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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 1447, Fri Aug 25 20:38:36 2006 UTC revision 1747, Mon Jan 29 20:17:33 2007 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) {
9              if (class(from) != "dgeMatrix")
10                  .Call(dup_mMatrix_as_dgeMatrix, from)
11              else from
12          })
13    
14  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
15  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
16  setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)  setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
17  setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)  setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
18  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
19  setAs("dspMatrix", "lspMatrix", d2l_Matrix)  setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
20    
21    setAs("ddenseMatrix", "CsparseMatrix",
22          function(from) {
23              if (class(from) != "dgeMatrix")
24                  from <- .Call(dup_mMatrix_as_dgeMatrix, from)
25              .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) {
34                if(is.numeric(from))
35                    .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from))
36                else if(is.logical(from)) ## FIXME: this works, but maybe wastefully
37                    as(Matrix(from, sparse=TRUE), "CsparseMatrix")
38                else stop('not-yet-implemented coercion to "CsparseMatrix"')
39          })
40    
41    
42    ## special case needed in the Matrix function
43    setAs("matrix", "dgCMatrix",
44          function(from) {
45              storage.mode(from) <- "double"
46              .Call(dense_to_Csparse, from)
47          })
48    
49    setAs("numeric", "CsparseMatrix",
50          function(from)
51          .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
52    
53  setMethod("as.numeric", signature(x = "ddenseMatrix"),  setMethod("as.numeric", signature(x = "ddenseMatrix"),
54            function(x, ...) as(x, "dgeMatrix")@x)            function(x, ...) as(x, "dgeMatrix")@x)
# Line 45  Line 82 
82            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
83    
84  setMethod("diag", signature(x = "ddenseMatrix"),  setMethod("diag", signature(x = "ddenseMatrix"),
85            function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))            function(x, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
86    
87  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  ## These methods cause an infinite loop in pre-2.4.0
88            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
89    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
90  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  
91            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))  ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
92    ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
93    
94    ## General method for dense matrix multiplication in case specific methods
95    ## have not been defined.
96    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
97              function(x, y) .Call(dgeMatrix_matrix_mm,
98                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
99              valueClass = "dgeMatrix")
100    
101  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
102            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) callGeneric(as(x, "dgeMatrix")))
103    
104    setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
105    
106  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
107            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
108    
# Line 74  Line 121 
121            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
122    
123    
 ## 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")))  
   
124  setMethod("Math",  setMethod("Math",
125            signature(x = "ddenseMatrix"),            signature(x = "ddenseMatrix"),
126            function(x) callGeneric(as(x, "dgeMatrix")))            function(x) callGeneric(as(x, "dgeMatrix")))
127    
128    
129    ### FIXME: band() et al should be extended from "ddense" to "dense" !
130    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
131    
132  ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
133    ##     for triangular ["dtr" and "dtp"]
134  ### cbind2  setMethod("tril", "ddenseMatrix",
135  setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),            function(x, k = 0, ...) {
136            function(x, y) {                k <- as.integer(k[1])
137                d <- dim(x); nr <- d[1]; nc <- d[2]                dd <- dim(x); sqr <- dd[1] == dd[2]
138                y <- rep(y, length.out = nr) # 'silent procrustes'                stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
139                ## beware of (packed) triangular, symmetric, ...                ## returns "lower triangular" if k <= 0 && sqr
140                x <- as(x, "dgeMatrix")                .Call(ddense_band, x, -dd[1], k)
141                x@x <- c(x@x, as.double(y))            })
142                x@Dim[2] <- nc + 1:1  
143                if(is.character(dn <- x@Dimnames[[2]]))  setMethod("triu", "ddenseMatrix",
144                    x@Dimnames[[2]] <- c(dn, "")            function(x, k = 0, ...) {
145                x                k <- as.integer(k[1])
146            })                dd <- dim(x); sqr <- dd[1] == dd[2]
147  ## the same, (x,y) <-> (y,x):                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
148  setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),                ## returns "upper triangular" if k >= 0
149            function(x, y) {                .Call(ddense_band, x, k, dd[2])
150                d <- dim(y); nr <- d[1]; nc <- d[2]            })
151                x <- rep(x, length.out = nr)  
152                y <- as(y, "dgeMatrix")  setMethod("band", "ddenseMatrix",
153                y@x <- c(as.double(x), y@x)            function(x, k1, k2, ...) {
154                y@Dim[2] <- nc + 1:1                k1 <- as.integer(k1[1])
155                if(is.character(dn <- y@Dimnames[[2]]))                k2 <- as.integer(k2[1])
156                    y@Dimnames[[2]] <- c("", dn)                dd <- dim(x); sqr <- dd[1] == dd[2]
157                y                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
158            })                r <- .Call(ddense_band, x, k1, k2)
159                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
160  setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),                    as(r, paste(.M.kind(x), "syMatrix", sep=''))
161            function(x, y) callGeneric(x, as(y, "dgeMatrix")))                else
162  setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),                    r
           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"))))  
163            })            })

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