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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 925, Mon Sep 19 19:01:31 2005 UTC revision 1708, Fri Dec 22 19:53:37 2006 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    ## Should this method return 'from' without duplication when it has
8    ## class dgeMatrix?
9    setAs("ddenseMatrix", "dgeMatrix",
10          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):
17    setAs("dgeMatrix", "lgeMatrix", d2l_Matrix)
18    setAs("dtrMatrix", "ltrMatrix", d2l_Matrix)
19    setAs("dtpMatrix", "ltpMatrix", d2l_Matrix)
20    setAs("dsyMatrix", "lsyMatrix", d2l_Matrix)
21    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"),
56              function(x, ...) as(x, "dgeMatrix")@x)
57    
58  ## -- see also ./Matrix.R  e.g., for a show() method  ## -- see also ./Matrix.R  e.g., for a show() method
59    
60  ## These methods are the 'fallback' methods for all dense numeric  ## These methods are the 'fallback' methods for all dense numeric
# Line 18  Line 73 
73  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),  setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
74            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))            function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
75    
76  setMethod("t", signature(x = "ddenseMatrix"),  ## Not really useful; now require *identical* class for result:
77            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("t", signature(x = "ddenseMatrix"),
78    ##        function(x) callGeneric(as(x, "dgeMatrix")))
79    
80  setMethod("tcrossprod", signature(x = "ddenseMatrix"),  setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81            function(x) callGeneric(as(x, "dgeMatrix")))            function(x, y = NULL) callGeneric(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) callGeneric(as(x, "dgeMatrix")))
# Line 30  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 46  Line 112 
112            function(x, logarithm, ...)            function(x, logarithm, ...)
113            callGeneric(as(x, "dgeMatrix"), logarithm))            callGeneric(as(x, "dgeMatrix"), logarithm))
114    
115  setMethod("expm", signature(x = "ddenseMatrix"),  ## now done for "dMatrix":
116            function(x) callGeneric(as(x, "dgeMatrix")))  ## setMethod("expm", signature(x = "ddenseMatrix"),
117    ##           function(x) callGeneric(as(x, "dgeMatrix")))
118    
119  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),  setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
120            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
# Line 56  Line 123 
123            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))            function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
124    
125    
126  ### NAMESPACE must export this -- also only for R version 2.2.x:  ## Cheap version: work via "dgeMatrix" and use the group methods there:
127  if(paste(R.version$major, R.version$minor, sep=".") >= "2.2") {  ## FIXME(?): try to preserve "symmetric", "triangular", ...
128      ## for R 2.2.x (and later):  setMethod("Arith", ##  "+", "-", "*", "^", "%%", "%/%", "/"
129              signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
130  ### cbind2            function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
131      setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),                                         as(e2, "dgeMatrix")))
132                function(x, y) {  setMethod("Arith",
133                    d <- dim(x); nr <- d[1]; nc <- d[2]            signature(e1 = "ddenseMatrix", e2 = "numeric"),
134                    y <- rep(y, length.out = nr)# 'silent procrustes'            function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
135                    ## beware of (packed) triangular, symmetric, ...  setMethod("Arith",
136                    x <- as(x, "dgeMatrix")            signature(e1 = "numeric", e2 = "ddenseMatrix"),
137                    x@x <- c(x@x, as.double(y))            function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
138                    x@Dim[2] <- nc + 1:1  
139                    if(is.character(dn <- x@Dimnames[[2]]))  setMethod("Math",
140                        x@Dimnames[[2]] <- c(dn, "")            signature(x = "ddenseMatrix"),
141                    x            function(x) callGeneric(as(x, "dgeMatrix")))
142                })  
     ## 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"))))  
               })  
143    
144  }## R-2.2.x ff  ### FIXME: band() et al should be extended from "ddense" to "dense" !
145    ###        However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
146    
147    ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
148    ##     for triangular ["dtr" and "dtp"]
149    setMethod("tril", "ddenseMatrix",
150              function(x, k = 0, ...) {
151                  k <- as.integer(k[1])
152                  dd <- dim(x); sqr <- dd[1] == dd[2]
153                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
154                  ## returns "lower triangular" if k <= 0 && sqr
155                  .Call(ddense_band, x, -dd[1], k)
156              })
157    
158    setMethod("triu", "ddenseMatrix",
159              function(x, k = 0, ...) {
160                  k <- as.integer(k[1])
161                  dd <- dim(x); sqr <- dd[1] == dd[2]
162                  stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
163                  ## returns "upper triangular" if k >= 0
164                  .Call(ddense_band, x, k, dd[2])
165              })
166    
167    setMethod("band", "ddenseMatrix",
168              function(x, k1, k2, ...) {
169                  k1 <- as.integer(k1[1])
170                  k2 <- as.integer(k2[1])
171                  dd <- dim(x); sqr <- dd[1] == dd[2]
172                  stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
173                  r <- .Call(ddense_band, x, k1, k2)
174                  if (k1 < 0  &&  k1 == -k2  && isSymmetric(x)) ## symmetric
175                      as(r, paste(.M.kind(x), "syMatrix", sep=''))
176                  else
177                      r
178              })

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