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

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pkg/R/ddenseMatrix.R revision 1453, Sun Aug 27 16:16:35 2006 UTC pkg/Matrix/R/ddenseMatrix.R revision 3092, Thu Apr 2 10:56:59 2015 UTC
# Line 3  Line 3 
3  ## This replaces many "d..Matrix" -> "dgeMatrix" ones  ## This replaces many "d..Matrix" -> "dgeMatrix" ones
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  setAs("ddenseMatrix", "dgeMatrix",  
7        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))  setAs("ddenseMatrix", "dgeMatrix", ..2dge)
8    
9    setAs("ddenseMatrix", "matrix",
10          function(from) as(..2dge(from), "matrix"))
11    
12  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
13  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
14  setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)  setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
15  setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)  setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
16  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
17  setAs("dspMatrix", "lspMatrix", d2l_Matrix)  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",
21          function(from) {
22              if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
23                  as_Csparse(from)
24              else .Call(dense_to_Csparse, from)
25          })
26    
27    ## special case
28    setAs("dgeMatrix", "dgCMatrix",
29          function(from) .Call(dense_to_Csparse, from))
30    
31    setAs("matrix", "CsparseMatrix",
32          function(from) .Call(dense_to_Csparse, from))
33    
34    ## for historical i.e. backcompatibility reasons ..
35    setAs("matrix", "dgCMatrix",
36          function(from) {
37              storage.mode(from) <- "double"
38              .Call(dense_to_Csparse, from)
39          })
40    
41    setAs("numeric", "CsparseMatrix",
42          function(from)
43          .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 23  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")))  
68    
69  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")))  
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    for(.b in c("matrix","numeric")) ## << against ambiguity notes
78    setMethod("solve", signature(a = "ddenseMatrix", b = .b),
79              function(a, b, ...) solve(..2dge(a), Matrix(b)))
80    rm(.b)
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"), 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))  
   
   
 ## Cheap version: work via "dgeMatrix" and use the group methods there:  
 ## FIXME(?): try to preserve "symmetric", "triangular", ...  
 setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"  
           signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),  
           function(e1, e2) callGeneric(as(e1, "dgeMatrix"),  
                                        as(e2, "dgeMatrix")))  
 setMethod("Arith",  
           signature(e1 = "ddenseMatrix", e2 = "numeric"),  
           function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))  
 setMethod("Arith",  
           signature(e1 = "numeric", e2 = "ddenseMatrix"),  
           function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))  
   
 setMethod("Math",  
           signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
   
98    
99    
100  ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --  .trilDense <- function(x, k = 0, ...) {
101        k <- as.integer(k[1])
102  ### cbind2      d <- dim(x)
103  setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
104            function(x, y) {      ## returns "lower triangular" if k <= 0 && sqr
105                d <- dim(x); nr <- d[1]; nc <- d[2]      .Call(dense_band, x, -d[1], k)
               y <- rep(y, length.out = nr) # 'silent procrustes'  
               ## beware of (packed) triangular, symmetric, ...  
               x <- as(x, "dgeMatrix")  
               x@x <- c(x@x, as.double(y))  
               x@Dim[2] <- nc + 1:1  
               if(is.character(dn <- x@Dimnames[[2]]))  
                   x@Dimnames[[2]] <- c(dn, "")  
               x  
           })  
 ## the same, (x,y) <-> (y,x):  
 setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),  
           function(x, y) {  
               d <- dim(y); nr <- d[1]; nc <- d[2]  
               x <- rep(x, length.out = nr)  
               y <- as(y, "dgeMatrix")  
               y@x <- c(as.double(x), y@x)  
               y@Dim[2] <- nc + 1:1  
               if(is.character(dn <- y@Dimnames[[2]]))  
                   y@Dimnames[[2]] <- c("", dn)  
               y  
           })  
   
 setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),  
           function(x, y) callGeneric(x, as(y, "dgeMatrix")))  
 setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),  
           function(x, y) callGeneric(as(x, "dgeMatrix"), y))  
   
 setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
           function(x, y) {  
               nr <- rowCheck(x,y)  
               ncx <- x@Dim[2]  
               ncy <- y@Dim[2]  
               ## beware of (packed) triangular, symmetric, ...  
               hasDN <- !is.null(dnx <- dimnames(x)) |  
               !is.null(dny <- dimnames(y))  
               x <- as(x, "dgeMatrix")  
               y <- as(y, "dgeMatrix")  
               x@x <- c(x@x, y@x)  
               x@Dim[2] <- ncx + ncy  
               if(hasDN) {  
                   ## R and S+ are different in which names they take  
                   ## if they differ -- but there's no warning in any case  
                   rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]  
                   cx <- dnx[[2]] ; cy <- dny[[2]]  
                   cn <- if(is.null(cx) && is.null(cy)) NULL  
                   else c(if(!is.null(cx)) cx else rep.int("", ncx),  
                          if(!is.null(cy)) cy else rep.int("", ncy))  
                   x@Dimnames <- list(rn, cn)  
106                }                }
               x  
           })  
   
 ### rbind2 -- analogous to cbind2 --- more to do for @x though:  
   
 setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),  
           function(x, y) {  
               if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")  
               new("dgeMatrix", Dim = x@Dim + 1:0,  
                   Dimnames = list(dn, x@Dimnames[[2]]),  
                   x = c(rbind2(as(x,"matrix"), y)))  
           })  
 ## the same, (x,y) <-> (y,x):  
 setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),  
           function(x, y) {  
               if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)  
               new("dgeMatrix", Dim = y@Dim + 1:0,  
                   Dimnames = list(dn, y@Dimnames[[2]]),  
                   x = c(rbind2(x, as(y,"matrix"))))  
           })  
   
 setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),  
           function(x, y) callGeneric(x, as(y, "dgeMatrix")))  
 setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),  
           function(x, y) callGeneric(as(x, "dgeMatrix"), y))  
   
 setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
           function(x, y) {  
               nc <- colCheck(x,y)  
               nrx <- x@Dim[1]  
               nry <- y@Dim[1]  
               dn <-  
                   if(!is.null(dnx <- dimnames(x)) |  
                      !is.null(dny <- dimnames(y))) {  
                       ## R and S+ are different in which names they take  
                       ## if they differ -- but there's no warning in any case  
                       list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))  
                            NULL else  
                            c(if(!is.null(rx)) rx else rep.int("", nrx),  
                              if(!is.null(ry)) ry else rep.int("", nry)),  
                            if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])  
   
                   } else list(NULL, NULL)  
               ## beware of (packed) triangular, symmetric, ...  
               new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,  
                   x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))  
           })  
107  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
108  ##     for triangular ["dtr" and "dtp"]  ##     for triangular ["dtr" and "dtp"]
109  setMethod("tril", "ddenseMatrix",  setMethod("tril", "denseMatrix", .trilDense)
110            function(x, k = 0, ...) {  setMethod("tril",      "matrix", .trilDense)
               k <- as.integer(k[1])  
               dd <- dim(x); sqr <- dd[1] == dd[2]  
               stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0  
               ## returns "lower triangular" if k <= 0 && sqr  
               .Call(ddense_band, x, -dd[1], k)  
           })  
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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