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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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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 : maechler 1575
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 : maechler 1618 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 : bates 1460
43 : maechler 1618
44 : bates 1460 ## 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 : maechler 1391 setMethod("as.numeric", signature(x = "ddenseMatrix"),
56 :     function(x, ...) as(x, "dgeMatrix")@x)
57 :    
58 : maechler 792 ## -- see also ./Matrix.R e.g., for a show() method
59 :    
60 : bates 686 ## These methods are the 'fallback' methods for all dense numeric
61 : maechler 792 ## matrices in that they simply coerce the ddenseMatrix to a
62 :     ## dgeMatrix. Methods for special forms override these.
63 : bates 686
64 :     setMethod("norm", signature(x = "ddenseMatrix", type = "missing"),
65 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
66 :    
67 :     setMethod("norm", signature(x = "ddenseMatrix", type = "character"),
68 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
69 :    
70 :     setMethod("rcond", signature(x = "ddenseMatrix", type = "missing"),
71 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix")))
72 :    
73 :     setMethod("rcond", signature(x = "ddenseMatrix", type = "character"),
74 :     function(x, type, ...) callGeneric(as(x, "dgeMatrix"), type))
75 :    
76 : maechler 946 ## Not really useful; now require *identical* class for result:
77 :     ## setMethod("t", signature(x = "ddenseMatrix"),
78 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
79 : bates 686
80 : maechler 1087 setMethod("tcrossprod", signature(x = "ddenseMatrix", y = "missing"),
81 :     function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
82 : bates 686
83 :     setMethod("crossprod", signature(x = "ddenseMatrix", y = "missing"),
84 :     function(x, y = NULL) callGeneric(as(x, "dgeMatrix")))
85 :    
86 :     setMethod("diag", signature(x = "ddenseMatrix"),
87 :     function(x = 1, nrow, ncol = n) callGeneric(as(x, "dgeMatrix")))
88 :    
89 : bates 1463 ## These methods cause an infinite loop in pre-2.4.0
90 :     ## setMethod("solve", signature(a = "ddenseMatrix", b = "missing"),
91 :     ## function(a, b, ...) callGeneric(as(a, "dgeMatrix")))
92 : bates 686
93 : bates 1463 ## setMethod("solve", signature(a = "ddenseMatrix", b = "ANY"),
94 :     ## function(a, b, ...) callGeneric(as(a, "dgeMatrix"), b))
95 : bates 686
96 : bates 1463 ## 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 : bates 686 setMethod("lu", signature(x = "ddenseMatrix"),
104 :     function(x, ...) callGeneric(as(x, "dgeMatrix")))
105 :    
106 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "missing"),
107 : bates 686 function(x, logarithm, ...) callGeneric(as(x, "dgeMatrix")))
108 :    
109 : maechler 856 setMethod("determinant", signature(x = "ddenseMatrix", logarithm = "logical"),
110 : bates 686 function(x, logarithm, ...)
111 :     callGeneric(as(x, "dgeMatrix"), logarithm))
112 :    
113 : maechler 954 ## now done for "dMatrix":
114 :     ## setMethod("expm", signature(x = "ddenseMatrix"),
115 :     ## function(x) callGeneric(as(x, "dgeMatrix")))
116 : bates 686
117 :     setMethod("Schur", signature(x = "ddenseMatrix", vectors = "missing"),
118 :     function(x, vectors, ...) callGeneric(as(x, "dgeMatrix")))
119 :    
120 :     setMethod("Schur", signature(x = "ddenseMatrix", vectors = "logical"),
121 :     function(x, vectors, ...) callGeneric(as(x, "dgeMatrix"), vectors))
122 :    
123 : maechler 792
124 : maechler 1331 ## Cheap version: work via "dgeMatrix" and use the group methods there:
125 :     ## FIXME(?): try to preserve "symmetric", "triangular", ...
126 :     setMethod("Arith", ## "+", "-", "*", "^", "%%", "%/%", "/"
127 :     signature(e1 = "ddenseMatrix", e2 = "ddenseMatrix"),
128 :     function(e1, e2) callGeneric(as(e1, "dgeMatrix"),
129 :     as(e2, "dgeMatrix")))
130 :     setMethod("Arith",
131 :     signature(e1 = "ddenseMatrix", e2 = "numeric"),
132 :     function(e1, e2) callGeneric(as(e1, "dgeMatrix"), e2))
133 :     setMethod("Arith",
134 :     signature(e1 = "numeric", e2 = "ddenseMatrix"),
135 :     function(e1, e2) callGeneric(e1, as(e2, "dgeMatrix")))
136 : maechler 908
137 : maechler 1331 setMethod("Math",
138 :     signature(x = "ddenseMatrix"),
139 :     function(x) callGeneric(as(x, "dgeMatrix")))
140 :    
141 :    
142 :    
143 :     ### for R 2.2.x (and later): -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
144 :    
145 : maechler 925 ### cbind2
146 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "numeric"),
147 :     function(x, y) {
148 :     d <- dim(x); nr <- d[1]; nc <- d[2]
149 :     y <- rep(y, length.out = nr) # 'silent procrustes'
150 :     ## beware of (packed) triangular, symmetric, ...
151 :     x <- as(x, "dgeMatrix")
152 :     x@x <- c(x@x, as.double(y))
153 :     x@Dim[2] <- nc + 1:1
154 :     if(is.character(dn <- x@Dimnames[[2]]))
155 :     x@Dimnames[[2]] <- c(dn, "")
156 :     x
157 :     })
158 :     ## the same, (x,y) <-> (y,x):
159 :     setMethod("cbind2", signature(x = "numeric", y = "ddenseMatrix"),
160 :     function(x, y) {
161 :     d <- dim(y); nr <- d[1]; nc <- d[2]
162 :     x <- rep(x, length.out = nr)
163 :     y <- as(y, "dgeMatrix")
164 :     y@x <- c(as.double(x), y@x)
165 :     y@Dim[2] <- nc + 1:1
166 :     if(is.character(dn <- y@Dimnames[[2]]))
167 :     y@Dimnames[[2]] <- c("", dn)
168 :     y
169 :     })
170 : maechler 908
171 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "matrix"),
172 :     function(x, y) callGeneric(x, as(y, "dgeMatrix")))
173 :     setMethod("cbind2", signature(x = "matrix", y = "ddenseMatrix"),
174 :     function(x, y) callGeneric(as(x, "dgeMatrix"), y))
175 : maechler 908
176 : maechler 1331 setMethod("cbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
177 :     function(x, y) {
178 :     nr <- rowCheck(x,y)
179 :     ncx <- x@Dim[2]
180 :     ncy <- y@Dim[2]
181 :     ## beware of (packed) triangular, symmetric, ...
182 :     hasDN <- !is.null(dnx <- dimnames(x)) |
183 :     !is.null(dny <- dimnames(y))
184 :     x <- as(x, "dgeMatrix")
185 :     y <- as(y, "dgeMatrix")
186 :     x@x <- c(x@x, y@x)
187 :     x@Dim[2] <- ncx + ncy
188 :     if(hasDN) {
189 :     ## R and S+ are different in which names they take
190 :     ## if they differ -- but there's no warning in any case
191 :     rn <- if(!is.null(dnx[[1]])) dnx[[1]] else dny[[1]]
192 :     cx <- dnx[[2]] ; cy <- dny[[2]]
193 :     cn <- if(is.null(cx) && is.null(cy)) NULL
194 :     else c(if(!is.null(cx)) cx else rep.int("", ncx),
195 :     if(!is.null(cy)) cy else rep.int("", ncy))
196 :     x@Dimnames <- list(rn, cn)
197 :     }
198 :     x
199 :     })
200 : maechler 908
201 : maechler 925 ### rbind2 -- analogous to cbind2 --- more to do for @x though:
202 : maechler 908
203 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "numeric"),
204 :     function(x, y) {
205 :     if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
206 :     new("dgeMatrix", Dim = x@Dim + 1:0,
207 :     Dimnames = list(dn, x@Dimnames[[2]]),
208 :     x = c(rbind2(as(x,"matrix"), y)))
209 :     })
210 :     ## the same, (x,y) <-> (y,x):
211 :     setMethod("rbind2", signature(x = "numeric", y = "ddenseMatrix"),
212 :     function(x, y) {
213 :     if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
214 :     new("dgeMatrix", Dim = y@Dim + 1:0,
215 :     Dimnames = list(dn, y@Dimnames[[2]]),
216 :     x = c(rbind2(x, as(y,"matrix"))))
217 :     })
218 : maechler 925
219 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "matrix"),
220 :     function(x, y) callGeneric(x, as(y, "dgeMatrix")))
221 :     setMethod("rbind2", signature(x = "matrix", y = "ddenseMatrix"),
222 :     function(x, y) callGeneric(as(x, "dgeMatrix"), y))
223 : maechler 925
224 : maechler 1331 setMethod("rbind2", signature(x = "ddenseMatrix", y = "ddenseMatrix"),
225 :     function(x, y) {
226 :     nc <- colCheck(x,y)
227 :     nrx <- x@Dim[1]
228 :     nry <- y@Dim[1]
229 :     dn <-
230 :     if(!is.null(dnx <- dimnames(x)) |
231 :     !is.null(dny <- dimnames(y))) {
232 :     ## R and S+ are different in which names they take
233 :     ## if they differ -- but there's no warning in any case
234 :     list(if(is.null(rx <- dnx[[1]]) && is.null(ry <- dny[[1]]))
235 :     NULL else
236 :     c(if(!is.null(rx)) rx else rep.int("", nrx),
237 :     if(!is.null(ry)) ry else rep.int("", nry)),
238 :     if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
239 : maechler 925
240 : maechler 1331 } else list(NULL, NULL)
241 :     ## beware of (packed) triangular, symmetric, ...
242 :     new("dgeMatrix", Dim = c(nrx + nry, nc), Dimnames = dn,
243 :     x = c(rbind2(as(x,"matrix"), as(y,"matrix"))))
244 :     })
245 : maechler 1575
246 :     ### FIXME: band() et al should be extended from "ddense" to "dense" !
247 :     ### However, needs much work to generalize dup_mMatrix_as_dgeMatrix()
248 :    
249 : bates 1453 ## NB: have extra tril(), triu() methods for symmetric ["dsy" and "dsp"] and
250 :     ## for triangular ["dtr" and "dtp"]
251 :     setMethod("tril", "ddenseMatrix",
252 :     function(x, k = 0, ...) {
253 :     k <- as.integer(k[1])
254 :     dd <- dim(x); sqr <- dd[1] == dd[2]
255 :     stopifnot(-dd[1] <= k, k <= dd[1]) # had k <= 0
256 :     ## returns "lower triangular" if k <= 0 && sqr
257 :     .Call(ddense_band, x, -dd[1], k)
258 :     })
259 :    
260 :     setMethod("triu", "ddenseMatrix",
261 :     function(x, k = 0, ...) {
262 :     k <- as.integer(k[1])
263 :     dd <- dim(x); sqr <- dd[1] == dd[2]
264 :     stopifnot(-dd[1] <= k, k <= dd[1]) # had k >= 0
265 :     ## returns "upper triangular" if k >= 0
266 :     .Call(ddense_band, x, k, dd[2])
267 :     })
268 :    
269 :     setMethod("band", "ddenseMatrix",
270 :     function(x, k1, k2, ...) {
271 :     k1 <- as.integer(k1[1])
272 :     k2 <- as.integer(k2[1])
273 :     dd <- dim(x); sqr <- dd[1] == dd[2]
274 :     stopifnot(-dd[1] <= k1, k1 <= k2, k2 <= dd[1])
275 :     r <- .Call(ddense_band, x, k1, k2)
276 :     if (k1 < 0 && k1 == -k2 && isSymmetric(x)) ## symmetric
277 :     as(r, paste(.M.kind(x), "syMatrix", sep=''))
278 :     else
279 :     r
280 :     })

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