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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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revision 925, Mon Sep 19 19:01:31 2005 UTC revision 2551, Sat Jun 19 20:45:45 2010 UTC
# Line 1  Line 1 
1  ### Define Methods that can be inherited for all subclasses  ### Define Methods that can be inherited for all subclasses
2    
3    ## This replaces many "d..Matrix" -> "dgeMatrix" ones
4    ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5    ##   -----  in  ../src/Mutils.c
6    
7    setAs("ddenseMatrix", "dgeMatrix",
8          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):
14    setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
15    setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
16    setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
17    setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
18    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    ##       function(from) {
35    ##          if(is.numeric(from))
36    ##              .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
37    ##          else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
38    ##                 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
44    setAs("matrix", "dgCMatrix",
45          function(from) {
46              storage.mode(from) <- "double"
47              .Call(dense_to_Csparse, from)
48          })
49    
50    setAs("numeric", "CsparseMatrix",
51          function(from)
52          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
53    
54    setMethod("as.numeric", signature(x = "ddenseMatrix"),
55              function(x, ...) as(x, "dgeMatrix")@x)
56    
57  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
58    
59  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 7  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  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
76            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
77    ##        function(x) callGeneric(as(x, "dgeMatrix")))
 setMethod("tcrossprod", signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
78    
79  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
80            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x, nrow, ncol) diag(as(x, "dgeMatrix")))
81    
82  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
83            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(as(a, "dgeMatrix")))
84    
85  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
86            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
87              function(a, b, ...) solve(as(a, "dgeMatrix"), b))
88    for(.b in c("matrix","numeric")) ## << against ambiguity notes
89    setMethod("solve", signature(a = "ddenseMatrix", b = .b),
90              function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
91    
92  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
93            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) lu(as(x, "dgeMatrix"), ...))
94    
95    setMethod("chol", signature(x = "ddenseMatrix"), cholMat)
96    
97  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
98            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
99    
100  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
101            function(x, logarithm, ...)            function(x, logarithm, ...)
102            callGeneric(as(x, "dgeMatrix"), logarithm))            determinant(as(x, "dgeMatrix"), logarithm))
   
 setMethod("expm", signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
103    
104  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  ## now done for "dMatrix":
105            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
106    ##           function(x) callGeneric(as(x, "dgeMatrix")))
107    
108  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),  setMethod("Math",
109            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            signature(x = "ddenseMatrix"),
110              function(x) callGeneric(as(x, "dgeMatrix")))
111    
112    
 ### NAMESPACE must export this -- also only for R version 2.2.x:  
 if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {  
     ## 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  
               })  
113    
114      setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),  .trilDense <- function(x, k = 0, ...) {
115                function(x, y) callGeneric(x, as(y, "dgeMatrix")))      k <- as.integer(k[1])
116      setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),      d <- dim(x)
117                function(x, y) callGeneric(as(x, "dgeMatrix"), y))      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
118        ## returns "lower triangular" if k <= 0 && sqr
119      setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),      .Call(dense_band, x, -d[1], k)
               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)  
120                    }                    }
121                    x  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
122                })  ##     for triangular ["dtr" and "dtp"]
123    setMethod("tril", "denseMatrix", .trilDense)
124    setMethod("tril",      "matrix", .trilDense)
125    
126    .triuDense <- function(x, k = 0, ...) {
127        k <- as.integer(k[1])
128        d <- dim(x)
129        stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
130        ## returns "upper triangular" if k >= 0
131        .Call(dense_band, x, k, d[2])
132    }
133    setMethod("triu", "denseMatrix", .triuDense)
134    setMethod("triu",      "matrix", .triuDense)
135    
136  ### rbind2 -- analogous to cbind2 --- more to do for @x though:  .bandDense <- function(x, k1, k2, ...) {
137        k1 <- as.integer(k1[1])
138        k2 <- as.integer(k2[1])
139        dd <- dim(x)
140        sqr <- dd[1] == dd[2]
141        stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
142        r <- .Call(dense_band, x, k1, k2)
143        if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
144            forceSymmetric(r)
145        else
146            r
147    }
148    setMethod("band", "denseMatrix", .bandDense)
149    setMethod("band",      "matrix", .bandDense)
150    
     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"))))  
               })  
151    
152      setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),  setMethod("symmpart", signature(x = "ddenseMatrix"),
153                function(x, y) callGeneric(x, as(y, "dgeMatrix")))            function(x) .Call(ddense_symmpart, x))
154      setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),  setMethod("skewpart", signature(x = "ddenseMatrix"),
155                function(x, y) callGeneric(as(x, "dgeMatrix"), y))            function(x) .Call(ddense_skewpart, x))
   
     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"))))  
               })  
156    
 }## R-2.2.x ff  

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