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
|
setAs("matrix", "dgeMatrix",
function(from) .Call(dup_mMatrix_as_dgeMatrix, from))
if(FALSE)## the above is MUCH faster than
setAs("matrix", "dgeMatrix",
function(from) {
new("dgeMatrix",
x = as.double(from),
Dim = as.integer(dim(from)),
Dimnames = .M.DN(from))
})
setAs("dgeMatrix", "matrix",
function(from) {
array(from@x, dim = from@Dim, dimnames = from@Dimnames)
})
## Group Methods, see ?Arith (e.g.)
## ----- only work with NAMESPACE importFrom(methods, ..)
setMethod("Arith", ## "+", "-", "*", "^", "%%", "%/%", "/"
signature(e1 = "dgeMatrix", e2 = "dgeMatrix"),
function(e1, e2) {
## NB: triangular, symmetric, etc may need own method
d1 <- e1@Dim
d2 <- e2@Dim
eqD <- d1 == d2
if (!eqD[1])
stop("Matrices must have same number of rows for arithmetic")
same.dim <- eqD[2]
if (same.dim) {
d <- d1
dn <- dimNamesCheck(e1, e2)
}
else { # nrows differ ----> maybe recycling
if(d2[2] %% d1[2] == 0) { # nrow(e2) is a multiple
e1@x <- rep.int(e1@x, d2[2] %/% d1[2])
d <- d2
dn <- e2@Dimnames
} else if(d1[2] %% d2[2] == 0) { # nrow(e1) is a multiple
e2@x <- rep.int(e2@x, d1[2] %/% d2[2])
d <- d1
dn <- e1@Dimnames
} else
stop("number of rows are not compatible for ", .Generic)
}
## be smart and preserve, e.g., triangular, or symmetric
## but this sucks: For these,
## 'uplo' and 'diag' also must coincide or be dealt with properly
## ==> triangular, symmetric, etc may need own method
## also since their @x is `non-typical'
## if(same.dim) {
## if(extends(class(e1), class(e2))) {
## e2@x <- callGeneric(e1@x, e2@x)
## e2@Dimnames <- dn
## e2
## }
## else if(extends(class(e2), class(e1))) {
## e1@x <- callGeneric(e1@x, e2@x)
## e1@Dimnames <- dn
## e1
## }
## }
## else
new("dgeMatrix", Dim = d, Dimnames = dn,
x = callGeneric(e1@x, e2@x))
})
setMethod("Arith",
signature(e1 = "dgeMatrix", e2 = "numeric"),
function(e1, e2) {
d <- e1@Dim
le <- length(e2)
if(le == 1 || le == d[1] || prod(d) == le) { # matching dim
e1@x <- callGeneric(e1@x, as.vector(e2))
e1
} else stop ("length of 2nd arg does not match dimension of first")
})
setMethod("Arith",
signature(e1 = "numeric", e2 = "dgeMatrix"),
function(e1, e2) {
d <- e2@Dim
le <- length(e1)
if(le == 1 || le == d[1] || prod(d) == le) { # matching dim
e2@x <- callGeneric(as.vector(e1), e2@x)
e2
} else stop ("length of 1st arg does not match dimension of 2nd")
})
setMethod("Math",
signature(x = "dgeMatrix"),
function(x) {
x@x <- callGeneric(x@x)
x
})
## "Math2" is in ./dMatrix.R
## "Summary"
## "Compare" now happens in ./dMatrix.R
## -- end{group generics} -----------------------
## "[" settings are "up in" Matrix.R & denseMatrix.R
setMethod("as.vector", signature(x = "dgeMatrix", mode = "missing"),
function(x) x@x)
setMethod("norm", signature(x = "dgeMatrix", type = "missing"),
function(x, type, ...) norm(x, type = "O", ...))
setMethod("norm", signature(x = "dgeMatrix", type = "character"),
function(x, type, ...)
.Call(dgeMatrix_norm, x, type),
valueClass = "numeric")
setMethod("rcond", signature(x = "dgeMatrix", type = "missing"),
function(x, type, ...) rcond(x, type = "O", ...))
setMethod("rcond", signature(x = "dgeMatrix", type = "character"),
function(x, type, ...)
.Call(dgeMatrix_rcond, x, type),
valueClass = "numeric")
setMethod("t", signature(x = "dgeMatrix"), t_geMatrix)
## crossprod(x) & tcrossprod(x) :
setMethod("crossprod", signature(x = "dgeMatrix", y = "missing"),
function(x, y = NULL) .Call(dgeMatrix_crossprod, x, FALSE),
valueClass = "dpoMatrix")
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "missing"),
function(x, y = NULL) .Call(dgeMatrix_crossprod, x, TRUE),
valueClass = "dpoMatrix")
if(FALSE) { ## this would mask 'base::tcrossprod'
setMethod("tcrossprod", signature(x = "matrix", y = "missing"),
function(x, y = NULL)
.Call(dgeMatrix_crossprod, as(x, "dgeMatrix"), TRUE),
valueClass = "dpoMatrix")
setMethod("tcrossprod", signature(x = "numeric", y = "missing"),
function(x, y = NULL) callGeneric(as.matrix(as.double(x))))
}
## crossprod (x,y)
setMethod("crossprod", signature(x = "dgeMatrix", y = "dgeMatrix"),
function(x, y = NULL) .Call(dgeMatrix_dgeMatrix_crossprod, x, y, FALSE),
valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "dgeMatrix", y = "matrix"),
function(x, y = NULL) .Call(dgeMatrix_matrix_crossprod, x, y, FALSE),
valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "dgeMatrix", y = "numeric"),
function(x, y = NULL)
.Call(dgeMatrix_matrix_crossprod, x, as.matrix(as.double(y)), FALSE),
valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "matrix", y = "dgeMatrix"),
function(x, y = NULL) callGeneric(as(x, "dgeMatrix"), y),
valueClass = "dgeMatrix")
setMethod("crossprod", signature(x = "numeric", y = "dgeMatrix"),
function(x, y = NULL) callGeneric(as.matrix(as.double(x)), y),
valueClass = "dgeMatrix")
## tcrossprod (x,y)
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "dgeMatrix"),
function(x, y = NULL) .Call(dgeMatrix_dgeMatrix_crossprod, x, y, TRUE),
valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "matrix"),
function(x, y = NULL) .Call(dgeMatrix_matrix_crossprod, x, y, TRUE),
valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "dgeMatrix", y = "numeric"),
function(x, y = NULL)
.Call(dgeMatrix_matrix_crossprod, x, rbind(as.double(y)), TRUE),
valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "matrix", y = "dgeMatrix"),
function(x, y = NULL) callGeneric(as(x, "dgeMatrix"), y),
valueClass = "dgeMatrix")
setMethod("tcrossprod", signature(x = "numeric", y = "dgeMatrix"),
function(x, y = NULL) callGeneric(rbind(as.double(x)), y),
valueClass = "dgeMatrix")
## %*% methods
setMethod("%*%", signature(x = "dgeMatrix", y = "dgeMatrix"),
function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
valueClass = "dgeMatrix")
setMethod("%*%", signature(x = "dgeMatrix", y = "matrix"),
function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
valueClass = "dgeMatrix")
setMethod("%*%", signature(x = "matrix", y = "dgeMatrix"),
function(x, y) .Call(dgeMatrix_matrix_mm, y, x, TRUE),
valueClass = "dgeMatrix")
## DB: Should we retain these methods? Does the shortcut save enough
## to justify additional signatures?
## dgeMatrix <-> numeric: conceptually dispatch to "matrix" one, but shortcut
setMethod("%*%", signature(x = "dgeMatrix", y = "numeric"),
function(x, y) .Call(dgeMatrix_matrix_mm, x, y, FALSE),
valueClass = "dgeMatrix")
setMethod("%*%", signature(x = "numeric", y = "dgeMatrix"),
function(x, y)
.Call(dgeMatrix_matrix_mm, y, rbind(x), TRUE),
valueClass = "dgeMatrix")
setMethod("diag", signature(x = "dgeMatrix"),
function(x = 1, nrow, ncol = n)
.Call(dgeMatrix_getDiag, x))
setMethod("chol", signature(x = "dgeMatrix", pivot = "ANY"), cholMat)
setMethod("solve", signature(a = "dgeMatrix", b = "missing"),
function(a, b, ...) .Call(dgeMatrix_solve, a),
valueClass = "dgeMatrix")
setMethod("solve", signature(a = "dgeMatrix", b = "ddenseMatrix"),
function(a, b, ...) .Call(dgeMatrix_matrix_solve, a, b),
valueClass = "dgeMatrix")
setMethod("solve", signature(a = "dgeMatrix", b = "matrix"),
function(a, b, ...) .Call(dgeMatrix_matrix_solve, a, b),
valueClass = "dgeMatrix")
## not needed - method for numeric defined for Matrix class
## setMethod("solve", signature(a = "dgeMatrix", b = "numeric"),
## function(a, b, ...)
## .Call(dgeMatrix_matrix_solve, a, as.matrix(as.double(b))))
setMethod("lu", signature(x = "dgeMatrix"),
function(x, ...) .Call(dgeMatrix_LU, x),
valueClass = "denseLU")
setMethod("determinant", signature(x = "dgeMatrix", logarithm = "missing"),
function(x, logarithm, ...)
.Call(dgeMatrix_determinant, x, TRUE))
setMethod("determinant", signature(x = "dgeMatrix", logarithm = "logical"),
function(x, logarithm, ...)
.Call(dgeMatrix_determinant, x, logarithm))
setMethod("expm", signature(x = "dgeMatrix"),
function(x) .Call(dgeMatrix_exp, x),
valueClass = "dgeMatrix")
setMethod("colSums", signature(x = "dgeMatrix"),
function(x, na.rm = FALSE, dims = 1)
.Call(dgeMatrix_colsums, x, na.rm, TRUE, FALSE),
valueClass = "numeric")
setMethod("colMeans", signature(x = "dgeMatrix"),
function(x, na.rm = FALSE, dims = 1)
.Call(dgeMatrix_colsums, x, na.rm, TRUE, TRUE),
valueClass = "numeric")
setMethod("rowSums", signature(x = "dgeMatrix"),
function(x, na.rm = FALSE, dims = 1)
.Call(dgeMatrix_colsums, x, na.rm, FALSE, FALSE),
valueClass = "numeric")
setMethod("rowMeans", signature(x = "dgeMatrix"),
function(x, na.rm = FALSE, dims = 1)
.Call(dgeMatrix_colsums, x, na.rm, FALSE, TRUE),
valueClass = "numeric")
|
