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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 1447, Fri Aug 25 20:38:36 2006 UTC pkg/Matrix/R/ddenseMatrix.R revision 3079, Tue Mar 31 15:29:43 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    
7  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix",
8        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))        function(from) .Call(dup_mMatrix_as_dgeMatrix, 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", 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",
22          function(from) {
23              if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24                  as_Csparse(from)
25              else .Call(dense_to_Csparse, from)
26          })
27    
28    ## special case
29    setAs("dgeMatrix", "dgCMatrix",
30          function(from) .Call(dense_to_Csparse, from))
31    
32    setAs("matrix", "CsparseMatrix",
33          function(from) .Call(dense_to_Csparse, from))
34    
35    ## for historical i.e. backcompatibility reasons ..
36    setAs("matrix", "dgCMatrix",
37          function(from) {
38              storage.mode(from) <- "double"
39              .Call(dense_to_Csparse, from)
40          })
41    
42    setAs("numeric", "CsparseMatrix",
43          function(from)
44          .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 23  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)))
   
 setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
69    
70  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")))  
71    
72  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
73            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(..2dge(a)))
74    
75  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
76            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
77              function(a, b, ...) solve(..2dge(a), b))
78    for(.b in c("matrix","numeric")) ## << against ambiguity notes
79    setMethod("solve", signature(a = "ddenseMatrix", b = .b),
80              function(a, b, ...) solve(..2dge(a), Matrix(b)))
81    rm(.b)
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"), 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)))
99    
 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")))  
100    
101    .trilDense <- function(x, k = 0, ...) {
102        k <- as.integer(k[1])
103        d <- dim(x)
104        stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
105        ## returns "lower triangular" if k <= 0 && sqr
106        .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    .triuDense <- function(x, k = 0, ...) {
114        k <- as.integer(k[1])
115        d <- dim(x)
116        stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
117        ## returns "upper triangular" if k >= 0
118        .Call(dense_band, x, k, d[2])
119    }
120    setMethod("triu", "denseMatrix", .triuDense)
121    setMethod("triu",      "matrix", .triuDense)
122    
123    .bandDense <- function(x, k1, k2, ...) {
124        k1 <- as.integer(k1[1])
125        k2 <- as.integer(k2[1])
126        dd <- dim(x)
127        sqr <- dd[1] == dd[2]
128        stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
129        r <- .Call(dense_band, x, k1, k2)
130        if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
131            forceSymmetric(r)
132        else
133            r
134    }
135    setMethod("band", "denseMatrix", .bandDense)
136    setMethod("band",      "matrix", .bandDense)
137    
 ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --  
   
 ### cbind2  
 setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),  
           function(x, y) {  
               d <- dim(x); nr <- d[1]; nc <- d[2]  
               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  
           })  
138    
139  setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),  setMethod("symmpart", signature(x = "ddenseMatrix"),
140            function(x, y) callGeneric(x, as(y, "dgeMatrix")))            function(x) .Call(ddense_symmpart, x))
141  setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),  setMethod("skewpart", signature(x = "ddenseMatrix"),
142            function(x, y) callGeneric(as(x, "dgeMatrix"), y))            function(x) .Call(ddense_skewpart, x))
143    
144  setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
145            function(x, y) {  setMethod("is.finite", signature(x = "dgeMatrix"),
146                nr <- rowCheck(x,y)            function(x) {
147                ncx <- x@Dim[2]                if(all(ifin <- is.finite(x@x)))
148                ncy <- y@Dim[2]                    allTrueMat(x)
149                ## beware of (packed) triangular, symmetric, ...                else if(any(ifin)) {
150                hasDN <- !is.null(dnx <- dimnames(x)) |                    r <- as(x, "lMatrix") #-> logical x-slot
151                !is.null(dny <- dimnames(y))                    r@x <- ifin
152                x <- as(x, "dgeMatrix")                    as(r, "nMatrix")
               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)  
153                }                }
154                x                else is.na_nsp(x)
155            })            })
156    
157  ### rbind2 -- analogous to cbind2 --- more to do for @x though:  ## TODO? -- rather methods for specific subclasses of ddenseMatrix
158    setMethod("is.finite", signature(x = "ddenseMatrix"),
159  setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),            function(x) {
160            function(x, y) {                if(all(ifin <- is.finite(x@x))) return(allTrueMat(x))
161                if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")                ## *NOT* dge, i.e., either triangular or symmetric
162                new("dgeMatrix", Dim = x@Dim + 1:0,                ## (possibly packed): has finite 0-triangle
163                    Dimnames = list(dn, x@Dimnames[[2]]),                cdx <- getClassDef(class(x))
164                    x = c(rbind2(as(x,"matrix"), y)))  
165            })                r <- new(if(extends(cdx,"symmetricMatrix"))"nsyMatrix" else "ngeMatrix")
166  ## the same, (x,y) <-> (y,x):                r@Dim <- (d <- x@Dim)
167  setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),                r@Dimnames <- x@Dimnames
168            function(x, y) {                isPacked <- (le <- prod(d)) > length(ifin)
169                if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)                r@x <- rep.int(TRUE, le)
170                new("dgeMatrix", Dim = y@Dim + 1:0,                iTr <- indTri(d[1], upper= x@uplo == "U", diag= TRUE)
171                    Dimnames = list(dn, y@Dimnames[[2]]),                if(isPacked) { ## x@x is "usable"
172                    x = c(rbind2(x, as(y,"matrix"))))                    r@x[iTr] <- ifin
173                  } else {
174                      r@x[iTr] <- ifin[iTr]
175                  }
176                  r
177            })            })
178    
179  setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),  setMethod("is.infinite", signature(x = "ddenseMatrix"),
180            function(x, y) callGeneric(x, as(y, "dgeMatrix")))            function(x) {
181  setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),                if(any((isInf <- is.infinite(x@x)))) {
182            function(x, y) callGeneric(as(x, "dgeMatrix"), y))                    r <- as(x, "lMatrix")#-> logical x-slot; 0 |--> FALSE
183                      r@x <- isInf
184  setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),                    as(r, "nMatrix")# often sparse .. better way?
185            function(x, y) {                }
186                nc <- colCheck(x,y)                else is.na_nsp(x)
               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"))))  
187            })            })

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