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Diff of /pkg/man/sparseMatrix-class.Rd

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revision 871, Fri Aug 26 17:26:49 2005 UTC revision 1903, Sat Jun 16 18:31:51 2007 UTC
# Line 1  Line 1 
1  \name{sparseMatrix-class}  \name{sparseMatrix-class}
2  \docType{class}  \docType{class}
3    \title{Virtual Class "sparseMatrix" --- Mother of Sparse Matrices}
4  \alias{sparseMatrix-class}  \alias{sparseMatrix-class}
5    %% Group methods
6    \alias{Math,sparseMatrix-method}
7    %\alias{Math2,sparseMatrix,numeric-method}
8    \alias{Ops,sparseMatrix,sparseMatrix-method}
9    \alias{Ops,sparseMatrix,numeric-method}
10    \alias{Ops,numeric,sparseMatrix-method}
11    \alias{Ops,diagonalMatrix,sparseMatrix-method}
12    \alias{Ops,sparseMatrix,diagonalMatrix-method}
13    %
14    \alias{cbind2,sparseMatrix,sparseMatrix-method}
15    \alias{cbind2,sparseMatrix,matrix-method}
16    \alias{cbind2,matrix,sparseMatrix-method}
17    \alias{cbind2,sparseMatrix,numeric-method}
18    \alias{cbind2,numeric,sparseMatrix-method}
19    \alias{rbind2,sparseMatrix,sparseMatrix-method}
20    \alias{rbind2,sparseMatrix,matrix-method}
21    \alias{rbind2,matrix,sparseMatrix-method}
22    \alias{rbind2,sparseMatrix,numeric-method}
23    \alias{rbind2,numeric,sparseMatrix-method}
24    %
25    \alias{coerce,ANY,sparseMatrix-method}
26    \alias{coerce,factor,sparseMatrix-method}
27    \alias{coerce,sparseMatrix,generalMatrix-method}
28    \alias{coerce,sparseMatrix,symmetricMatrix-method}
29    \alias{coerce,sparseMatrix,triangularMatrix-method}
30    \alias{-,sparseMatrix,missing-method}
31    \alias{diag,sparseMatrix-method}
32    \alias{dim<-,sparseMatrix-method}
33    \alias{print,sparseMatrix-method}
34  \alias{show,sparseMatrix-method}  \alias{show,sparseMatrix-method}
35  \alias{\%*\%,sparseMatrix,ddenseMatrix-method}  \alias{summary,sparseMatrix-method}
36  \alias{\%*\%,ddenseMatrix,sparseMatrix-method}  %\alias{colMeans,..} etc are now in ./colSums.Rd
37  \alias{crossprod,sparseMatrix,ddenseMatrix-method}  % graph stuff
 \alias{crossprod,ddenseMatrix,sparseMatrix-method}  
38  \alias{coerce,graph,sparseMatrix-method}  \alias{coerce,graph,sparseMatrix-method}
39  \alias{coerce,graphNEL,sparseMatrix-method}  \alias{coerce,graph,CsparseMatrix-method}
40  \title{Virtual Class "sparseMatrix" --- Mother of Sparse Matrices}  \alias{coerce,graphAM,sparseMatrix-method}
41    \alias{coerce,graphNEL,CsparseMatrix-method}
42    \alias{coerce,graphNEL,TsparseMatrix-method}
43    \alias{coerce,sparseMatrix,graph-method}
44    \alias{coerce,sparseMatrix,graphNEL-method}
45    \alias{coerce,TsparseMatrix,graphNEL-method}
46    \alias{coerce,dgTMatrix,graphNEL-method}
47    %
48  \description{Virtual Mother Class of All Sparse Matrices}  \description{Virtual Mother Class of All Sparse Matrices}
49  \section{Slots}{  \section{Slots}{
50    \code{Dim}, and \code{Dimnames}, see \code{\link{Matrix-class}}.    \describe{
51  % Should this be "written in stone" or should they be added?      \item{\code{Dim}:}{Object of class \code{"integer"} - the dimensions
52  %   Note that the current implementation keeps \code{Dimnames} empty for       of the matrix - must be an integer vector with exactly two
53  %   sparse matrices.       non-negative values.}
54        \item{\code{Dimnames}:}{a list of length two - inherited from class
55          \code{Matrix}, see \code{\linkS4class{Matrix}}.}
56        \item{\code{factors}:}{Object of class \code{"list"} - a list
57          of factorizations of the matrix. }
58      }
59  }  }
60  \section{Extends}{  \section{Extends}{
61    Class \code{"Matrix"}, directly.    Class \code{"Matrix"}, directly.
62  }  }
63  \section{Methods}{  \section{Methods}{
64    \describe{    \describe{
65      \item{show}{\code{signature(object = "sparseMatrix")}: The  %% FIXME: better description of print() / show(); notably explain the
66    %% print() arguments !
67        \item{show}{\code{(object = "sparseMatrix")}: The
68        \code{\link{show}} method for sparse matrices prints        \code{\link{show}} method for sparse matrices prints
69        \emph{\dQuote{structural}} zeroes as \code{"."} or blank.}        \emph{\dQuote{structural}} zeroes as \code{"."} using the
70          non-exported \code{prSpMatrix} function which allows further
71          customization such as replacing \code{"."} by \code{" "} (blank).
72    
73          Note that \code{\link{options}(max.print)} will influence how many
74          entries of large matrices are printed at all.}
75        \item{print}{\code{signature(x = "sparseMatrix")}, extra arguments
76          \code{digits = getOption("digits"), maxp = getOption("max.print"),
77            zero.print = ".", col.names = FALSE, note.dropping.colnames = TRUE,
78            col.trailer = '', align = c("fancy", "right")}: The
79          \code{\link{print}} method for sparse matrices by default is the
80          same as \code{show()} but can be called with extra optional arguments.}
81    
82        \item{summary}{\code{(object = "sparseMatrix")}: Returns
83          an object of S3 class \code{"sparseSummary"} which is basically a
84          \code{\link{data.frame}} with columns \code{(i,j,x)} with the
85          non-zero entries.   The \code{\link{print}} method resemble's
86          Matlab's way of printing sparse matrices.}
87        \item{diag}{\code{(x = "sparseMatrix")}: extracts the diagonal of a
88          sparse matrix.}
89        \item{dim<-}{\code{signature(x = "sparseMatrix", value = "ANY")}:
90          allows to \emph{reshape} a sparse matrix to a sparse matrix with
91          the same entries but different dimensions. \code{value} must be of
92          length two and fulfill \code{prod(value) == prod(dim(x))}.}
93        \item{coerce}{\code{signature(from = "factor", to = "sparseMatrix")}:
94          Coercion of a factor to \code{"sparseMatrix"} produces the matrix
95          of indicator \bold{rows} stored as an object of class
96          \code{"dgCMatrix"}.  To obtain columns representing the interaction
97          of the factor and a numeric covariate, replace the \code{"x"} slot
98          of the result by the numeric covariate then take the transpose.}
99    }    }
100      See also \code{\link{colSums}}, ... %% FIXME
101      for methods with separate help pages.
102  }  }
103  \note{  \note{
104    In method selection for multiplication operations (i.e. \code{\%*\%}    In method selection for multiplication operations (i.e. \code{\%*\%}
# Line 37  Line 111 
111  %\author{Martin}  %\author{Martin}
112  \examples{  \examples{
113  showClass("sparseMatrix") ## and look at the help() of its subclasses  showClass("sparseMatrix") ## and look at the help() of its subclasses
114    M <- Matrix(0, 10000, 100)
115    M[1,1] <- M[2,3] <- 3.14
116    M  ## show(.) method suppresses printing of the majority of rows
117    
118    ## factor -> t( <sparse design matrix> ) :
119    (fact <- gl(5, 3, 30, labels = LETTERS[1:5]))
120    (Xt <- as(fact, "sparseMatrix"))  # indicator rows
121    X <- t(Xt)
122    ## printing :
123    X ## <==>  show(X)  <==>  print(X)
124    print(X, zero.print = "", col.names = TRUE)
125    
126    \dontshow{% show() was slow in 0.9975-8 because of slow adjust="fancy"
127    op <- options(max.print = 25000, width = 80)
128    sink(print(tempfile()))
129    stopifnot((st <- system.time(show(M)))[1] < 1.0) # only 0.09 on cmath-3
130    sink()
131    st
132    options(op)
133    }
134  }  }
135  \keyword{classes}  \keyword{classes}

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