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Annotation of OpenXM/src/R/r-client/Ropenxm/man/oxm.markov.Rd, Revision 1.2

1.2     ! takayama    1: % $OpenXM$
1.1       takayama    2: \name{oxm.markov}
                      3: \alias{oxm.markov}
                      4: %- Also NEED an '\alias' for EACH other topic documented here.
                      5: \title{
1.2     ! takayama    6:   The function oxm.markov obtains the Markov basis for a given set of points by 4ti2 through an OpenXM server.
1.1       takayama    7: }
                      8: \description{
1.2     ! takayama    9:   The function oxm.markov obtains the Markov basis for a given set of points by 4ti2 through an OpenXM server.
        !            10:   It is provided also for a sample implementation to call OpenXM servers from R.
1.1       takayama   11: }
                     12: \usage{
1.2     ! takayama   13: oxm.markov(mat,url="http://polymake.math.kobe-u.ac.jp/cgi-bin/cgi-asir-r-markov.sh")
1.1       takayama   14: }
                     15: %- maybe also 'usage' for other objects documented here.
                     16: \arguments{
                     17:   \item{mat}{
1.2     ! takayama   18:      A matrix which represents a set of integer points.
        !            19:      Each column of the matrix is each point of the set.
        !            20:   }
        !            21:   \item{url}{
        !            22:     This argument specifies the URL of an OpenXM server.
        !            23:   The default is an anonymous server in public set by the openxm.org.
        !            24:   Note that all inputs are recorded in the server
        !            25:   and the privacy policy of the public server declares
        !            26:   that the record is used only for debugging and for security tasks.
        !            27:   You can specify your own server.
        !            28:   }
1.1       takayama   29: }
                     30: \details{
1.2     ! takayama   31:   A general algorithm to obtain the Markov basis for a set of points
        !            32:   was given in
        !            33:   "P.Diaconis and B.Sturmfels, Algebraic algorithms for sampling from
        !            34:    conditional distributions, Annals of Statistics, 26, (1998) 363--397".
        !            35:   4ti2 is an efficient implementation of this algorithm.
        !            36:   The function oxm.markov calls the 4ti2 through an OpenXM server.
        !            37:   In order to set up your own server,
        !            38:   please refer to \url{http://www.openxm.org.}
        !            39:   The function utilizes \code{\link{oxm.matrix_r2tfb}} and
        !            40:   \code{\link[RCurl]{postForm}}.
1.1       takayama   41: }
                     42: \value{
1.2     ! takayama   43: The output is given by a list with the following named entries.
        !            44:   \item{markov}{Markov basis in a list.}
        !            45:   \item{text}{The string returned from the server. It is used to get errors.}
1.1       takayama   46: }
                     47: \references{
1.2     ! takayama   48:   \url{http://www.4ti2.de}
        !            49:
        !            50:   P.Diaconis and B.Sturmfels (1998), Algebraic algorithms for sampling from
        !            51:   conditional distributions, Annals of Statistics, 26, 363--397.
1.1       takayama   52: }
                     53: \author{
1.2     ! takayama   54: %%
1.1       takayama   55: }
                     56: \note{
                     57: %%  ~~further notes~~
                     58: }
                     59:
                     60: %% ~Make other sections like Warning with \section{Warning }{....} ~
                     61:
                     62: \seealso{
1.2     ! takayama   63: \code{\link{oxm.matrix_r2tfb}}
1.1       takayama   64: }
                     65: \examples{
1.2     ! takayama   66: ## =====================================================
        !            67: ## Example 1. Markov basis of 2 x 3 contingency table.
        !            68: ## =====================================================
        !            69: mat<-matrix(c(1,0,0,0, 1,0,1,0, 1,0,0,1,
        !            70:               1,1,0,0, 1,1,1,0, 1,1,0,1),nrow=4,ncol=6)
        !            71: mb<-oxm.markov(mat)
        !            72: mb$markov
1.1       takayama   73: }
                     74: % Add one or more standard keywords, see file 'KEYWORDS' in the
                     75: % R documentation directory.
1.2     ! takayama   76: \keyword{ Markov basis }
        !            77: \keyword{ 4ti2 }
        !            78: \keyword{ OpenXM }