LeBauer:Software/Statistics

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(Installing JAGS)
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**Document -> Settings -> Document Class -> article (Sweave noweb)
**Document -> Settings -> Document Class -> article (Sweave noweb)
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==JAGS==
 
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=====Installing JAGS=====
 
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1. download the file
 
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<pre>
 
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wget http://sourceforge.net/projects/mcmc-jags/files/JAGS/2.x/Source/JAGS-2.2.0.tar.gz
 
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</pre>
 
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2. unpack the gzipped file
 
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<pre> tar xvfz  JAGS-<version>.tar.gz</pre>
 
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3. change directory to folder with unpacked JAGS files
 
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<pre> cd JAGS-<version></pre>
 
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4. Run configuration file to check system and set system dependent variables
 
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*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.
 
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<pre> ./configure --prefix=/usr</pre>
 
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5. build program
 
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<pre> make</pre>
 
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6.  install (requires root access)
 
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<pre> sudo make install</pre>
 
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7. remove files no longer needed after installation
 
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<pre> make clean
 
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cd ..
 
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rm -rf JAGS-<version> </pre>
 
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=====Specific Code for JAGS version 2.1.0=====
 
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<pre>
 
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wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-2.1.0.tar.gz
 
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tar xvfz  JAGS-2.1.0.tar.gz
 
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cd JAGS-2.1.0/
 
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./configure --prefix=/usr
 
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make
 
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sudo make install
 
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make clean
 
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cd ..
 
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rm -rf JAGS-2.1.0
 
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</pre>
 
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=====Installing Jags packages (rjags and R2jags) in R=====
 
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<pre>
 
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wget http://cran.r-project.org/src/contrib/R2jags_0.01-26.tar.gz
 
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sudo R CMD INSTALL R2jags_0.01-26.tar.gz
 
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wget http://cran.r-project.org/src/contrib/rjags_1.0.3-11.tar.gz
 
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sudo R CMD INSTALL rjags_1.0.3-11.tar.gz
 
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</pre>
 
==Kepler==
==Kepler==

Revision as of 12:46, 10 November 2010


Contents

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

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)


Kepler

Kelper project homepage

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/
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