Difference between revisions of "LeBauer:Software/Statistics"

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===Custom R packages===
 
===Custom R packages===
 
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.
====PECAn====
+
====Building the PECAn library====
Building the code
+
 
 
<pre>
 
<pre>
 
rsync ~/pecan/dev/* ~/pecan/PECAN/
 
rsync ~/pecan/dev/* ~/pecan/PECAN/

Revision as of 13:54, 2 September 2010


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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.

Building the PECAn library

rsync ~/pecan/dev/* ~/pecan/PECAN/
cd ~/pecan
R CMD build PECAn

JAGS

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

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/