Difference between revisions of "LeBauer:Software/Statistics"

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*'''coda''' tools for analysis of mcmc chains
 
*'''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].
 
*'''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].
 
+
*[http://www.bioconductor.org/packages/2.2/bioc/html/EBImage.html '''EBImage'''] for image analysis
 +
<pre>
 +
$ R
 +
> source("http://bioconductor.org/biocLite.R")
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> biocLite("EBImage")
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</pre>
 
==JAGS==
 
==JAGS==
 
=====Installing Jags packages (rjags and R2jags) in R=====
 
=====Installing Jags packages (rjags and R2jags) in R=====

Revision as of 15:35, 28 July 2010


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R

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.
  • EBImage for image analysis
$ R
> source("http://bioconductor.org/biocLite.R")
> biocLite("EBImage")

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