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].
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*[http://www.bioconductor.org/packages/2.2/bioc/html/EBImage.html '''EBImage'''] for image analysis
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* '''adimpro'''] for image analysis
<pre>
<pre>
-
$ R
+
##example R code for extracting jpg to N x M x 3 matrix
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> source("http://bioconductor.org/biocLite.R")
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##much slower than Matlab imread()
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> biocLite("EBImage")
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a <- read.image('file.jpg')
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b <- extract.image(a)
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red  <- b[,,1]
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green <- b[,,2]
 +
blue  <- b[,,3]
</pre>
</pre>
 +
==JAGS==
==JAGS==
=====Installing Jags packages (rjags and R2jags) in R=====
=====Installing Jags packages (rjags and R2jags) in R=====

Revision as of 21:21, 28 July 2010


Contents

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.
  • 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]

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
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