[[2]] <- c("", dn)
162                  y
163              })
164    
165    setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
166              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
167    setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
168              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
169    
170    setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
171              function(x, y) {
172                  nr <- rowCheck(x,y)
173                  ncx <- x@Dim[2]
174                  ncy <- y@Dim[2]
175                  ## beware of (packed) triangular, symmetric, ...
176                  hasDN <- !is.null(dnx <- dimnames(x)) |
177                  !is.null(dny <- dimnames(y))
178                  x <- as(x, "dgeMatrix")
179                  y <- as(y, "dgeMatrix")
180                  x@x <- c(x@x, y@x)
181                  x@Dim[2] <- ncx + ncy
182                  if(hasDN) {
183                      ## R and S+ are different in which names they take
184                      ## if they differ -- but there's no warning in any case
185                      rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
186                      cx <- dnx[[2]] ; cy <- dny[[2]]
187                      cn <- if(is.null(cx) && is.null(cy)) NULL
188                      else c(if(!is.null(cx)) cx else rep.int("", ncx),
189                             if(!is.null(cy)) cy else rep.int("", ncy))
190                      x@Dimnames <- list(rn, cn)
191                  }
192                  x
193              })
194    
195    ### rbind2 -- analogous to cbind2 --- more to do for @x though:
196    
197    setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
198              function(x, y) {
199                  if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
200                  new("dgeMatrix", Dim = x@Dim + 1:0,
201                      Dimnames = list(dn, x@Dimnames[[2]]),
202                      x = c(rbind2(as(x,"matrix"), y)))
203              })
204    ## the same, (x,y) <-> (y,x):
205    setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
206              function(x, y) {
207                  if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
208                  new("dgeMatrix", Dim = y@Dim + 1:0,
209                      Dimnames = list(dn, y@Dimnames[[2]]),
210                      x = c(rbind2(x, as(y,"matrix"))))
211              })
212    
213    setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
214              function(x, y) callGeneric(x, as(y, "dgeMatrix")))
215    setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
216              function(x, y) callGeneric(as(x, "dgeMatrix"), y))
217    
218    setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
219              function(x, y) {
220                  nc <- colCheck(x,y)
221                  nrx <- x@Dim[1]
222                  nry <- y@Dim[1]
223                  dn <-
224                      if(!is.null(dnx <- dimnames(x)) |
225                         !is.null(dny <- dimnames(y))) {
226                          ## R and S+ are different in which names they take
227                          ## if they differ -- but there's no warning in any case
228                          list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
229                               NULL else
230                               c(if(!is.null(rx)) rx else rep.int("", nrx),
231                                 if(!is.null(ry)) ry else rep.int("", nry)),
232                               if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
233    
234                      } else list(NULL, NULL)
235                  ## beware of (packed) triangular, symmetric, ...
236                  new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
237                      x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
238              })
239    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
240    ##     for triangular ["dtr" and "dtp"]
241    setMethod("tril", "ddenseMatrix",
242              function(x, k = 0, ...) {
243                  k <- as.integer(k[1])
244                  dd <- dim(x); sqr <- dd[1] == dd[2]
245                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
246                  ## returns "lower triangular" if k <= 0 && sqr
247                  .Call(ddense_band, x, -dd[1], k)
248              })
249    
250    setMethod("triu", "ddenseMatrix",
251              function(x, k = 0, ...) {
252                  k <- as.integer(k[1])
253                  dd <- dim(x); sqr <- dd[1] == dd[2]
254                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
255                  ## returns "upper triangular" if k >= 0
256                  .Call(ddense_band, x, k, dd[2])
257              })
258    
259    setMethod("band", "ddenseMatrix",
260              function(x, k1, k2, ...) {
261                  k1 <- as.integer(k1[1])
262                  k2 <- as.integer(k2[1])
263                  dd <- dim(x); sqr <- dd[1] == dd[2]
264                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
265                  r <- .Call(ddense_band, x, k1, k2)
266                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
267                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
268                  else
269                      r
270              })

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