LeBauer:Software/Statistics: Difference between revisions
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**Document -> Settings -> Document Class -> article (Sweave noweb) | **Document -> Settings -> Document Class -> article (Sweave noweb) | ||
==Kepler== | ==Kepler== | ||
Revision as of 09:46, 10 November 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.
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
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/
