1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
|
#### Containing all cbind2() and rbind2() methods for all our Matrices
###-- General -----------------------------------------------------------
###-- Dense, incl Diagonal ----------------------------------------------
###-- Sparse ------------------------------------------------------------
setMethod("cbind2", signature(x = "sparseMatrix", y = "matrix"),
function(x, y) cbind2(x, .Call(dense_to_Csparse, y)))
setMethod("cbind2", signature(x = "matrix", y = "sparseMatrix"),
function(x, y) cbind2(.Call(dense_to_Csparse, x), y))
setMethod("rbind2", signature(x = "sparseMatrix", y = "matrix"),
function(x, y) rbind2(x, .Call(dense_to_Csparse, y)))
setMethod("rbind2", signature(x = "matrix", y = "sparseMatrix"),
function(x, y) rbind2(.Call(dense_to_Csparse, x), y))
## originally from ./Matrix.R : -------------------------------
## The trivial methods :
setMethod("cbind2", signature(x = "Matrix", y = "NULL"),
function(x, y) x)
setMethod("cbind2", signature(x = "Matrix", y = "missing"),
function(x, y) x)
setMethod("cbind2", signature(x = "NULL", y="Matrix"),
function(x, y) x)
## using "atomicVector" not just "numeric"
setMethod("cbind2", signature(x = "Matrix", y = "atomicVector"),
function(x, y) cbind2(x, matrix(y, nrow = nrow(x))))
setMethod("cbind2", signature(x = "atomicVector", y = "Matrix"),
function(x, y) cbind2(matrix(x, nrow = nrow(y)), y))
setMethod("cbind2", signature(x = "ANY", y = "Matrix"),
function(x, y) .bail.out.2(.Generic, class(x), class(y)))
setMethod("cbind2", signature(x = "Matrix", y = "ANY"),
function(x, y) .bail.out.2(.Generic, class(x), class(y)))
setMethod("rbind2", signature(x = "Matrix", y = "NULL"),
function(x, y) x)
setMethod("rbind2", signature(x = "Matrix", y = "missing"),
function(x, y) x)
setMethod("rbind2", signature(x = "NULL", y="Matrix"),
function(x, y) x)
setMethod("rbind2", signature(x = "Matrix", y = "atomicVector"),
function(x, y) rbind2(x, matrix(y, ncol = ncol(x))))
setMethod("rbind2", signature(x = "atomicVector", y = "Matrix"),
function(x, y) rbind2(matrix(x, ncol = ncol(y)), y))
setMethod("rbind2", signature(x = "ANY", y = "Matrix"),
function(x, y) .bail.out.2(.Generic, class(x), class(y)))
setMethod("rbind2", signature(x = "Matrix", y = "ANY"),
function(x, y) .bail.out.2(.Generic, class(x), class(y)))
## Makes sure one gets x decent error message for the unimplemented cases:
setMethod("cbind2", signature(x = "Matrix", y = "Matrix"),
function(x, y) {
rowCheck(x,y)
stop(gettextf("cbind2() method for (%s,%s) not-yet defined",
class(x), class(y)))
})
## Use a working fall back {particularly useful for sparse}:
## FIXME: implement rbind2 via "cholmod" for C* and Tsparse ones
setMethod("rbind2", signature(x = "Matrix", y = "Matrix"),
function(x, y) {
colCheck(x,y)
t(cbind2(t(x), t(y)))
})
## originally from ./denseMatrix.R : -------------------------------
### cbind2
setMethod("cbind2", signature(x = "denseMatrix", 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, geClass(x))
x@x <- c(x@x, as.double(y))
x@Dim[2] <- nc + 1L
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 = "denseMatrix"),
function(x, y) {
d <- dim(y); nr <- d[1]; nc <- d[2]
x <- rep(x, length.out = nr)
y <- as(y, geClass(y))
y@x <- c(as.double(x), y@x)
y@Dim[2] <- nc + 1L
if(is.character(dn <- y@Dimnames[[2]]))
y@Dimnames[[2]] <- c("", dn)
y
})
setMethod("cbind2", signature(x = "denseMatrix", y = "matrix"),
function(x, y) cbind2(x, as_geSimpl(y)))
setMethod("cbind2", signature(x = "matrix", y = "denseMatrix"),
function(x, y) cbind2(as_geSimpl(x), y))
setMethod("cbind2", signature(x = "denseMatrix", y = "denseMatrix"),
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, geClass(x))
y <- as(y, geClass(y))
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 character(ncx),
if(!is.null(cy)) cy else character(ncy))
x@Dimnames <- list(rn, cn)
}
x
})
### rbind2 -- analogous to cbind2 --- more to do for @x though:
setMethod("rbind2", signature(x = "denseMatrix", y = "numeric"),
function(x, y) {
if(is.character(dn <- x@Dimnames[[1]])) dn <- c(dn, "")
y <- rbind2(as(x,"matrix"), y)
new(paste(.M.kind(y), "geMatrix", sep=''), x = c(y),
Dim = x@Dim + 1:0, Dimnames = list(dn, x@Dimnames[[2]]))
})
## the same, (x,y) <-> (y,x):
setMethod("rbind2", signature(x = "numeric", y = "denseMatrix"),
function(x, y) {
if(is.character(dn <- y@Dimnames[[1]])) dn <- c("", dn)
x <- rbind2(x, as(y,"matrix"))
new(paste(.M.kind(x), "geMatrix", sep=''), x = c(x),
Dim = y@Dim + 1:0, Dimnames = list(dn, y@Dimnames[[2]]))
})
setMethod("rbind2", signature(x = "denseMatrix", y = "matrix"),
function(x, y) rbind2(x, as_geSimpl(y)))
setMethod("rbind2", signature(x = "matrix", y = "denseMatrix"),
function(x, y) rbind2(as_geSimpl(x), y))
setMethod("rbind2", signature(x = "denseMatrix", y = "denseMatrix"),
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 character(nrx),
if(!is.null(ry)) ry else character(nry)),
if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]])
} else list(NULL, NULL)
## beware of (packed) triangular, symmetric, -> "cheap" (FIXME):
x <- rbind2(as(x,"matrix"), as(y,"matrix"))
new(paste(.M.kind(x), "geMatrix", sep=''), x = c(x),
Dim = c(nrx + nry, nc), Dimnames = dn)
})
## originally from ./diagMatrix.R : --------------------------------------
## For diagonalMatrix: preserve sparseness {not always optimal, but "the law"}
## hack to suppress the obnoxious dispatch ambiguity warnings:
diag2Sp <- function(x) suppressWarnings(as(x, "CsparseMatrix"))
setMethod("cbind2", signature(x = "diagonalMatrix", y = "sparseMatrix"),
function(x,y) cbind2(diag2Sp(x), as(y,"CsparseMatrix")))
setMethod("cbind2", signature(x = "sparseMatrix", y = "diagonalMatrix"),
function(x,y) cbind2(as(x,"CsparseMatrix"), diag2Sp(y)))
setMethod("rbind2", signature(x = "diagonalMatrix", y = "sparseMatrix"),
function(x,y) rbind2(diag2Sp(x), as(y,"CsparseMatrix")))
setMethod("rbind2", signature(x = "sparseMatrix", y = "diagonalMatrix"),
function(x,y) rbind2(as(x,"CsparseMatrix"), diag2Sp(y)))
## in order to evade method dispatch ambiguity, but still remain "general"
## we use this hack instead of signature x = "diagonalMatrix"
for(cls in names(getClass("diagonalMatrix")@subclasses)) {
setMethod("cbind2", signature(x = cls, y = "matrix"),
function(x,y) cbind2(diag2Sp(x), .Call(dense_to_Csparse, y)))
setMethod("cbind2", signature(x = "matrix", y = cls),
function(x,y) cbind2(.Call(dense_to_Csparse, x), diag2Sp(y)))
setMethod("rbind2", signature(x = cls, y = "matrix"),
function(x,y) rbind2(diag2Sp(x), .Call(dense_to_Csparse, y)))
setMethod("rbind2", signature(x = "matrix", y = cls),
function(x,y) rbind2(.Call(dense_to_Csparse, x), diag2Sp(y)))
## These are already defined for "Matrix"
## -- repeated here for method dispatch disambiguation {"design-FIXME" ?}
setMethod("cbind2", signature(x = cls, y = "atomicVector"),
function(x, y) cbind2(x, matrix(y, nrow = nrow(x))))
setMethod("cbind2", signature(x = "atomicVector", y = cls),
function(x, y) cbind2(matrix(x, nrow = nrow(y)), y))
setMethod("rbind2", signature(x = cls, y = "atomicVector"),
function(x, y) rbind2(x, matrix(y, ncol = ncol(x))))
setMethod("rbind2", signature(x = "atomicVector", y = cls),
function(x, y) rbind2(matrix(x, ncol = ncol(y)), y))
}
## originally from ./dsparseMatrix.R : --------------------------------
## Fast - almost non-checking methods
.cbind2Csp <- function(x,y) .Call(Csparse_horzcat, as_Csp2(x), as_Csp2(y))
.rbind2Csp <- function(x,y) .Call(Csparse_vertcat, as_Csp2(x), as_Csp2(y))
setMethod("cbind2", signature(x = "sparseMatrix", y = "sparseMatrix"),
function(x, y) {
nr <- rowCheck(x,y)
## beware of (packed) triangular, symmetric, ...
hasDN <- !identical(c(dnx <- dimnames(x),
dny <- dimnames(y)),
list(NULL,NULL,NULL,NULL))
ans <- .Call(Csparse_horzcat, as_Csp2(x), as_Csp2(y))
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 character(ncol(x)),
if(!is.null(cy)) cy else character(ncol(y)))
ans@Dimnames <- list(rn, cn)
}
ans
})
setMethod("rbind2", signature(x = "sparseMatrix", y = "sparseMatrix"),
function(x, y) {
nc <- colCheck(x,y)
## beware of (packed) triangular, symmetric, ...
hasDN <- !identical(c(dnx <- dimnames(x),
dny <- dimnames(y)),
list(NULL,NULL,NULL,NULL))
ans <- .Call(Csparse_vertcat, as_Csp2(x), as_Csp2(y))
if(hasDN) {
## R and S+ are different in which names they take
## if they differ -- but there's no warning in any case
cn <- if(!is.null(dnx[[2]])) dnx[[2]] else dny[[2]]
rx <- dnx[[1]] ; ry <- dny[[1]]
rn <- if(is.null(rx) && is.null(ry)) NULL
else c(if(!is.null(rx)) rx else character(nrow(x)),
if(!is.null(ry)) ry else character(nrow(y)))
ans@Dimnames <- list(rn, cn)
}
ans
})
if(FALSE) {
## FIXME
##------------- maybe a bit faster --- but too much to maintain
## would have to be done for "rbind2" as well ...
setMethod("cbind2", signature(x = "sparseMatrix", y = "numeric"),
function(x, y) {
d <- dim(x); nr <- d[1]; nc <- d[2]; cl <- class(x)
x <- as(x, "CsparseMatrix")
if(nr > 0) {
y <- rep(y, length.out = nr) # 'silent procrustes'
n0y <- y != 0
n.e <- length(x@i)
x@i <- c(x@i, (0:(nr-1))[n0y])
x@p <- c(x@p, n.e + sum(n0y))
x@x <- c(x@x, y[n0y])
} else { ## nr == 0
}
x@Dim[2] <- nc + 1L
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 = "sparseMatrix"),
function(x, y) {
d <- dim(y); nr <- d[1]; nc <- d[2]; cl <- class(y)
y <- as(y, "CsparseMatrix")
if(nr > 0) {
x <- rep(x, length.out = nr) # 'silent procrustes'
n0x <- x != 0
y@i <- c((0:(nr-1))[n0x], y@i)
y@p <- c(0:0, sum(n0x) + y@p)
y@x <- c(x[n0x], y@x)
} else { ## nr == 0
}
y@Dim[2] <- nc + 1L
if(is.character(dn <- y@Dimnames[[2]]))
y@Dimnames[[2]] <- c(dn, "")
y
})
}## -- no longer
|
