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Annotation of OpenXM/src/R/r-client/Ropenxm/man/oxm.markov.Rd, Revision 1.3

1.3     ! takayama    1: % $OpenXM: OpenXM/src/R/r-client/Ropenxm/man/oxm.markov.Rd,v 1.2 2013/02/02 05:16:44 takayama Exp $
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{
1.3     ! takayama   13: oxm.markov(mat,url="http://asir.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 }