View source for LeBauer:Software/Statistics

{{Template:DLeBauer}}
==R==
===public R packages===
*[http://had.co.nz/ggplot2/ '''ggplot2'''] simplifies graphical data visualization and presentation
*'''coda''' tools for analysis of mcmc chains
*'''randtoolbox''' has function for generating pseudo-random samples; the [http://en.wikipedia.org/wiki/Halton_sequence 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 [http://128.174.125.122/wiki/index.php/ED2_Documentation ED2 ecosystem model].
* '''adimpro''' for image analysis
<pre>
##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]
</pre>

===Custom R packages===
See the [http://cran.r-project.org/doc/manuals/R-exts.html Writing R Extensions] guides for more information.

==Latex and Sweave==
useful links:
[http://cran.fhcrc.org/contrib/extra/lyx/ lyx sweave repository]
[http://www.r-project.org/doc/Rnews/Rnews_2008-1.pdf R news article about Lyx and Sweave]

<pre>
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
</pre>

*start Lyx
**Preferences -> Reconfigure
*restart Lyx
**File -> new
**Document -> Settings -> Document Class -> article (Sweave noweb)

==JAGS==
=====Installing JAGS=====
1. download the file
<pre>
 wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-<version>.tar.gz 
</pre>
2. unpack the gzipped file
<pre> tar xvfz  JAGS-<version>.tar.gz</pre>
3. change directory to folder with unpacked JAGS files
<pre> cd JAGS-<version></pre>
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.
<pre> ./configure --prefix=/usr</pre>
5. build program
 <pre> make</pre>
6.  install (requires root access)
<pre> sudo make install</pre>
7. remove files no longer needed after installation
<pre> make clean
cd ..
rm -rf JAGS-<version> </pre>

=====Specific Code for JAGS version 2.1.0=====
<pre>
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
</pre>
=====Installing Jags packages (rjags and R2jags) in R=====
<pre>
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
</pre>

==Kepler==
[https://kepler-project.org Kelper project homepage]

download Kepler
<pre>
wget https://code.kepler-project.org/code/kepler/releases/installers/2.0/Kepler-2.0-linux.jar
Kepler-2.0-linux.jar
</pre>
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

<pre>
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/
</pre>