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(Latex and Sweave)
(Installing JAGS)
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1. download the file
1. download the file
  wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-<version>.tar.gz  
  wget http://sourceforge.net/projects/mcmc-jags/files/JAGS/2.x/Source/JAGS-2.2.0.tar.gz
2. unpack the gzipped file
2. unpack the gzipped file

Revision as of 12:43, 10 November 2010



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

LaTeX plus Sweave facilitate documentation and reproduction of statistical analyses. I generally use Sweave and Latex in emacs, but I also find Lyx useful in some cases, and the learning curve is easier using the Lyx interface to Latex.

Lyx 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)


Installing JAGS

1. download the file

 wget http://sourceforge.net/projects/mcmc-jags/files/JAGS/2.x/Source/JAGS-2.2.0.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


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
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


Kelper project homepage

download Kepler

wget https://code.kepler-project.org/code/kepler/releases/installers/2.0/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/
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