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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 2123, Wed Mar 5 08:44:52 2008 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) {
9              if (class(from) != "dgeMatrix")
10                  .Call(dup_mMatrix_as_dgeMatrix, from)
11              else from
12          })
13    
14    
15    ## d(ouble) to l(ogical):
16    setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
17    setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
18    setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
19    setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
20    setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
21    
22    setAs("ddenseMatrix", "CsparseMatrix",
23          function(from) {
24              if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
25                  as_Csparse(from)
26              else .Call(dense_to_Csparse, from)
27          })
28    
29    ## special case
30    setAs("dgeMatrix", "dgCMatrix",
31          function(from) .Call(dense_to_Csparse, from))
32    
33    setAs("matrix", "CsparseMatrix",
34          function(from) .Call(dense_to_Csparse, from))
35    ##       function(from) {
36    ##          if(is.numeric(from))
37    ##              .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
38    ##          else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
39    ##                 as(Matrix(from, sparse=TRUE), "CsparseMatrix")
40    ##          else stop('not-yet-implemented coercion to "CsparseMatrix"')
41    ##       })
42    
43    
44    ## special case needed in the Matrix function
45    setAs("matrix", "dgCMatrix",
46          function(from) {
47              storage.mode(from) <- "double"
48              .Call(dense_to_Csparse, from)
49          })
50    
51    setAs("numeric", "CsparseMatrix",
52          function(from)
53          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
54    
55    setMethod("as.numeric", signature(x = "ddenseMatrix"),
56              function(x, ...) as(x, "dgeMatrix")@x)
57    
58  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
59    
60  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 7  Line 62 
62  ## dgeMatrix. Methods for special forms override these.  ## dgeMatrix. Methods for special forms override these.
63    
64  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),  setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
65            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, type, ...) norm(as(x, "dgeMatrix")))
66    
67  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),  setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
68            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) norm(as(x, "dgeMatrix"), type))
69    
70  setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),
71            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, type, ...) rcond(as(x, "dgeMatrix")))
72    
73  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
74            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) rcond(as(x, "dgeMatrix"), type))
75    
76  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
77            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
78    ##        function(x) callGeneric(as(x, "dgeMatrix")))
79    
80  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) tcrossprod(as(x, "dgeMatrix")))
82    
83  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
84            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) crossprod(as(x, "dgeMatrix")))
85    
86  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
87            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x, nrow, ncol) diag(as(x, "dgeMatrix")))
88    
89  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
90            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) solve(as(a, "dgeMatrix")))
91    
92  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
93            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))            function(a, b, ...) solve(as(a, "dgeMatrix"), b))
94    
95    ## General method for dense matrix multiplication in case specific methods
96    ## have not been defined.
97    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
98              function(x, y) .Call(dgeMatrix_matrix_mm,
99                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
100              valueClass = "dgeMatrix")
101    
102  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
103            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) lu(as(x, "dgeMatrix")))
104    
105    setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
106    
107  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
108            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) determinant(as(x, "dgeMatrix")))
109    
110  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
111            function(x, logarithm, ...)            function(x, logarithm, ...)
112            callGeneric(as(x, "dgeMatrix"), logarithm))            determinant(as(x, "dgeMatrix"), logarithm))
   
 setMethod("expm", signature(x = "ddenseMatrix"),  
           function(x) callGeneric(as(x, "dgeMatrix")))  
113    
114  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  ## now done for "dMatrix":
115            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
116    ##           function(x) callGeneric(as(x, "dgeMatrix")))
117    
118  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),  setMethod("Math",
119            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            signature(x = "ddenseMatrix"),
120              function(x) callGeneric(as(x, "dgeMatrix")))
121    
122    
 ### 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  
               })  
123    
124      setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),  .trilDense <- function(x, k = 0, ...) {
125                function(x, y) callGeneric(x, as(y, "dgeMatrix")))      k <- as.integer(k[1])
126      setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),      d <- dim(x)
127                function(x, y) callGeneric(as(x, "dgeMatrix"), y))      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
128        ## returns "lower triangular" if k <= 0 && sqr
129      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)  
130                    }                    }
131                    x  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
132                })  ##     for triangular ["dtr" and "dtp"]
133    setMethod("tril", "denseMatrix", .trilDense)
134    setMethod("tril",      "matrix", .trilDense)
135    
136    .triuDense <- function(x, k = 0, ...) {
137        k <- as.integer(k[1])
138        d <- dim(x)
139        stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
140        ## returns "upper triangular" if k >= 0
141        .Call(dense_band, x, k, d[2])
142    }
143    setMethod("triu", "denseMatrix", .triuDense)
144    setMethod("triu",      "matrix", .triuDense)
145    
146  ### rbind2 -- analogous to cbind2 --- more to do for @x though:  .bandDense <- function(x, k1, k2, ...) {
147        k1 <- as.integer(k1[1])
148        k2 <- as.integer(k2[1])
149        dd <- dim(x); sqr <- dd[1] == dd[2]
150        stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
151        r <- .Call(dense_band, x, k1, k2)
152        if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
153            forceSymmetric(r)
154        else
155            r
156    }
157    setMethod("band", "denseMatrix", .bandDense)
158    setMethod("band",      "matrix", .bandDense)
159    
     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"))))  
               })  
160    
161      setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),  setMethod("symmpart", signature(x = "ddenseMatrix"),
162                function(x, y) callGeneric(x, as(y, "dgeMatrix")))            function(x) .Call(ddense_symmpart, x))
163      setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),  setMethod("skewpart", signature(x = "ddenseMatrix"),
164                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"))))  
               })  
165    
 }## R-2.2.x ff  

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