Xpose 4

by Andrew C. Hooker, Justin J. Wilkins, Mats O. Karlsson and E. Niclas Jonsson

http://xpose.sourceforge.net/

Introduction

Xpose 4 is a ground-floor rewrite of Xpose 3.1. Chief amongst the enhancements in the new version is the migration from S-PLUS to R, a free, multi-platform statistical environment. We have also added direct access to Xpose functions from the command line, and, through R, access to Xpose tools by third-party applications.

R and required package installation

To install xpose you will need:

• R version >=2.2.0. Download the latest version of R from www.r-project.org.
• the gam package. Install the latest version from CRAN. Write at the R command line (type ?install.packages in R for more details):

install.packages("gam")

Xpose 4 Installation

Install xpose in R using one of the following methods:

• latest stable release -- From CRAN. Write at the R command line:

install.packages("xpose4")

• Latest development version -- from Github. Note that the command below installs the "master" (development) branch; if you want the release branch from Github add ref="release" to the install_github() call. The install_github() approach requires that you build from source, i.e. make and compilers must be installed on your system -- see the R FAQ for your operating system; you may also need to install dependencies manually.

devtools::install_github("xpose4",username="andrewhooker")

Additional recommended packages

The Hmisc package is also recommended. to install, write at the R command line (type ?install.packages in R for more details):

install.packages("Hmisc")

Running Xpose 4

Start R

To use the classic menu system, type at the R command prompt:

library(xpose4)
xpose4()

Each function is independently available from the command line, once the Xpose library is loaded. For example, assuming your run is called 'run5.mod', you might do the following:

• Import data

  xpdb5 <- xpose.data(5)

• Display goodness-of-fit plots

  basic.gof(xpdb5)

More help is available in the online documentation, which can be found by typing (for example) ?xpose at the R command line.

The Xpose 4 Bestiary

A more detailed description of Xpose with example plots and explanaitions for most of the functions in the package is available in our Bestiarium: http://xpose.sourceforge.net/bestiarium_v1.0.pdf

Don't Panic

Andrew Hooker (andrew.hooker at farmbio.uu.se) should be able to get you an answer if you run into trouble. The website http://xpose.sf.net should also be of help.

Release Schedule

Bugfix releases will be released regularly, fixing any problems that are found.

License

Xpose 4 is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details http://www.gnu.org/licenses/.

Known Bugs

None at present, but there will certainly be a few