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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 1945, Wed Jul 4 18:07:07 2007 UTC pkg/Matrix/R/ddenseMatrix.R revision 3000, Tue Aug 12 10:29:50 2014 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))
9            if (class(from) != "dgeMatrix")  
10                .Call(dup_mMatrix_as_dgeMatrix, from)  setAs("ddenseMatrix", "matrix",
11            else from        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 18  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 30  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))
34              if(is.numeric(from))  ##       function(from) {
35                  .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))  ##          if(is.numeric(from))
36              else if(is.logical(from)) ## FIXME: this works, but maybe wastefully  ##              .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
37                  as(Matrix(from, sparse=TRUE), "CsparseMatrix")  ##          else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
38              else stop('not-yet-implemented coercion to "CsparseMatrix"')  ##                 as(Matrix(from, sparse=TRUE), "CsparseMatrix")
39        })  ##          else stop('not-yet-implemented coercion to "CsparseMatrix"')
40    ##       })
41    
42    
43  ## special case needed in the Matrix function  ## special case needed in the Matrix function
# Line 60  Line 61 
61  ## dgeMatrix. Methods for special forms override these.  ## dgeMatrix. Methods for special forms override these.
62    
63  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
64            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, type, ...) norm(as(x, "dgeMatrix")))
65    
66  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
67            function(x, type, ...) callGeneric(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, ...) callGeneric(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, ...) callGeneric(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) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("diag", signature(x = "ddenseMatrix"),  
           function(x, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))  
80    
81  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
82            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(as(a, "dgeMatrix")))
   
 setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  
83    
84  ## General method for dense matrix multiplication in case specific methods  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
85  ## have not been defined.  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
86  setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),            function(a, b, ...) solve(as(a, "dgeMatrix"), b))
87            function(x, y) .Call(dgeMatrix_matrix_mm,  for(.b in c("matrix","numeric")) ## << against ambiguity notes
88                                 .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
89            valueClass = "dgeMatrix")            function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
90    rm(.b)
91    
92  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
93            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...)
94              .set.factors(x, "LU", lu(as(x, "dgeMatrix"), ...)))
95    
96  setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)  setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
97    
98  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
99            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
100    
101  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
102            function(x, logarithm, ...)            function(x, logarithm, ...)
103            callGeneric(as(x, "dgeMatrix"), logarithm))            determinant(as(x, "dgeMatrix"), logarithm))
104    
105  ## now done for "dMatrix":  ## now done for "dMatrix":
106  ## setMethod("expm", signature(x = "ddenseMatrix"),  ## setMethod("expm", signature(x = "ddenseMatrix"),
107  ##           function(x) callGeneric(as(x, "dgeMatrix")))  ##           function(x) callGeneric(as(x, "dgeMatrix")))
108    
 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))  
   
   
 setMethod("Math",  
           signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
109    
110    .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, ...) {  
111                k <- as.integer(k[1])                k <- as.integer(k[1])
112                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
113                stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
114                ## returns "lower triangular" if k <= 0 && sqr                ## returns "lower triangular" if k <= 0 && sqr
115                .Call(ddense_band, x, -dd[1], k)      .Call(dense_band, x, -d[1], k)
116            })  }
117    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
118    ##     for triangular ["dtr" and "dtp"]
119    setMethod("tril", "denseMatrix", .trilDense)
120    setMethod("tril",      "matrix", .trilDense)
121    
122  setMethod("triu", "ddenseMatrix",  .triuDense <- function(x, k = 0, ...) {
           function(x, k = 0, ...) {  
123                k <- as.integer(k[1])                k <- as.integer(k[1])
124                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
125                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
126                ## returns "upper triangular" if k >= 0                ## returns "upper triangular" if k >= 0
127                .Call(ddense_band, x, k, dd[2])      .Call(dense_band, x, k, d[2])
128            })  }
129    setMethod("triu", "denseMatrix", .triuDense)
130    setMethod("triu",      "matrix", .triuDense)
131    
132  setMethod("band", "ddenseMatrix",  .bandDense <- function(x, k1, k2, ...) {
           function(x, k1, k2, ...) {  
133                k1 <- as.integer(k1[1])                k1 <- as.integer(k1[1])
134                k2 <- as.integer(k2[1])                k2 <- as.integer(k2[1])
135                dd <- dim(x); sqr <- dd[1] == dd[2]      dd <- dim(x)
136                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])      sqr <- dd[1] == dd[2]
137                r <- .Call(ddense_band, x, k1, k2)      stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
138                if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric      r <- .Call(dense_band, x, k1, k2)
139                    as(r, paste(.M.kind(x), "syMatrix", sep=''))      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
140            forceSymmetric(r)
141                else                else
142                    r                    r
143    }
144    setMethod("band", "denseMatrix", .bandDense)
145    setMethod("band",      "matrix", .bandDense)
146    
147    
148    setMethod("symmpart", signature(x = "ddenseMatrix"),
149              function(x) .Call(ddense_symmpart, x))
150    setMethod("skewpart", signature(x = "ddenseMatrix"),
151              function(x) .Call(ddense_skewpart, x))
152    
153    
154    setMethod("is.finite", signature(x = "dgeMatrix"),
155              function(x) {
156                  if(all(ifin <- is.finite(x@x)))
157                      allTrueMat(x)
158                  else if(any(ifin)) {
159                      r <- as(x, "lMatrix") #-> logical x-slot
160                      r@x <- ifin
161                      as(r, "nMatrix")
162                  }
163                  else is.na_nsp(x)
164              })
165    
166    ## TODO? -- rather methods for specific subclasses of ddenseMatrix
167    setMethod("is.finite", signature(x = "ddenseMatrix"),
168              function(x) {
169                  if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
170                  ## *NOT* dge, i.e., either triangular or symmetric
171                  ## (possibly packed): has finite 0-triangle
172                  cdx <- getClassDef(class(x))
173    
174                  r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
175                  r@Dim <- (d <- x@Dim)
176                  r@Dimnames <- x@Dimnames
177                  isPacked <- (le <- prod(d)) > length(ifin)
178                  r@x <- rep.int(TRUE, le)
179                  iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
180                  if(isPacked) { ## x@x is "usable"
181                      r@x[iTr] <- ifin
182                  } else {
183                      r@x[iTr] <- ifin[iTr]
184                  }
185                  r
186              })
187    
188    setMethod("is.infinite", signature(x = "ddenseMatrix"),
189              function(x) {
190                  if(any((isInf <- is.infinite(x@x)))) {
191                      r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
192                      r@x <- isInf
193                      as(r, "nMatrix")# often sparse .. better way?
194                  }
195                  else is.na_nsp(x)
196            })            })

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