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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 925, Mon Sep 19 19:01:31 2005 UTC revision 1575, Mon Sep 18 14:47:40 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  ### NAMESPACE must export this -- also only for R version 2.2.x:  ## Cheap version: work via "dgeMatrix" and use the group methods there:
119  if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {  ## FIXME(?): try to preserve "symmetric", "triangular", ...
120      ## for R 2.2.x (and later):  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  ### cbind2
140      setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),      setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
# Line 161  Line 237 
237                        x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))                        x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
238                })                })
239    
240  }## R-2.2.x ff  ### FIXME: band() et al should be extended from "ddense" to "dense" !
241    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
242    
243    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
244    ##     for triangular ["dtr" and "dtp"]
245    setMethod("tril", "ddenseMatrix",
246              function(x, k = 0, ...) {
247                  k <- as.integer(k[1])
248                  dd <- dim(x); sqr <- dd[1] == dd[2]
249                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
250                  ## returns "lower triangular" if k <= 0 && sqr
251                  .Call(ddense_band, x, -dd[1], k)
252              })
253    
254    setMethod("triu", "ddenseMatrix",
255              function(x, k = 0, ...) {
256                  k <- as.integer(k[1])
257                  dd <- dim(x); sqr <- dd[1] == dd[2]
258                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
259                  ## returns "upper triangular" if k >= 0
260                  .Call(ddense_band, x, k, dd[2])
261              })
262    
263    setMethod("band", "ddenseMatrix",
264              function(x, k1, k2, ...) {
265                  k1 <- as.integer(k1[1])
266                  k2 <- as.integer(k2[1])
267                  dd <- dim(x); sqr <- dd[1] == dd[2]
268                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
269                  r <- .Call(ddense_band, x, k1, k2)
270                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
271                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
272                  else
273                      r
274              })

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