by Andrew C. Hooker, Justin J. Wilkins, Mats O. Karlsson -and E. Niclas Jonsson
- - - -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.
- -To install you will need:
- -All of these are freely available from the Comprehensive R-Project -Archive Network (http://cran.r-project.org). To install Hmisc and gam, -you have a number of options.
- -Option 1: The GUI
- -Start the R GUI, and then select “Packages” -> “Install Package(s)…” - from the menus at the top of the screen. You will be asked for a - mirror - select the one that seems closest to you, geographically, - and click OK. Select “Hmisc” from the list, and click OK. Repeat all - steps for “gam”.
- -Option 2: The R console
- -Start R. Enter
- --- -install.packages(“Hmisc”) -install.packages(“gam”)
-
and the Hmisc and gam packages will be downloaded and installed from the - default mirror.
- -Type ?install.packages in R for more details.
- -Download the correct archive for your operating system
- -where VERSION.NUMBER should be replaced by the most recent version of -xposed released. Once you have downloaded the archive, you will need to -install the Xpose package bundle.
- -Option 1: The GUI (Windows)
- -Install from R, by using the GUI. Choose the menu item “Packages” -> - “Install packages from local zip files…” and select the zip file - you have downloaded (e.g. xpose4_4.0.1_win32.zip).
- -Option 2: The R console (Linux & Windows)
- -Start R. Enter
- --- -install.packages(“C:/temp/xpose4_4.0.1_win32.zip”,repos=NULL)
-
if you are using Windows, or
- --- -install.packages(“/tmp/xpose4_4.0.1.tar.gz”,repos=NULL)
-
if you are using Linux. Note that this assumes that you have stored - your downloaded files in “C:\temp” or “/tmp/”. Substitute as - needed.
- -NOTE: for windows, ensure you have downloaded the BINARY -distribution. If you have the source code release -(e.g. xpose4_4.0.1_src.zip), you will need to either (a) build the -packages from source code, as below, or download the correct file and -start again.
- -For Windows users, you will need to download the source distribution -(e.g. xpose4_4.0.1_src.zip) from the website. In addition you will -need to download some package building toolsets from the web. We -direct you to this rather useful tutorial on building R packages under -Windows:
- -http://www.maths.bris.ac.uk/~maman/computerstuff/Rhelp/Rpackages.html
- -This description is a bit outdated but useful as well
- - - -In addition the R help manuals give lots of information:
- -http://cran.r-project.org/doc/manuals/R-admin.html#The-Windows-toolset -http://cran.r-project.org/doc/manuals/R-exts.html
- -Your task under Linux should be much simpler. All the tools you need ought -to be available already in almost all distributions. Simply follow the -instructions (option 2) above. The *.tar.gz release version of xpose -4 is a compressed source distribution that can be built using the -command above. For more help on building R packages see:
- -http://cran.r-project.org/doc/manuals/R-exts.html
- -At the R command prompt, type:
- -library(xpose4)
and use the menu system!
Each function in the bundle is now independently available from the command -line, once libraries are 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) ?basic.gof at the R command line. Using the GUI -(Windows): From the menu system in R choose 'Help' -> 'Html help' -> -'Search Engine & Keywords' and search for “xpose4”.
- -Andrew Hooker (andrew.hooker@farmbio.uu.se) -should be able to get you a quick answer if you run into trouble. The -website http://xpose.sf.net should also be of help.
- -Bugfix releases will be released regularly, fixing any problems that are -found.
- -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.
- -You should have received a copy of the GNU Lesser General Public License
-along with this program (available in <RHOME>\share\licenses).
-If not, see http://www.gnu.org/licenses/.