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Revision 2312 - (download) (as text) (annotate)
Sat Jan 10 14:01:26 2009 UTC (10 years, 1 month ago) by mmaechler
File size: 7065 byte(s)
new sparseMatrix(): construct *sorted* Csparse from un-sorted input, using modify-in-place under the hood
\name{CsparseMatrix-class}
\docType{class}
\alias{CsparseMatrix-class}
\alias{\%*\%,CsparseMatrix,CsparseMatrix-method}
\alias{\%*\%,CsparseMatrix,ddenseMatrix-method}
\alias{\%*\%,CsparseMatrix,matrix-method}
\alias{\%*\%,CsparseMatrix,numeric-method}
\alias{\%*\%,ddenseMatrix,CsparseMatrix-method}
\alias{\%*\%,matrix,CsparseMatrix-method}
\alias{\%*\%,numeric,CsparseMatrix-method}
\alias{coerce,CsparseMatrix,lsparseMatrix-method}
\alias{coerce,CsparseMatrix,lMatrix-method}
\alias{coerce,CsparseMatrix,nsparseMatrix-method}
\alias{coerce,CsparseMatrix,nMatrix-method}
\alias{coerce,CsparseMatrix,TsparseMatrix-method}
\alias{coerce,CsparseMatrix,denseMatrix-method}
\alias{coerce,CsparseMatrix,matrix-method}
\alias{coerce,matrix,CsparseMatrix-method}
\alias{coerce,numeric,CsparseMatrix-method}
\alias{crossprod,CsparseMatrix,missing-method}
\alias{crossprod,CsparseMatrix,CsparseMatrix-method}
\alias{crossprod,CsparseMatrix,ddenseMatrix-method}
\alias{crossprod,CsparseMatrix,matrix-method}
\alias{crossprod,CsparseMatrix,numeric-method}
\alias{diag,CsparseMatrix-method}
\alias{t,CsparseMatrix-method}
\alias{tcrossprod,CsparseMatrix,CsparseMatrix-method}
\alias{tcrossprod,CsparseMatrix,missing-method}
%% Group methods --------- FIXME: not tested yet (or documented)
\alias{Compare,CsparseMatrix,CsparseMatrix-method}
\alias{Arith,CsparseMatrix,CsparseMatrix-method}
\alias{Arith,CsparseMatrix,numeric-method}
\alias{Arith,numeric,CsparseMatrix-method}
\alias{Logic,CsparseMatrix,CsparseMatrix-method}
\alias{Math,CsparseMatrix-method}
%
\alias{.validateCsparse}
%
\title{Class "CsparseMatrix" of Sparse Matrices in Column-compressed Form}
\description{The \code{"CsparseMatrix"} class is the virtual class of
  all sparse matrices coded in sorted compressed column-oriented form.
  Since it is a virtual class, no objects may be created from it.  See
  \code{showClass("CsparseMatrix")} for its subclasses.
}

\section{Slots}{
  \describe{
    \item{\code{i}:}{Object of class \code{"integer"} of length nnzero
      (number of non-zero elements).  These are the \emph{0-based} row numbers for
      each non-zero element in the matrix, i.e., \code{i} must be in
      \code{0:(nrow(.)-1)}}.
    \item{\code{p}:}{Object of class \code{"integer"} for providing pointers, one
      for each column, to the initial (zero-based) index of elements in
      the column.  \code{.@p} is of length \code{ncol(.) + 1}, with
      \code{p[1] == 0} and \code{p[length(p)] == nnzero}, such that in
      fact, \code{diff(.@p)} are the number of non-zero elements for
      each column.}
    \item{\code{factors}, \code{Dim}, \code{Dimnames}:}{inherited from
      the superclass, see the \code{\linkS4class{sparseMatrix}} class.}
  }
}
\section{Extends}{
Class \code{"sparseMatrix"}, directly.
Class \code{"Matrix"}, by class \code{"sparseMatrix"}.
}
\section{Methods}{
  \describe{%% The following is generated by promptClass(..) --
    %% FIXME: write a script that update all the *-class.Rd files
    \item{Arith}{\code{signature(e1 = "CsparseMatrix", e2 = "numeric")}: ... }
    \item{Arith}{\code{signature(e1 = "numeric", e2 = "CsparseMatrix")}: ... }
    \item{Math}{\code{signature(x = "CsparseMatrix")}: ... }

    \item{band}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{-}{\code{signature(e1 = "CsparseMatrix", e2 = "numeric")}: ... }
    \item{-}{\code{signature(e1 = "numeric", e2 = "CsparseMatrix")}: ... }
    \item{[<-}{\code{signature(x = "CsparseMatrix", i = "index", j = "missing", value = "replValue")}: ... }
    \item{[<-}{\code{signature(x = "CsparseMatrix", i = "index", j = "index", value = "replValue")}: ... }
    \item{[<-}{\code{signature(x = "CsparseMatrix", i = "missing", j = "index", value = "replValue")}: ... }
    \item{\%*\%}{\code{signature(x = "CsparseMatrix", y = "CsparseMatrix")}: ... }
    \item{\%*\%}{\code{signature(x = "CsparseMatrix", y = "denseMatrix")}: ... }
    \item{\%*\%}{\code{signature(x = "CsparseMatrix", y = "matrix")}: ... }
    \item{+}{\code{signature(e1 = "CsparseMatrix", e2 = "numeric")}: ... }
    \item{+}{\code{signature(e1 = "numeric", e2 = "CsparseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "CsparseMatrix", to = "TsparseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "CsparseMatrix", to = "denseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "CsparseMatrix", to = "matrix")}: ... }
    \item{coerce}{\code{signature(from = "CsparseMatrix", to = "lsparseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "CsparseMatrix", to = "nsparseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "TsparseMatrix", to = "CsparseMatrix")}: ... }
    \item{coerce}{\code{signature(from = "denseMatrix", to = "CsparseMatrix")}: ... }
    \item{crossprod}{\code{signature(x = "CsparseMatrix", y = "CsparseMatrix")}: ... }
    \item{crossprod}{\code{signature(x = "CsparseMatrix", y = "missing")}: ... }
    \item{crossprod}{\code{signature(x = "CsparseMatrix", y = "dgeMatrix")}: ... }
    \item{crossprod}{\code{signature(x = "CsparseMatrix", y = "matrix")}: ... }
    \item{diag}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{gamma}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{lgamma}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{log}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{t}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{tcrossprod}{\code{signature(x = "CsparseMatrix", y = "CsparseMatrix")}: ... }
    \item{tcrossprod}{\code{signature(x = "CsparseMatrix", y = "missing")}: ... }
    \item{tril}{\code{signature(x = "CsparseMatrix")}: ... }
    \item{triu}{\code{signature(x = "CsparseMatrix")}: ... }
  }
}
\note{
  All classes extending \code{CsparseMatrix} have a common validity
  (see \code{\link{validObject}}) check function.  That function
  additionally checks the \code{i} slot for each column to contain
  increasing row numbers. \cr
  In earlier versions of \pkg{Matrix} (\code{<= 0.999375-16}),
  \code{\link{validObject}} automatically re-sorted the entries when
  necessary, and hence \code{new()} calls with somewhat permuted
  \code{i} and \code{x} slots worked, as \code{\link{new}(...)}
  (\emph{with} slot arguments) automatically checks the validity.

  Now, you have to use \code{\link{sparseMatrix}} to achieve the same
  functionality or know how to use \code{.validateCsparse()} to do so.
}
\seealso{
  \code{\link{colSums}}, \code{\link{kronecker}}, and other such methods
  with own help pages.

  Further, the super class of \code{CsparseMatrix},
  \code{\linkS4class{sparseMatrix}}, and, e.g.,
  class \code{\linkS4class{dgCMatrix}} for the links to other classes.
}
\examples{
getClass("CsparseMatrix")

## The common validity check function (based on C code):
getValidity(getClass("CsparseMatrix"))

## This behavior has been changed
# un-sorted i-slot on input is automatically "sorted" :
#M <- new("dgCMatrix", Dim = 2:3, p = as.integer(c(0,1,1,3)),
#         i = c(1L, 1:0), x= c(2,2,1))
#stopifnot(M@i == c(1L, 0:1), M@x == c(2,1,2))
}
\keyword{classes}

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