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| ==R==
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| ===R packages===
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| *[http://had.co.nz/ggplot2/ '''ggplot2'''] simplifies graphical data visualization and presentation
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| *'''coda''' tools for analysis of mcmc chains
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| *'''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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| * '''adimpro''' for image analysis
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| <pre>
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| ##example R code for extracting jpg to N x M x 3 matrix
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| ##much slower than Matlab imread()
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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]
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| blue <- b[,,3]
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| </pre>
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|
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| ==JAGS==
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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>
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|
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| ==Kepler==
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| [https://kepler-project.org Kelper project homepage]
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|
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| download Kepler
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| <pre>
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| wget https://code.kepler-project.org/code/kepler/releases/installers/2.0/Kepler-2.0-linux.jar
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| Kepler-2.0-linux.jar
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| </pre>
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| follow the instructions to install Kepler, if installation does not begin, double-click on the file
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|
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| after installation, need to download jar file for jdbc java connection
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| <pre>
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| wget http://www.mysql.com/get/Downloads/Connector-J/mysql-connector-java-5.1.13.tar.gz/from/ftp://mirror.anl.gov/pub/mysql/
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| tar -zcf mysql-connector-java-5.1.13.tar.gz
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| cp mysql-connector-java-5.1.13.tar.gz ~/Kepler-2.0/
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| </pre>
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Latest revision as of 09:53, 10 November 2010
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