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
|
\name{symmetricMatrix-class}
\title{Virtual Class of Symmetric Matrices in Package Matrix}
%
\docType{class}
\keyword{array}
\keyword{classes}
%
\alias{symmetricMatrix-class}
%
\alias{coerce,matrix,symmetricMatrix-method}
\alias{dimnames,symmetricMatrix-method}
\alias{dimnames<-,symmetricMatrix,NULL-method}
\alias{dimnames<-,symmetricMatrix,list-method}
%
\description{
The virtual class of symmetric matrices, \code{"symmetricMatrix"},
from the package \pkg{Matrix} contains numeric and logical, dense and
sparse matrices, e.g., see the examples with the \dQuote{actual}
subclasses.
The main use is in methods (and C functions) that can deal with
all symmetric matrices, and in \code{as(*, "symmetricMatrix")}.
}
% \section{Objects from the Class}{A virtual Class: No objects may be created from it.}
\section{Slots}{
\describe{
\item{\code{Dim, Dimnames}}{inherited from virtual class
\code{\linkS4class{Matrix}}. See comments below about
symmetry of \code{Dimnames}.}
\item{\code{factors}}{a list of
\code{\linkS4class{MatrixFactorization}} objects caching
factorizations of the matrix. Typically, it is initialized
as an empty list and updated \dQuote{automagically} whenever
a factorization is computed.}
\item{\code{uplo}}{a character string, either \code{"U"} or
\code{"L"} indicating that only entries in the upper or lower
triangle are referenced.}
}
}
\section{Extends}{
Class \code{"Matrix"}, directly.
}
\section{Methods}{
\describe{
\item{dimnames}{\code{signature(object = "symmetricMatrix")}:
returns \emph{symmetric} \code{\link{dimnames}}, even when the
\code{Dimnames} slot only has row or column names. This allows to
save storage for large (typically sparse) symmetric matrices.}
\item{isSymmetric}{\code{signature(object = "symmetricMatrix")}:
returns \code{TRUE} trivially.}
}
There's a C function \code{symmetricMatrix_validate()}% in ../src/dsyMatrix.c
called by the internal validity checking functions, and also from
\code{\link{getValidity}(getClass("symmetricMatrix"))}.
}
\section{Validity and \code{\link{dimnames}}}{
The validity checks do not require a symmetric \code{Dimnames} slot,
so it can be \code{list(NULL, <character>)}, e.g., for efficiency.
However, \code{\link{dimnames}()} and other functions and methods
should behave as if the dimnames were symmetric, i.e., with both list
components identical.
}
\seealso{
\code{\link{isSymmetric}} which has efficient methods
(\link{isSymmetric-methods}) for the \pkg{Matrix} classes.
Classes \code{\linkS4class{triangularMatrix}}, and, e.g.,
\code{\linkS4class{dsyMatrix}} for numeric \emph{dense} matrices, or
\code{\linkS4class{lsCMatrix}} for a logical \emph{sparse} matrix class.
}
\examples{
## An example about the symmetric Dimnames:
sy <- sparseMatrix(i= c(2,4,3:5), j= c(4,7:5,5), x = 1:5, dims = c(7,7),
symmetric=TRUE, dimnames = list(NULL, letters[1:7]))
sy # shows symmetrical dimnames
sy@Dimnames # internally only one part is stored
dimnames(sy) # both parts - as sy *is* symmetrical
\dontshow{
local({ nm <- letters[1:7]
stopifnot(identical(dimnames(sy), list( nm, nm)),
identical(sy@Dimnames , list(NULL, nm)))
})
}%dont
showClass("symmetricMatrix")
## The names of direct subclasses:
scl <- getClass("symmetricMatrix")@subclasses
directly <- sapply(lapply(scl, slot, "by"), length) == 0
names(scl)[directly]
## Methods -- applicaple to all subclasses above:
showMethods(classes = "symmetricMatrix")
}
|
