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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 1453, Sun Aug 27 16:16:35 2006 UTC revision 1714, Thu Dec 28 22:11:32 2006 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    ## Should this method return 'from' without duplication when it has
8    ## class dgeMatrix?
9  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix",
10        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))        function(from) {
11              if (class(from) != "dgeMatrix")
12                  from <- .Call(dup_mMatrix_as_dgeMatrix, from)
13              from
14          })
15    
16  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
17  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)
# Line 13  Line 20 
20  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
21  setAs("dspMatrix", "lspMatrix", d2l_Matrix)  setAs("dspMatrix", "lspMatrix", d2l_Matrix)
22    
23    setAs("ddenseMatrix", "CsparseMatrix",
24          function(from) {
25              if (class(from) != "dgeMatrix")
26                  from <- .Call(dup_mMatrix_as_dgeMatrix, from)
27              .Call(dense_to_Csparse, from)
28          })
29    
30    ## special case
31    setAs("dgeMatrix", "dgCMatrix",
32          function(from) .Call(dense_to_Csparse, from))
33    
34    setAs("matrix", "CsparseMatrix",
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"),  setMethod("as.numeric", signature(x = "ddenseMatrix"),
56            function(x, ...) as(x, "dgeMatrix")@x)            function(x, ...) as(x, "dgeMatrix")@x)
57    
# Line 47  Line 86 
86  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
87            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
88    
89  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  ## These methods cause an infinite loop in pre-2.4.0
90            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
91    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
92  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
93            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
94    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
95    
96    ## General method for dense matrix multiplication in case specific methods
97    ## have not been defined.
98    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
99              function(x, y) .Call(dgeMatrix_matrix_mm,
100                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
101              valueClass = "dgeMatrix")
102    
103  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
104            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) callGeneric(as(x, "dgeMatrix")))
105    
106    setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
107    
108  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
109            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
110    
# Line 74  Line 123 
123            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
124    
125    
 ## 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")))  
   
126  setMethod("Math",  setMethod("Math",
127            signature(x = "ddenseMatrix"),            signature(x = "ddenseMatrix"),
128            function(x) callGeneric(as(x, "dgeMatrix")))            function(x) callGeneric(as(x, "dgeMatrix")))
129    
130    
131    ### FIXME: band() et al should be extended from "ddense" to "dense" !
132    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
133    
 ### 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  
           })  
   
 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)  
               }  
               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"))))  
           })  
134  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
135  ##     for triangular ["dtr" and "dtp"]  ##     for triangular ["dtr" and "dtp"]
136  setMethod("tril", "ddenseMatrix",  setMethod("tril", "ddenseMatrix",

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