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Diff of /pkg/Matrix/R/ddenseMatrix.R

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pkg/R/ddenseMatrix.R revision 792, Sat Jul 2 20:58:14 2005 UTC pkg/Matrix/R/ddenseMatrix.R revision 3079, Tue Mar 31 15:29:43 2015 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    setAs("ddenseMatrix", "dgeMatrix",
8          function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
9    
10    setAs("ddenseMatrix", "matrix",
11          function(from) as(as(from, "dgeMatrix"), "matrix"))
12    
13    ## d(ouble) to l(ogical):
14    setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
15    setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
16    setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
17    setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
18    setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
19    
20    if(FALSE) ## FIXME, this fails for ("dtpMatrix" -> "CsparseMatrix") where .dense2C() works
21    setAs("ddenseMatrix", "CsparseMatrix",
22          function(from) {
23              if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24                  as_Csparse(from)
25              else .Call(dense_to_Csparse, from)
26          })
27    
28    ## special case
29    setAs("dgeMatrix", "dgCMatrix",
30          function(from) .Call(dense_to_Csparse, from))
31    
32    setAs("matrix", "CsparseMatrix",
33          function(from) .Call(dense_to_Csparse, from))
34    
35    ## for historical i.e. backcompatibility reasons ..
36    setAs("matrix", "dgCMatrix",
37          function(from) {
38              storage.mode(from) <- "double"
39              .Call(dense_to_Csparse, from)
40          })
41    
42    setAs("numeric", "CsparseMatrix",
43          function(from)
44          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
45    
46    setMethod("as.numeric", "ddenseMatrix", function(x, ...) ..2dge(x)@x)
47    
48  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
49    
50  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 7  Line 52 
52  ## dgeMatrix. Methods for special forms override these.  ## dgeMatrix. Methods for special forms override these.
53    
54  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
55            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, type, ...) norm(..2dge(x)))
56    
57  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
58            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) norm(..2dge(x), type))
   
 setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),  
           function(x, type, ...) callGeneric(as(x, "dgeMatrix")))  
59    
60  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
61            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, norm, ...) rcond(..2dge(x), ...))
62    
63  setMethod("t", signature(x = "ddenseMatrix"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
64            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, norm, ...) rcond(..2dge(x), norm, ...))
65    
66  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
67            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
68    ##        function(x) callGeneric(..2dge(x)))
69    
70  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("diag", signature(x = "ddenseMatrix"),  
           function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))  
71    
72  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
73            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(..2dge(a)))
74    
75  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
76            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
77              function(a, b, ...) solve(..2dge(a), b))
78    for(.b in c("matrix","numeric")) ## << against ambiguity notes
79    setMethod("solve", signature(a = "ddenseMatrix", b = .b),
80              function(a, b, ...) solve(..2dge(a), Matrix(b)))
81    rm(.b)
82    
83  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
84            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...)
85              .set.factors(x, "LU", lu(..2dge(x), ...)))
86    
87  setMethod("determinant", signature(x = "dgeMatrix", logarithm = "missing"),  setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
           function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))  
88    
89  setMethod("determinant", signature(x = "dgeMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
90            function(x, logarithm, ...)            function(x, logarithm, ...) determinant(..2dge(x)))
           callGeneric(as(x, "dgeMatrix"), logarithm))  
   
 setMethod("expm", signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  
           function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),  
           function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))  
91    
92    setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
93              function(x, logarithm, ...)
94              determinant(..2dge(x), logarithm))
95    
96    ## now done for "dMatrix":
97    ## setMethod("expm", signature(x = "ddenseMatrix"),
98    ##           function(x) callGeneric(..2dge(x)))
99    
100    
101    .trilDense <- function(x, k = 0, ...) {
102        k <- as.integer(k[1])
103        d <- dim(x)
104        stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
105        ## returns "lower triangular" if k <= 0 && sqr
106        .Call(dense_band, x, -d[1], k)
107    }
108    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
109    ##     for triangular ["dtr" and "dtp"]
110    setMethod("tril", "denseMatrix", .trilDense)
111    setMethod("tril",      "matrix", .trilDense)
112    
113    .triuDense <- function(x, k = 0, ...) {
114        k <- as.integer(k[1])
115        d <- dim(x)
116        stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
117        ## returns "upper triangular" if k >= 0
118        .Call(dense_band, x, k, d[2])
119    }
120    setMethod("triu", "denseMatrix", .triuDense)
121    setMethod("triu",      "matrix", .triuDense)
122    
123    .bandDense <- function(x, k1, k2, ...) {
124        k1 <- as.integer(k1[1])
125        k2 <- as.integer(k2[1])
126        dd <- dim(x)
127        sqr <- dd[1] == dd[2]
128        stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
129        r <- .Call(dense_band, x, k1, k2)
130        if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
131            forceSymmetric(r)
132        else
133            r
134    }
135    setMethod("band", "denseMatrix", .bandDense)
136    setMethod("band",      "matrix", .bandDense)
137    
138    
139    setMethod("symmpart", signature(x = "ddenseMatrix"),
140              function(x) .Call(ddense_symmpart, x))
141    setMethod("skewpart", signature(x = "ddenseMatrix"),
142              function(x) .Call(ddense_skewpart, x))
143    
144    
145    setMethod("is.finite", signature(x = "dgeMatrix"),
146              function(x) {
147                  if(all(ifin <- is.finite(x@x)))
148                      allTrueMat(x)
149                  else if(any(ifin)) {
150                      r <- as(x, "lMatrix") #-> logical x-slot
151                      r@x <- ifin
152                      as(r, "nMatrix")
153                  }
154                  else is.na_nsp(x)
155              })
156    
157    ## TODO? -- rather methods for specific subclasses of ddenseMatrix
158    setMethod("is.finite", signature(x = "ddenseMatrix"),
159              function(x) {
160                  if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
161                  ## *NOT* dge, i.e., either triangular or symmetric
162                  ## (possibly packed): has finite 0-triangle
163                  cdx <- getClassDef(class(x))
164    
165                  r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
166                  r@Dim <- (d <- x@Dim)
167                  r@Dimnames <- x@Dimnames
168                  isPacked <- (le <- prod(d)) > length(ifin)
169                  r@x <- rep.int(TRUE, le)
170                  iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
171                  if(isPacked) { ## x@x is "usable"
172                      r@x[iTr] <- ifin
173                  } else {
174                      r@x[iTr] <- ifin[iTr]
175                  }
176                  r
177              })
178    
179    setMethod("is.infinite", signature(x = "ddenseMatrix"),
180              function(x) {
181                  if(any((isInf <- is.infinite(x@x)))) {
182                      r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
183                      r@x <- isInf
184                      as(r, "nMatrix")# often sparse .. better way?
185                  }
186                  else is.na_nsp(x)
187              })

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