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[matrix] Diff of /pkg/Matrix/R/ddenseMatrix.R
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Diff of /pkg/Matrix/R/ddenseMatrix.R

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pkg/R/ddenseMatrix.R revision 2123, Wed Mar 5 08:44:52 2008 UTC pkg/Matrix/R/ddenseMatrix.R revision 2814, Tue Jul 24 14:02:28 2012 UTC
# Line 5  Line 5 
5  ##   -----  in  ../src/Mutils.c  ##   -----  in  ../src/Mutils.c
6    
7  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix",
8        function(from) {        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
           if (class(from) != "dgeMatrix")  
               .Call(dup_mMatrix_as_dgeMatrix, from)  
           else from  
       })  
9    
10    setAs("ddenseMatrix", "matrix",
11          function(from) as(as(from, "dgeMatrix"), "matrix"))
12    
13  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
14  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
# Line 19  Line 17 
17  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
18  setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))  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",  setAs("ddenseMatrix", "CsparseMatrix",
22        function(from) {        function(from) {
23            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
# Line 67  Line 66 
66  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
67            function(x, type, ...) norm(as(x, "dgeMatrix"), type))            function(x, type, ...) norm(as(x, "dgeMatrix"), type))
68    
69  setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
70            function(x, type, ...) rcond(as(x, "dgeMatrix")))            function(x, norm, ...) rcond(as(x, "dgeMatrix"), ...))
71    
72  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
73            function(x, type, ...) rcond(as(x, "dgeMatrix"), type))            function(x, norm, ...) rcond(as(x, "dgeMatrix"), norm, ...))
74    
75  ## Not really useful; now require *identical* class for result:  ## Not really useful; now require *identical* class for result:
76  ## setMethod("t", signature(x = "ddenseMatrix"),  ## setMethod("t", signature(x = "ddenseMatrix"),
77  ##        function(x) callGeneric(as(x, "dgeMatrix")))  ##        function(x) callGeneric(as(x, "dgeMatrix")))
78    
79  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
           function(x, y = NULL) tcrossprod(as(x, "dgeMatrix")))  
   
 setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) crossprod(as(x, "dgeMatrix")))  
   
 setMethod("diag", signature(x = "ddenseMatrix"),  
           function(x, nrow, ncol) diag(as(x, "dgeMatrix")))  
80    
81  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
82            function(a, b, ...) solve(as(a, "dgeMatrix")))            function(a, b, ...) solve(as(a, "dgeMatrix")))
83    
84  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
85    setMethod("solve", signature(a = "ddenseMatrix", b = .b),
86            function(a, b, ...) solve(as(a, "dgeMatrix"), b))            function(a, b, ...) solve(as(a, "dgeMatrix"), b))
87    for(.b in c("matrix","numeric")) ## << against ambiguity notes
88  ## General method for dense matrix multiplication in case specific methods  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
89  ## have not been defined.            function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
 setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
           function(x, y) .Call(dgeMatrix_matrix_mm,  
                                .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),  
           valueClass = "dgeMatrix")  
90    
91  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
92            function(x, ...) lu(as(x, "dgeMatrix")))            function(x, ...) lu(as(x, "dgeMatrix"), ...))
93    
94  setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)  setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
95    
96  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
97            function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
# Line 146  Line 135 
135  .bandDense <- function(x, k1, k2, ...) {  .bandDense <- function(x, k1, k2, ...) {
136      k1 <- as.integer(k1[1])      k1 <- as.integer(k1[1])
137      k2 <- as.integer(k2[1])      k2 <- as.integer(k2[1])
138      dd <- dim(x); sqr <- dd[1] == dd[2]      dd <- dim(x)
139      stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])      sqr <- dd[1] == dd[2]
140        stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
141      r <- .Call(dense_band, x, k1, k2)      r <- .Call(dense_band, x, k1, k2)
142      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
143          forceSymmetric(r)          forceSymmetric(r)
# Line 163  Line 153 
153  setMethod("skewpart", signature(x = "ddenseMatrix"),  setMethod("skewpart", signature(x = "ddenseMatrix"),
154            function(x) .Call(ddense_skewpart, x))            function(x) .Call(ddense_skewpart, x))
155    
156    
157    setMethod("is.finite", signature(x = "dgeMatrix"),
158              function(x) {
159                  if(all(ifin <- is.finite(x@x)))
160                      allTrueMat(x)
161                  else if(any(ifin)) {
162                      r <- as(x, "lMatrix") #-> logical x-slot
163                      r@x <- ifin
164                      as(r, "nMatrix")
165                  }
166                  else is.na_nsp(x)
167              })
168    
169    ## TODO? -- rather methods for specific subclasses of ddenseMatrix
170    setMethod("is.finite", signature(x = "ddenseMatrix"),
171              function(x) {
172                  if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
173                  ## *NOT* dge, i.e., either triangular or symmetric
174                  ## (possibly packed): has finite 0-triangle
175                  cdx <- getClassDef(class(x))
176    
177                  r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
178                  r@Dim <- (d <- x@Dim)
179                  r@Dimnames <- x@Dimnames
180                  isPacked <- (le <- prod(d)) > length(ifin)
181                  r@x <- rep.int(TRUE, le)
182                  iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
183                  if(isPacked) { ## x@x is "usable"
184                      r@x[iTr] <- ifin
185                  } else {
186                      r@x[iTr] <- ifin[iTr]
187                  }
188                  r
189              })
190    
191    setMethod("is.infinite", signature(x = "ddenseMatrix"),
192              function(x) {
193                  if(any((isInf <- is.infinite(x@x)))) {
194                      r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
195                      r@x <- isInf
196                      as(r, "nMatrix")# often sparse .. better way?
197                  }
198                  else is.na_nsp(x)
199              })

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