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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 2158, Fri Mar 28 17:07:54 2008 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) {
9            if (class(from) != "dgeMatrix")            if (class(from) != "dgeMatrix")
10                from <- .Call(dup_mMatrix_as_dgeMatrix, from)                .Call(dup_mMatrix_as_dgeMatrix, from)
11            from            else from
12        })        })
13    
14    
15  ## d(ouble) to l(ogical):  ## d(ouble) to l(ogical):
16  setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)  setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
17  setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)  setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
18  setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)  setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
19  setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)  setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
20  setAs("dspMatrix", "lspMatrix", d2l_Matrix)  setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
21    
22  setAs("ddenseMatrix", "CsparseMatrix",  setAs("ddenseMatrix", "CsparseMatrix",
23        function(from) {        function(from) {
24            if (class(from) != "dgeMatrix")            if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
25                from <- .Call(dup_mMatrix_as_dgeMatrix, from)                as_Csparse(from)
26            .Call(dense_to_Csparse, from)            else .Call(dense_to_Csparse, from)
27        })        })
28    
29  ## special case  ## special case
# Line 32  Line 31 
31        function(from) .Call(dense_to_Csparse, from))        function(from) .Call(dense_to_Csparse, from))
32    
33  setAs("matrix", "CsparseMatrix",  setAs("matrix", "CsparseMatrix",
34        function(from)        function(from) .Call(dense_to_Csparse, from))
35        .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))  ##       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  ## special case needed in the Matrix function
45  setAs("matrix", "dgCMatrix",  setAs("matrix", "dgCMatrix",
# Line 56  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", norm = "missing"),
71            function(x, type, ...) callGeneric(as(x, "dgeMatrix")))            function(x, norm, ...) rcond(as(x, "dgeMatrix"), ...))
72    
73  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", norm = "character"),
74            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, norm, ...) rcond(as(x, "dgeMatrix"), norm, ...))
75    
76  ## Not really useful; now require *identical* class for result:  ## Not really useful; now require *identical* class for result:
77  ## setMethod("t", signature(x = "ddenseMatrix"),  ## setMethod("t", signature(x = "ddenseMatrix"),
78  ##        function(x) callGeneric(as(x, "dgeMatrix")))  ##        function(x) callGeneric(as(x, "dgeMatrix")))
79    
80  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81            function(x, y = NULL) 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  ## These methods cause an infinite loop in pre-2.4.0  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
90  ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),            function(a, b, ...) solve(as(a, "dgeMatrix")))
 ##           function(a, b, ...) callGeneric(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  ## General method for dense matrix multiplication in case specific methods
96  ## have not been defined.  ## have not been defined.
# Line 95  Line 100 
100            valueClass = "dgeMatrix")            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"), 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))
113    
114  ## now done for "dMatrix":  ## now done for "dMatrix":
115  ## setMethod("expm", signature(x = "ddenseMatrix"),  ## setMethod("expm", signature(x = "ddenseMatrix"),
116  ##           function(x) callGeneric(as(x, "dgeMatrix")))  ##           function(x) callGeneric(as(x, "dgeMatrix")))
117    
 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")))  
   
118  setMethod("Math",  setMethod("Math",
119            signature(x = "ddenseMatrix"),            signature(x = "ddenseMatrix"),
120            function(x) callGeneric(as(x, "dgeMatrix")))            function(x) callGeneric(as(x, "dgeMatrix")))
121    
122    
123    
124  ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --  .trilDense <- function(x, k = 0, ...) {
125        k <- as.integer(k[1])
126  ### cbind2      d <- dim(x)
127  setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),      stopifnot(-d[1] <= k, k <= d[1]) # had k <= 0
128            function(x, y) {      ## returns "lower triangular" if k <= 0 && sqr
129                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)  
130                }                }
               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()  
   
131  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and  ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
132  ##     for triangular ["dtr" and "dtp"]  ##     for triangular ["dtr" and "dtp"]
133  setMethod("tril", "ddenseMatrix",  setMethod("tril", "denseMatrix", .trilDense)
134            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)  
           })  
135    
136  setMethod("triu", "ddenseMatrix",  .triuDense <- function(x, k = 0, ...) {
           function(x, k = 0, ...) {  
137                k <- as.integer(k[1])                k <- as.integer(k[1])
138                dd <- dim(x); sqr <- dd[1] == dd[2]      d <- dim(x)
139                stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0      stopifnot(-d[1] <= k, k <= d[1]) # had k >= 0
140                ## returns "upper triangular" if k >= 0                ## returns "upper triangular" if k >= 0
141                .Call(ddense_band, x, k, dd[2])      .Call(dense_band, x, k, d[2])
142            })  }
143    setMethod("triu", "denseMatrix", .triuDense)
144    setMethod("triu",      "matrix", .triuDense)
145    
146  setMethod("band", "ddenseMatrix",  .bandDense <- function(x, k1, k2, ...) {
           function(x, k1, k2, ...) {  
147                k1 <- as.integer(k1[1])                k1 <- as.integer(k1[1])
148                k2 <- as.integer(k2[1])                k2 <- as.integer(k2[1])
149                dd <- dim(x); sqr <- dd[1] == dd[2]                dd <- dim(x); sqr <- dd[1] == dd[2]
150                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])                stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
151                r <- .Call(ddense_band, x, k1, k2)      r <- .Call(dense_band, x, k1, k2)
152                if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric      if (sqr &&  k1 < 0 &&  k1 == -k2  && isSymmetric(x)) ## symmetric
153                    as(r, paste(.M.kind(x), "syMatrix", sep=''))          forceSymmetric(r)
154                else                else
155                    r                    r
156            })  }
157    setMethod("band", "denseMatrix", .bandDense)
158    setMethod("band",      "matrix", .bandDense)
159    
160    
161    setMethod("symmpart", signature(x = "ddenseMatrix"),
162              function(x) .Call(ddense_symmpart, x))
163    setMethod("skewpart", signature(x = "ddenseMatrix"),
164              function(x) .Call(ddense_skewpart, x))
165    

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