LeBauer:Software/Statistics: Difference between revisions
From OpenWetWare
Jump to navigationJump to search
| Line 19: | Line 19: | ||
See the [http://cran.r-project.org/doc/manuals/R-exts.html Writing R Extensions] guides for more information. | See the [http://cran.r-project.org/doc/manuals/R-exts.html Writing R Extensions] guides for more information. | ||
==Latex and Sweave== | |||
useful links: | useful links: | ||
[http://cran.fhcrc.org/contrib/extra/lyx/ lyx sweave repository] | [http://cran.fhcrc.org/contrib/extra/lyx/ lyx sweave repository] | ||
Revision as of 11:33, 29 September 2010
<html> <script type="text/javascript">
var _gaq = _gaq || []; _gaq.push(['_setAccount', 'UA-3103850-6']); _gaq.push(['_trackPageview']);
(function() {
var ga = document.createElement('script'); ga.type = 'text/javascript'; ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl' : 'http://www') + '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0]; s.parentNode.insertBefore(ga, s);
})();
</script> </html>
R
public R packages
- ggplot2 simplifies graphical data visualization and presentation
- coda tools for analysis of mcmc chains
- randtoolbox has function for generating pseudo-random samples; the halton() function produces a pseudo-random over-dispersed matrix that I use to sampling from the distributions of ~20 parameters used in ensemble runs of the ED2 ecosystem model.
- adimpro for image analysis
##example R code for extracting jpg to N x M x 3 matrix
##much slower than Matlab imread()
a <- read.image('file.jpg')
b <- extract.image(a)
red <- b[,,1]
green <- b[,,2]
blue <- b[,,3]
Custom R packages
See the Writing R Extensions guides for more information.
Latex and Sweave
useful links: lyx sweave repository R news article about Lyx and Sweave
sudo apt-get install lyx cd ~./lyx wget http://cran.fhcrc.org/contrib/extra/lyx/preferences cd layouts wget http://cran.fhcrc.org/contrib/extra/lyx/literate* wget http://cran.fhcrc.org/contrib/extra/lyx/literate-article.layout wget http://cran.fhcrc.org/contrib/extra/lyx/literate-book.layout wget http://cran.fhcrc.org/contrib/extra/lyx/literate-report.layout wget http://cran.fhcrc.org/contrib/extra/lyx/literate-scrap.inc cd ~/texmf/tex wget http://www.biostat.jhsph.edu/~rpeng/ENAR2009/Sweave.sty
- start Lyx
- Preferences -> Reconfigure
- restart Lyx
- File -> new
- Document -> Settings -> Document Class -> article (Sweave noweb)
JAGS
Installing JAGS
1. download the file
wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-<version>.tar.gz
2. unpack the gzipped file
tar xvfz JAGS-<version>.tar.gz
3. change directory to folder with unpacked JAGS files
cd JAGS-<version>
4. Run configuration file to check system and set system dependent variables
- optional, for consistency with the ebi-forecast and ebi-cluster servers: include the --prefix=/usr/ to specify JAGS install location, /usr/ is default on Red Hat, which runs the ebi-forecast server but /usr/local/ is the default installation folder on Ubuntu, so --prefix=/usr/ is required when installing on Ubuntu to mirror Red Hat.
./configure --prefix=/usr
5. build program
make
6. install (requires root access)
sudo make install
7. remove files no longer needed after installation
make clean cd .. rm -rf JAGS-<version>
Specific Code for JAGS version 2.1.0
wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-2.1.0.tar.gz tar xvfz JAGS-2.1.0.tar.gz cd JAGS-2.1.0/ ./configure --prefix=/usr make sudo make install make clean cd .. rm -rf JAGS-2.1.0
Installing Jags packages (rjags and R2jags) in R
wget http://cran.r-project.org/src/contrib/R2jags_0.01-26.tar.gz sudo R CMD INSTALL R2jags_0.01-26.tar.gz wget http://cran.r-project.org/src/contrib/rjags_1.0.3-11.tar.gz sudo R CMD INSTALL rjags_1.0.3-11.tar.gz
Kepler
download Kepler
wget https://code.kepler-project.org/code/kepler/releases/installers/2.0/Kepler-2.0-linux.jar Kepler-2.0-linux.jar
follow the instructions to install Kepler, if installation does not begin, double-click on the file
after installation, to use mysql with Open Database Connection actor, may need to download jar file for jdbc java connection
wget http://www.mysql.com/get/Downloads/Connector-J/mysql-connector-java-5.1.13.tar.gz/from/ftp://mirror.anl.gov/pub/mysql/ tar -zxf mysql-connector-java-5.1.13.tar.gz cp mysql-connector-java-5.1.13/mysql-connector-java-5.1.13-bin.jar Kepler-2.0/
