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

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pkg/R/ddenseMatrix.R revision 1714, Thu Dec 28 22:11:32 2006 UTC pkg/Matrix/R/ddenseMatrix.R revision 3079, Tue Mar 31 15:29:43 2015 UTC
# Line 4  Line 4 
4  ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed  ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5  ##   -----  in  ../src/Mutils.c  ##   -----  in  ../src/Mutils.c
6    
 ## Should this method return 'from' without duplication when it has  
 ## class dgeMatrix?  
7  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix",
8        function(from) {        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
9            if (class(from) != "dgeMatrix")  
10                from <- .Call(dup_mMatrix_as_dgeMatrix, from)  setAs("ddenseMatrix", "matrix",
11            from        function(from) as(as(from, "dgeMatrix"), "matrix"))
       })  
12    
13  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
14  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
15  setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)  setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
16  setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)  setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
17  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
18  setAs("dspMatrix", "lspMatrix", d2l_Matrix)  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")            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24                from <- .Call(dup_mMatrix_as_dgeMatrix, from)                as_Csparse(from)
25            .Call(dense_to_Csparse, from)            else .Call(dense_to_Csparse, from)
26        })        })
27    
28  ## special case  ## special case
# Line 32  Line 30 
30        function(from) .Call(dense_to_Csparse, from))        function(from) .Call(dense_to_Csparse, from))
31    
32  setAs("matrix", "CsparseMatrix",  setAs("matrix", "CsparseMatrix",
33        function(from) {        function(from) .Call(dense_to_Csparse, from))
             if(is.numeric(from))  
                 .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))  
             else if(is.logical(from)) ## FIXME: this works, but maybe wastefully  
                 as(Matrix(from, sparse=TRUE), "CsparseMatrix")  
             else stop('not-yet-implemented coercion to "CsparseMatrix"')  
       })  
   
34    
35  ## special case needed in the Matrix function  ## for historical i.e. backcompatibility reasons ..
36  setAs("matrix", "dgCMatrix",  setAs("matrix", "dgCMatrix",
37        function(from) {        function(from) {
38            storage.mode(from) <- "double"            storage.mode(from) <- "double"
# Line 52  Line 43 
43        function(from)        function(from)
44        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
45    
46  setMethod("as.numeric", signature(x = "ddenseMatrix"),  setMethod("as.numeric", "ddenseMatrix", function(x, ...) ..2dge(x)@x)
           function(x, ...) as(x, "dgeMatrix")@x)  
47    
48  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
49    
# Line 62  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))
59    
60  setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
61            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, norm, ...) rcond(..2dge(x), ...))
62    
63  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
64            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, norm, ...) rcond(..2dge(x), norm, ...))
65    
66  ## Not really useful; now require *identical* class for result:  ## Not really useful; now require *identical* class for result:
67  ## setMethod("t", signature(x = "ddenseMatrix"),  ## setMethod("t", signature(x = "ddenseMatrix"),
68  ##        function(x) callGeneric(as(x, "dgeMatrix")))  ##        function(x) callGeneric(..2dge(x)))
69    
70  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
71    
72  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
73            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))            function(a, b, ...) solve(..2dge(a)))
74    
75  setMethod("diag", signature(x = "ddenseMatrix"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
76            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
77              function(a, b, ...) solve(..2dge(a), b))
78  ## These methods cause an infinite loop in pre-2.4.0  for(.b in c("matrix","numeric")) ## << against ambiguity notes
79  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
80  ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(..2dge(a), Matrix(b)))
81    rm(.b)
 ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
 ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  
   
 ## General method for dense matrix multiplication in case specific methods  
 ## have not been defined.  
 setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
           function(x, y) .Call(dgeMatrix_matrix_mm,  
                                .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),  
           valueClass = "dgeMatrix")  
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("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)  setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
88    
89  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
90            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(..2dge(x)))
91    
92  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
93            function(x, logarithm, ...)            function(x, logarithm, ...)
94            callGeneric(as(x, "dgeMatrix"), logarithm))            determinant(..2dge(x), logarithm))
95    
96  ## now done for "dMatrix":  ## now done for "dMatrix":
97  ## setMethod("expm", signature(x = "ddenseMatrix"),  ## setMethod("expm", signature(x = "ddenseMatrix"),
98  ##           function(x) callGeneric(as(x, "dgeMatrix")))  ##           function(x) callGeneric(..2dge(x)))
   
 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))  
   
99    
 setMethod("Math",  
           signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
100    
101    .trilDense <- function(x, k = 0, ...) {
 ### FIXME: band() et al should be extended from "ddense" to "dense" !  
 ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()  
   
 ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and  
 ##     for triangular ["dtr" and "dtp"]  
 setMethod("tril", "ddenseMatrix",  
           function(x, k = 0, ...) {  
102                k <- as.integer(k[1])                k <- as.integer(k[1])
103                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
104                stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
105                ## returns "lower triangular" if k <= 0 && sqr                ## returns "lower triangular" if k <= 0 && sqr
106                .Call(ddense_band, x, -dd[1], k)      .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  setMethod("triu", "ddenseMatrix",  .triuDense <- function(x, k = 0, ...) {
           function(x, k = 0, ...) {  
114                k <- as.integer(k[1])                k <- as.integer(k[1])
115                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
116                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
117                ## returns "upper triangular" if k >= 0                ## returns "upper triangular" if k >= 0
118                .Call(ddense_band, x, k, dd[2])      .Call(dense_band, x, k, d[2])
119            })  }
120    setMethod("triu", "denseMatrix", .triuDense)
121    setMethod("triu",      "matrix", .triuDense)
122    
123  setMethod("band", "ddenseMatrix",  .bandDense <- function(x, k1, k2, ...) {
           function(x, k1, k2, ...) {  
124                k1 <- as.integer(k1[1])                k1 <- as.integer(k1[1])
125                k2 <- as.integer(k2[1])                k2 <- as.integer(k2[1])
126                dd <- dim(x); sqr <- dd[1] == dd[2]      dd <- dim(x)
127                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])      sqr <- dd[1] == dd[2]
128                r <- .Call(ddense_band, x, k1, k2)      stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
129                if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric      r <- .Call(dense_band, x, k1, k2)
130                    as(r, paste(.M.kind(x), "syMatrix", sep=''))      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
131            forceSymmetric(r)
132                else                else
133                    r                    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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