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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 2052, Wed Aug 15 13:33:19 2007 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    ## d(ouble) to l(ogical):
15    setAs("dgeMatrix", "lgeMatrix", function(from) d2l_Matrix(from, "dgeMatrix"))
16    setAs("dsyMatrix", "lsyMatrix", function(from) d2l_Matrix(from, "dsyMatrix"))
17    setAs("dspMatrix", "lspMatrix", function(from) d2l_Matrix(from, "dspMatrix"))
18    setAs("dtrMatrix", "ltrMatrix", function(from) d2l_Matrix(from, "dtrMatrix"))
19    setAs("dtpMatrix", "ltpMatrix", function(from) d2l_Matrix(from, "dtpMatrix"))
20    
21    setAs("ddenseMatrix", "CsparseMatrix",
22          function(from) {
23              if (class(from) != "dgeMatrix") # don't lose symmetry/triangularity/...
24                  as_Csparse(from)
25              else .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"),
54              function(x, ...) as(x, "dgeMatrix")@x)
55    
56  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
57    
58  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 18  Line 71 
71  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
72            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
73    
74  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
75            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
76    ##        function(x) callGeneric(as(x, "dgeMatrix")))
77    
78  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
79            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
80    
81  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),  setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
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) callGeneric(as(x, "dgeMatrix")))
86    
87  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),  setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
88            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))            function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
# Line 36  Line 90 
90  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),  setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
91            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))            function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
92    
93    ## General method for dense matrix multiplication in case specific methods
94    ## have not been defined.
95    setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
96              function(x, y) .Call(dgeMatrix_matrix_mm,
97                                   .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
98              valueClass = "dgeMatrix")
99    
100  setMethod("lu", signature(x = "ddenseMatrix"),  setMethod("lu", signature(x = "ddenseMatrix"),
101            function(x, ...) callGeneric(as(x, "dgeMatrix")))            function(x, ...) callGeneric(as(x, "dgeMatrix")))
102    
103    setMethod("chol", signature(x = "ddenseMatrix", pivot = "ANY"), cholMat)
104    
105  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),  setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
106            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))            function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
107    
# Line 46  Line 109 
109            function(x, logarithm, ...)            function(x, logarithm, ...)
110            callGeneric(as(x, "dgeMatrix"), logarithm))            callGeneric(as(x, "dgeMatrix"), logarithm))
111    
112  setMethod("expm", signature(x = "ddenseMatrix"),  ## now done for "dMatrix":
113            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
114    ##           function(x) callGeneric(as(x, "dgeMatrix")))
115    
116  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
117            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
# Line 56  Line 120 
120            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
121    
122    
123  ### NAMESPACE must export this -- also only for R version 2.2.x:  setMethod("Math",
124  if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {            signature(x = "ddenseMatrix"),
125      ## for R 2.2.x (and later):            function(x) callGeneric(as(x, "dgeMatrix")))
126    
 ### 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"))))  
               })  
127    
128  }## R-2.2.x ff  ### FIXME: band() et al should be extended from "ddense" to "dense" !
129    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
130    
131    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
132    ##     for triangular ["dtr" and "dtp"]
133    setMethod("tril", "ddenseMatrix",
134              function(x, k = 0, ...) {
135                  k <- as.integer(k[1])
136                  dd <- dim(x); sqr <- dd[1] == dd[2]
137                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
138                  ## returns "lower triangular" if k <= 0 && sqr
139                  .Call(ddense_band, x, -dd[1], k)
140              })
141    
142    setMethod("triu", "ddenseMatrix",
143              function(x, k = 0, ...) {
144                  k <- as.integer(k[1])
145                  dd <- dim(x); sqr <- dd[1] == dd[2]
146                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
147                  ## returns "upper triangular" if k >= 0
148                  .Call(ddense_band, x, k, dd[2])
149              })
150    
151    setMethod("band", "ddenseMatrix",
152              function(x, k1, k2, ...) {
153                  k1 <- as.integer(k1[1])
154                  k2 <- as.integer(k2[1])
155                  dd <- dim(x); sqr <- dd[1] == dd[2]
156                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
157                  r <- .Call(ddense_band, x, k1, k2)
158                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
159                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
160                  else
161                      r
162              })

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