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
|
#### Symmetric Sparse Matrices in compressed column-oriented format
setAs("dgCMatrix", "dsCMatrix",
function(from) {
if(isSymmetric(from))
## FIXME: should be able to *not* need Tsparse route
as(as(as(from, "dgTMatrix"), "dsTMatrix"), "dsCMatrix")
else stop("not a symmetric matrix")})
## Specific conversions, should they be necessary. Better to convert as
## as(x, "TsparseMatrix") or as(x, "denseMatrix")
## Moved to ./Csparse.R
## setAs("dsCMatrix", "dsTMatrix",
## function(from) .Call(Csparse_to_Tsparse, from, FALSE))
setAs("dsCMatrix", "dgTMatrix", # needed for show(), image()
function(from)
## pre-Cholmod -- FIXME: get rid of
.Call(dsCMatrix_to_dgTMatrix, from))
setAs("dsCMatrix", "dgeMatrix",
function(from) as(as(from, "dgTMatrix"), "dgeMatrix"))
setAs("dgeMatrix", "dsCMatrix",
function(from) as(as(from, "dsyMatrix"), "dsTMatrix"))
setAs("dsCMatrix", "matrix",
function(from) as(as(from, "dgTMatrix"), "matrix"))
setAs("matrix", "dsCMatrix",
function(from) as(as(from, "dgTMatrix"), "dsCMatrix"))
setAs("dsCMatrix", "lsCMatrix",
function(from) new("lsCMatrix", i = from@i, p = from@p, uplo = from@uplo,
x = as.logical(from@x),
Dim = from@Dim, Dimnames = from@Dimnames))
setAs("dsCMatrix", "nsCMatrix",
function(from) new("nsCMatrix", i = from@i, p = from@p, uplo = from@uplo,
Dim = from@Dim, Dimnames = from@Dimnames))
setAs("dsCMatrix", "dgCMatrix",
function(from) .Call(Csparse_symmetric_to_general, from))
setAs("dsCMatrix", "dsyMatrix",
function(from) as(as(from, "dsTMatrix"), "dsyMatrix"))
## have rather tril() and triu() methods than
## setAs("dsCMatrix", "dtCMatrix", ....)
setMethod("tril", "dsCMatrix",
function(x, k = 0, ...) {
if(x@uplo == "L" && k == 0)
## same internal structure (speedup potential !?)
new("dtCMatrix", uplo = x@uplo, i = x@i, p = x@p,
x = x@x, Dim = x@Dim, Dimnames = x@Dimnames)
else tril(as(x, "dgCMatrix"), k = k, ...)
})
setMethod("triu", "dsCMatrix",
function(x, k = 0, ...) {
if(x@uplo == "U" && k == 0)
## same internal structure (speedup potential !?)
new("dtCMatrix", uplo = x@uplo, i = x@i, p = x@p,
x = x@x, Dim = x@Dim, Dimnames = x@Dimnames)
else triu(as(x, "dgCMatrix"), k = k, ...)
})
setMethod("solve", signature(a = "dsCMatrix", b = "ddenseMatrix"),
function(a, b, ...) {
if (class(b) != "dgeMatrix")
b <- .Call(dup_mMatrix_as_dgeMatrix, b)
.Call(dsCMatrix_matrix_solve, a, b)
},
valueClass = "dgeMatrix")
setMethod("solve", signature(a = "dsCMatrix", b = "matrix"),
function(a, b, ...)
.Call(dsCMatrix_matrix_solve, a,
.Call(dup_mMatrix_as_dgeMatrix, b)),
valueClass = "dgeMatrix")
setMethod("solve", signature(a = "dsCMatrix", b = "numeric"),
function(a, b, ...)
.Call(dsCMatrix_matrix_solve, a,
.Call(dup_mMatrix_as_dgeMatrix, b)),
valueClass = "dgeMatrix")
## `` Fully-sparse'' solve() :
setMethod("solve", signature(a = "dsCMatrix", b = "dsparseMatrix"),
function(a, b, ...) {
if (!is(b, "CsparseMatrix"))
b <- as(b, "CsparseMatrix")
if (is(b, "symmetricMatrix")) ## not supported (yet) by cholmod_spsolve
b <- as(b, "dgCMatrix")
.Call(dsCMatrix_Csparse_solve, a, b)
})
setMethod("chol", signature(x = "dsCMatrix", pivot = "missing"),
function(x, pivot, ...) .Call(dsCMatrix_chol, x, FALSE),
valueClass = "dtCMatrix")
setMethod("chol", signature(x = "dsCMatrix", pivot = "logical"),
function(x, pivot, ...) .Call(dsCMatrix_chol, x, pivot),
valueClass = "dtCMatrix")
setMethod("Cholesky", signature(A = "dsCMatrix"),
function(A, perm = TRUE, LDL = TRUE, super = FALSE, ...)
.Call(dsCMatrix_Cholesky, A, perm, LDL, super))
setMethod("t", signature(x = "dsCMatrix"),
function(x) .Call(Csparse_transpose, x, FALSE),
valueClass = "dsCMatrix")
setMethod("determinant", signature(x = "dsCMatrix", logarithm = "missing"),
function(x, logarithm, ...) determinant(x, TRUE))
setMethod("determinant", signature(x = "dsCMatrix", logarithm = "logical"),
function(x, logarithm, ...)
{
stop("Temporarily disabled until we work out the LDL factorization diagonal")
ldet <- sum(log(chol(x)@D))
modulus <- if (logarithm) ldet else exp(ldet)
attr(modulus, "logarithm") <- logarithm
val <- list(modulus = modulus, sign = as.integer(1))
class(val) <- "det"
val
})
setMethod("writeHB", signature(obj = "dsCMatrix"),
function(obj, file, ...) {
.Deprecated("writeMM")
.Call(Matrix_writeHarwellBoeing,
if (obj@uplo == "U") t(obj) else obj,
as.character(file), "DSC")
})
setMethod("writeMM", signature(obj = "dsCMatrix"),
function(obj, file, ...)
.Call(Matrix_writeMatrixMarket,
if (obj@uplo == "U") t(obj) else obj,
as.character(file), "DSC"))
|
