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[matrix] Diff of /pkg/R/ddenseMatrix.R
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Diff of /pkg/R/ddenseMatrix.R

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revision 1575, Mon Sep 18 14:47:40 2006 UTC revision 2551, Sat Jun 19 20:45:45 2010 UTC
# Line 4  Line 4 
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    
 ## Should this method return 'from' without duplication when it has  
 ## class dgeMatrix?  
7  setAs("ddenseMatrix", "dgeMatrix",  setAs("ddenseMatrix", "dgeMatrix",
8        function(from) {        function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
9            if (class(from) != "dgeMatrix")  
10                from <- .Call(dup_mMatrix_as_dgeMatrix, from)  setAs("ddenseMatrix", "matrix",
11            from        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",  setAs("ddenseMatrix", "CsparseMatrix",
22        function(from) {        function(from) {
23            if (class(from) != "dgeMatrix")            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24                from <- .Call(dup_mMatrix_as_dgeMatrix, from)                as_Csparse(from)
25            .Call(dense_to_Csparse, from)            else .Call(dense_to_Csparse, from)
26        })        })
27    
28  ## special case  ## special case
# Line 32  Line 30 
30        function(from) .Call(dense_to_Csparse, from))        function(from) .Call(dense_to_Csparse, from))
31    
32  setAs("matrix", "CsparseMatrix",  setAs("matrix", "CsparseMatrix",
33        function(from)        function(from) .Call(dense_to_Csparse, from))
34        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))  ##       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  ## special case needed in the Matrix function
44  setAs("matrix", "dgCMatrix",  setAs("matrix", "dgCMatrix",
# Line 56  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  ## Not really useful; now require *identical* class for result:  ## Not really useful; now require *identical* class for result:
76  ## setMethod("t", signature(x = "ddenseMatrix"),  ## setMethod("t", signature(x = "ddenseMatrix"),
77  ##        function(x) callGeneric(as(x, "dgeMatrix")))  ##        function(x) callGeneric(as(x, "dgeMatrix")))
78    
 setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
   
 setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  
           function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))  
   
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"),
83              function(a, b, ...) solve(as(a, "dgeMatrix")))
84    
85  ## These methods cause an infinite loop in pre-2.4.0  for(.b in c("Matrix","ANY")) ## << against ambiguity notes
86  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
87  ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            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 = "ANY"),  setMethod("solve", signature(a = "ddenseMatrix", b = .b),
90  ##           function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))            function(a, b, ...) solve(as(a, "dgeMatrix"), Matrix(b)))
   
 ## General method for dense matrix multiplication in case specific methods  
 ## have not been defined.  
 setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),  
           function(x, y) .Call(dgeMatrix_matrix_mm,  
                                .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),  
           valueClass = "dgeMatrix")  
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))
103    
104  ## now done for "dMatrix":  ## now done for "dMatrix":
105  ## setMethod("expm", signature(x = "ddenseMatrix"),  ## setMethod("expm", signature(x = "ddenseMatrix"),
106  ##           function(x) callGeneric(as(x, "dgeMatrix")))  ##           function(x) callGeneric(as(x, "dgeMatrix")))
107    
 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")))  
   
108  setMethod("Math",  setMethod("Math",
109            signature(x = "ddenseMatrix"),            signature(x = "ddenseMatrix"),
110            function(x) callGeneric(as(x, "dgeMatrix")))            function(x) callGeneric(as(x, "dgeMatrix")))
111    
112    
113    
114  ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --  .trilDense <- function(x, k = 0, ...) {
115        k <- as.integer(k[1])
116  ### cbind2      d <- dim(x)
117  setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
118            function(x, y) {      ## returns "lower triangular" if k <= 0 && sqr
119                d <- dim(x); nr <- d[1]; nc <- d[2]      .Call(dense_band, x, -d[1], k)
               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)  
120                }                }
               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"))))  
           })  
   
 ### FIXME: band() et al should be extended from "ddense" to "dense" !  
 ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()  
   
121  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
122  ##     for triangular ["dtr" and "dtp"]  ##     for triangular ["dtr" and "dtp"]
123  setMethod("tril", "ddenseMatrix",  setMethod("tril", "denseMatrix", .trilDense)
124            function(x, k = 0, ...) {  setMethod("tril",      "matrix", .trilDense)
               k <- as.integer(k[1])  
               dd <- dim(x); sqr <- dd[1] == dd[2]  
               stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0  
               ## returns "lower triangular" if k <= 0 && sqr  
               .Call(ddense_band, x, -dd[1], k)  
           })  
125    
126  setMethod("triu", "ddenseMatrix",  .triuDense <- function(x, k = 0, ...) {
           function(x, k = 0, ...) {  
127                k <- as.integer(k[1])                k <- as.integer(k[1])
128                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
129                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
130                ## returns "upper triangular" if k >= 0                ## returns "upper triangular" if k >= 0
131                .Call(ddense_band, x, k, dd[2])      .Call(dense_band, x, k, d[2])
132            })  }
133    setMethod("triu", "denseMatrix", .triuDense)
134    setMethod("triu",      "matrix", .triuDense)
135    
136  setMethod("band", "ddenseMatrix",  .bandDense <- function(x, k1, k2, ...) {
           function(x, k1, k2, ...) {  
137                k1 <- as.integer(k1[1])                k1 <- as.integer(k1[1])
138                k2 <- as.integer(k2[1])                k2 <- as.integer(k2[1])
139                dd <- dim(x); sqr <- dd[1] == dd[2]      dd <- dim(x)
140                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])      sqr <- dd[1] == dd[2]
141                r <- .Call(ddense_band, x, k1, k2)      stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[2])
142                if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric      r <- .Call(dense_band, x, k1, k2)
143                    as(r, paste(.M.kind(x), "syMatrix", sep=''))      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
144            forceSymmetric(r)
145                else                else
146                    r                    r
147            })  }
148    setMethod("band", "denseMatrix", .bandDense)
149    setMethod("band",      "matrix", .bandDense)
150    
151    
152    setMethod("symmpart", signature(x = "ddenseMatrix"),
153              function(x) .Call(ddense_symmpart, x))
154    setMethod("skewpart", signature(x = "ddenseMatrix"),
155              function(x) .Call(ddense_skewpart, x))
156    

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