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[matrix] Annotation of /pkg/Matrix/R/ddenseMatrix.R
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Annotation of /pkg/Matrix/R/ddenseMatrix.R

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Revision 1463 - (view) (download)
Original Path: pkg/R/ddenseMatrix.R

1 : bates 686 ### Define Methods that can be inherited for all subclasses
2 :    
3 : maechler 1447 ## This replaces many "d..Matrix" -> "dgeMatrix" ones
4 :     ## >> but << needs all sub(sub(sub)) classes of "ddenseMatrix" listed
5 :     ## ----- in ../src/Mutils.c
6 : bates 1460
7 :     ## Should this method return 'from' without duplication when it has
8 :     ## class dgeMatrix?
9 : maechler 1447 setAs("ddenseMatrix", "dgeMatrix",
10 : bates 1463 function(from) {
11 :     if (class(from) != "dgeMatrix")
12 :     from <- .Call(dup_mMatrix_as_dgeMatrix, from)
13 :     from
14 :     })
15 :    
16 : maechler 1447 ## d(ouble) to l(ogical):
17 : maechler 956 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 : bates 1460 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 :     .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
37 :    
38 :     ## special case needed in the Matrix function
39 :     setAs("matrix", "dgCMatrix",
40 :     function(from) {
41 :     storage.mode(from) <- "double"
42 :     .Call(dense_to_Csparse, from)
43 :     })
44 :    
45 :     setAs("numeric", "CsparseMatrix",
46 :     function(from)
47 :     .Call(dense_to_Csparse, .Call(dup_mMatrix_as_dgeMatrix, from)))
48 :    
49 : maechler 1391 setMethod("as.numeric", signature(x = "ddenseMatrix"),
50 :     function(x, ...) as(x, "dgeMatrix")@x)
51 :    
52 : maechler 792 ## -- see also ./Matrix.R e.g., for a show() method
53 :    
54 : bates 686 ## These methods are the 'fallback' methods for all dense numeric
55 : maechler 792 ## matrices in that they simply coerce the ddenseMatrix to a
56 :     ## dgeMatrix. Methods for special forms override these.
57 : bates 686
58 :     setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
59 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
60 :    
61 :     setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
62 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
63 :    
64 :     setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),
65 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
66 :    
67 :     setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
68 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
69 :    
70 : maechler 946 ## Not really useful; now require *identical* class for result:
71 :     ## setMethod("t", signature(x = "ddenseMatrix"),
72 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
73 : bates 686
74 : maechler 1087 setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
75 :     function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
76 : bates 686
77 :     setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
78 :     function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
79 :    
80 :     setMethod("diag", signature(x = "ddenseMatrix"),
81 :     function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
82 :    
83 : bates 1463 ## These methods cause an infinite loop in pre-2.4.0
84 :     ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
85 :     ## function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
86 : bates 686
87 : bates 1463 ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
88 :     ## function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
89 : bates 686
90 : bates 1463 ## General method for dense matrix multiplication in case specific methods
91 :     ## have not been defined.
92 :     setMethod("%*%", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
93 :     function(x, y) .Call(dgeMatrix_matrix_mm,
94 :     .Call(dup_mMatrix_as_dgeMatrix, x), y, FALSE),
95 :     valueClass = "dgeMatrix")
96 :    
97 : bates 686 setMethod("lu", signature(x = "ddenseMatrix"),
98 :     function(x, ...) callGeneric(as(x, "dgeMatrix")))
99 :    
100 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
101 : bates 686 function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
102 :    
103 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
104 : bates 686 function(x, logarithm, ...)
105 :     callGeneric(as(x, "dgeMatrix"), logarithm))
106 :    
107 : maechler 954 ## now done for "dMatrix":
108 :     ## setMethod("expm", signature(x = "ddenseMatrix"),
109 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
110 : bates 686
111 :     setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
112 :     function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
113 :    
114 :     setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),
115 :     function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
116 :    
117 : maechler 792
118 : maechler 1331 ## Cheap version: work via "dgeMatrix" and use the group methods there:
119 :     ## FIXME(?): try to preserve "symmetric", "triangular", ...
120 :     setMethod("Arith", ## "+", "-", "*", "^", "%%", "%/%", "/"
121 :     signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
122 :     function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
123 :     as(e2, "dgeMatrix")))
124 :     setMethod("Arith",
125 :     signature(e1 = "ddenseMatrix", e2 = "numeric"),
126 :     function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
127 :     setMethod("Arith",
128 :     signature(e1 = "numeric", e2 = "ddenseMatrix"),
129 :     function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
130 : maechler 908
131 : maechler 1331 setMethod("Math",
132 :     signature(x = "ddenseMatrix"),
133 :     function(x) callGeneric(as(x, "dgeMatrix")))
134 :    
135 :    
136 :    
137 :     ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
138 :    
139 : maechler 925 ### cbind2
140 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
141 :     function(x, y) {
142 :     d <- dim(x); nr <- d[1]; nc <- d[2]
143 :     y <- rep(y, length.out = nr) # 'silent procrustes'
144 :     ## beware of (packed) triangular, symmetric, ...
145 :     x <- as(x, "dgeMatrix")
146 :     x@x <- c(x@x, as.double(y))
147 :     x@Dim[2] <- nc + 1:1
148 :     if(is.character(dn <- x@Dimnames[[2]]))
149 :     x@Dimnames[[2]] <- c(dn, "")
150 :     x
151 :     })
152 :     ## the same, (x,y) <-> (y,x):
153 :     setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
154 :     function(x, y) {
155 :     d <- dim(y); nr <- d[1]; nc <- d[2]
156 :     x <- rep(x, length.out = nr)
157 :     y <- as(y, "dgeMatrix")
158 :     y@x <- c(as.double(x), y@x)
159 :     y@Dim[2] <- nc + 1:1
160 :     if(is.character(dn <- y@Dimnames[[2]]))
161 :     y@Dimnames[[2]] <- c("", dn)
162 :     y
163 :     })
164 : maechler 908
165 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
166 :     function(x, y) callGeneric(x, as(y, "dgeMatrix")))
167 :     setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
168 :     function(x, y) callGeneric(as(x, "dgeMatrix"), y))
169 : maechler 908
170 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
171 :     function(x, y) {
172 :     nr <- rowCheck(x,y)
173 :     ncx <- x@Dim[2]
174 :     ncy <- y@Dim[2]
175 :     ## beware of (packed) triangular, symmetric, ...
176 :     hasDN <- !is.null(dnx <- dimnames(x)) |
177 :     !is.null(dny <- dimnames(y))
178 :     x <- as(x, "dgeMatrix")
179 :     y <- as(y, "dgeMatrix")
180 :     x@x <- c(x@x, y@x)
181 :     x@Dim[2] <- ncx + ncy
182 :     if(hasDN) {
183 :     ## R and S+ are different in which names they take
184 :     ## if they differ -- but there's no warning in any case
185 :     rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
186 :     cx <- dnx[[2]] ; cy <- dny[[2]]
187 :     cn <- if(is.null(cx) && is.null(cy)) NULL
188 :     else c(if(!is.null(cx)) cx else rep.int("", ncx),
189 :     if(!is.null(cy)) cy else rep.int("", ncy))
190 :     x@Dimnames <- list(rn, cn)
191 :     }
192 :     x
193 :     })
194 : maechler 908
195 : maechler 925 ### rbind2 -- analogous to cbind2 --- more to do for @x though:
196 : maechler 908
197 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
198 :     function(x, y) {
199 :     if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
200 :     new("dgeMatrix", Dim = x@Dim + 1:0,
201 :     Dimnames = list(dn, x@Dimnames[[2]]),
202 :     x = c(rbind2(as(x,"matrix"), y)))
203 :     })
204 :     ## the same, (x,y) <-> (y,x):
205 :     setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
206 :     function(x, y) {
207 :     if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
208 :     new("dgeMatrix", Dim = y@Dim + 1:0,
209 :     Dimnames = list(dn, y@Dimnames[[2]]),
210 :     x = c(rbind2(x, as(y,"matrix"))))
211 :     })
212 : maechler 925
213 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
214 :     function(x, y) callGeneric(x, as(y, "dgeMatrix")))
215 :     setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
216 :     function(x, y) callGeneric(as(x, "dgeMatrix"), y))
217 : maechler 925
218 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
219 :     function(x, y) {
220 :     nc <- colCheck(x,y)
221 :     nrx <- x@Dim[1]
222 :     nry <- y@Dim[1]
223 :     dn <-
224 :     if(!is.null(dnx <- dimnames(x)) |
225 :     !is.null(dny <- dimnames(y))) {
226 :     ## R and S+ are different in which names they take
227 :     ## if they differ -- but there's no warning in any case
228 :     list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
229 :     NULL else
230 :     c(if(!is.null(rx)) rx else rep.int("", nrx),
231 :     if(!is.null(ry)) ry else rep.int("", nry)),
232 :     if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
233 : maechler 925
234 : maechler 1331 } else list(NULL, NULL)
235 :     ## beware of (packed) triangular, symmetric, ...
236 :     new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
237 :     x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
238 :     })
239 : bates 1453 ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
240 :     ## for triangular ["dtr" and "dtp"]
241 :     setMethod("tril", "ddenseMatrix",
242 :     function(x, k = 0, ...) {
243 :     k <- as.integer(k[1])
244 :     dd <- dim(x); sqr <- dd[1] == dd[2]
245 :     stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
246 :     ## returns "lower triangular" if k <= 0 && sqr
247 :     .Call(ddense_band, x, -dd[1], k)
248 :     })
249 :    
250 :     setMethod("triu", "ddenseMatrix",
251 :     function(x, k = 0, ...) {
252 :     k <- as.integer(k[1])
253 :     dd <- dim(x); sqr <- dd[1] == dd[2]
254 :     stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
255 :     ## returns "upper triangular" if k >= 0
256 :     .Call(ddense_band, x, k, dd[2])
257 :     })
258 :    
259 :     setMethod("band", "ddenseMatrix",
260 :     function(x, k1, k2, ...) {
261 :     k1 <- as.integer(k1[1])
262 :     k2 <- as.integer(k2[1])
263 :     dd <- dim(x); sqr <- dd[1] == dd[2]
264 :     stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
265 :     r <- .Call(ddense_band, x, k1, k2)
266 :     if (k1 < 0 && k1 == -k2 && isSymmetric(x)) ## symmetric
267 :     as(r, paste(.M.kind(x), "syMatrix", sep=''))
268 :     else
269 :     r
270 :     })

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