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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 2052, Wed Aug 15 13:33:19 2007 UTC pkg/Matrix/R/ddenseMatrix.R revision 3092, Thu Apr 2 10:56:59 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    
7  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix", ..2dge)
8        function(from) {  
9            if (class(from) != "dgeMatrix")  setAs("ddenseMatrix", "matrix",
10                .Call(dup_mMatrix_as_dgeMatrix, from)        function(from) as(..2dge(from), "matrix"))
           else from  
       })  
11    
12  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
13  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
# Line 18  Line 16 
16  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
17  setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))  setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
18    
19    if(FALSE) ## FIXME, this fails for ("dtpMatrix" -> "CsparseMatrix") where .dense2C() works
20  setAs("ddenseMatrix", "CsparseMatrix",  setAs("ddenseMatrix", "CsparseMatrix",
21        function(from) {        function(from) {
22            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
# Line 30  Line 29 
29        function(from) .Call(dense_to_Csparse, from))        function(from) .Call(dense_to_Csparse, from))
30    
31  setAs("matrix", "CsparseMatrix",  setAs("matrix", "CsparseMatrix",
32        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"')  
       })  
   
33    
34  ## special case needed in the Matrix function  ## for historical i.e. backcompatibility reasons ..
35  setAs("matrix", "dgCMatrix",  setAs("matrix", "dgCMatrix",
36        function(from) {        function(from) {
37            storage.mode(from) <- "double"            storage.mode(from) <- "double"
# Line 50  Line 42 
42        function(from)        function(from)
43        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
44    
45  setMethod("as.numeric", signature(x = "ddenseMatrix"),  setMethod("as.numeric", "ddenseMatrix", function(x, ...) ..2dge(x)@x)
           function(x, ...) as(x, "dgeMatrix")@x)  
46    
47  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
48    
# Line 60  Line 51 
51  ## dgeMatrix. Methods for special forms override these.  ## dgeMatrix. Methods for special forms override these.
52    
53  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
54            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, type, ...) norm(..2dge(x)))
55    
56  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
57            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) norm(..2dge(x), type))
58    
59  setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "missing"),
60            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, norm, ...) rcond(..2dge(x), ...))
61    
62  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
63            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, norm, ...) rcond(..2dge(x), norm, ...))
64    
65  ## Not really useful; now require *identical* class for result:  ## Not really useful; now require *identical* class for result:
66  ## setMethod("t", signature(x = "ddenseMatrix"),  ## setMethod("t", signature(x = "ddenseMatrix"),
67  ##        function(x) callGeneric(as(x, "dgeMatrix")))  ##        function(x) callGeneric(..2dge(x)))
   
 setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
68    
69  setMethod("diag", signature(x = "ddenseMatrix"),  ## "diag" --> specific methods for dge, dtr,dtp, dsy,dsp
           function(x, nrow, ncol) callGeneric(as(x, "dgeMatrix")))  
70    
71  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
72            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(..2dge(a)))
73    
74  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
75            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
76              function(a, b, ...) solve(..2dge(a), b))
77  ## General method for dense matrix multiplication in case specific methods  for(.b in c("matrix","numeric")) ## << against ambiguity notes
78  ## have not been defined.  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
79  setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),            function(a, b, ...) solve(..2dge(a), Matrix(b)))
80            function(x, y) .Call(dgeMatrix_matrix_mm,  rm(.b)
                                .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),  
           valueClass = "dgeMatrix")  
81    
82  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
83            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...)
84              .set.factors(x, "LU", lu(..2dge(x), ...)))
85    
86  setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)  setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
87    
88  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
89            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(..2dge(x)))
90    
91  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
92            function(x, logarithm, ...)            function(x, logarithm, ...)
93            callGeneric(as(x, "dgeMatrix"), logarithm))            determinant(..2dge(x), logarithm))
94    
95  ## now done for "dMatrix":  ## now done for "dMatrix":
96  ## setMethod("expm", signature(x = "ddenseMatrix"),  ## setMethod("expm", signature(x = "ddenseMatrix"),
97  ##           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))  
98    
99    
100  setMethod("Math",  .trilDense <- function(x, k = 0, ...) {
           signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
   
   
 ### 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, ...) {  
101                k <- as.integer(k[1])                k <- as.integer(k[1])
102                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
103                stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
104                ## returns "lower triangular" if k <= 0 && sqr                ## returns "lower triangular" if k <= 0 && sqr
105                .Call(ddense_band, x, -dd[1], k)      .Call(dense_band, x, -d[1], k)
106            })  }
107    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
108    ##     for triangular ["dtr" and "dtp"]
109    setMethod("tril", "denseMatrix", .trilDense)
110    setMethod("tril",      "matrix", .trilDense)
111    
112  setMethod("triu", "ddenseMatrix",  .triuDense <- function(x, k = 0, ...) {
           function(x, k = 0, ...) {  
113                k <- as.integer(k[1])                k <- as.integer(k[1])
114                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
115                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
116                ## returns "upper triangular" if k >= 0                ## returns "upper triangular" if k >= 0
117                .Call(ddense_band, x, k, dd[2])      .Call(dense_band, x, k, d[2])
118            })  }
119    setMethod("triu", "denseMatrix", .triuDense)
120    setMethod("triu",      "matrix", .triuDense)
121    
122  setMethod("band", "ddenseMatrix",  .bandDense <- function(x, k1, k2, ...) {
           function(x, k1, k2, ...) {  
123                k1 <- as.integer(k1[1])                k1 <- as.integer(k1[1])
124                k2 <- as.integer(k2[1])                k2 <- as.integer(k2[1])
125                dd <- dim(x); sqr <- dd[1] == dd[2]      dd <- dim(x)
126                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])      sqr <- dd[1] == dd[2]
127                r <- .Call(ddense_band, x, k1, k2)      stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
128                if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric      r <- .Call(dense_band, x, k1, k2)
129                    as(r, paste(.M.kind(x), "syMatrix", sep=''))      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
130            forceSymmetric(r)
131                else                else
132                    r                    r
133    }
134    setMethod("band", "denseMatrix", .bandDense)
135    setMethod("band",      "matrix", .bandDense)
136    
137    
138    setMethod("symmpart", signature(x = "ddenseMatrix"),
139              function(x) .Call(ddense_symmpart, x))
140    setMethod("skewpart", signature(x = "ddenseMatrix"),
141              function(x) .Call(ddense_skewpart, x))
142    
143    
144    setMethod("is.finite", signature(x = "dgeMatrix"),
145              function(x) {
146                  if(all(ifin <- is.finite(x@x)))
147                      allTrueMat(x)
148                  else if(any(ifin)) {
149                      r <- as(x, "lMatrix") #-> logical x-slot
150                      r@x <- ifin
151                      as(r, "nMatrix")
152                  }
153                  else is.na_nsp(x)
154              })
155    
156    ## TODO? -- rather methods for specific subclasses of ddenseMatrix
157    setMethod("is.finite", signature(x = "ddenseMatrix"),
158              function(x) {
159                  if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
160                  ## *NOT* dge, i.e., either triangular or symmetric
161                  ## (possibly packed): has finite 0-triangle
162                  cdx <- getClassDef(class(x))
163    
164                  r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
165                  r@Dim <- (d <- x@Dim)
166                  r@Dimnames <- x@Dimnames
167                  isPacked <- (le <- prod(d)) > length(ifin)
168                  r@x <- rep.int(TRUE, le)
169                  iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
170                  if(isPacked) { ## x@x is "usable"
171                      r@x[iTr] <- ifin
172                  } else {
173                      r@x[iTr] <- ifin[iTr]
174                  }
175                  r
176              })
177    
178    setMethod("is.infinite", signature(x = "ddenseMatrix"),
179              function(x) {
180                  if(any((isInf <- is.infinite(x@x)))) {
181                      r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
182                      r@x <- isInf
183                      as(r, "nMatrix")# often sparse .. better way?
184                  }
185                  else is.na_nsp(x)
186            })            })

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