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| {{Template:DLeBauer}} | | {{Template:DLeBauer}} |
| ==R==
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| ===public 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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| ===Custom R packages===
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| See the [http://cran.r-project.org/doc/manuals/R-exts.html Writing R Extensions] guides for more information.
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|
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|
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| ==JAGS==
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| =====Installing JAGS=====
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| 1. download the file
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| <pre>
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| wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-<version>.tar.gz
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| </pre>
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| 2. unpack the gzipped file
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| <pre> tar xvfz JAGS-<version>.tar.gz</pre>
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| 3. change directory to folder with unpacked JAGS files
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| <pre> cd JAGS-<version></pre>
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| 4. run configuration file to check system and set system dependent variables (--prefix=/usr/ specifies where JAGS will install, /usr/ is default on Red Hat, which runs the ebi-forecast server but /usr/local/ is the default installation folder on Ubuntu
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| <pre> ./configure --prefix=/usr</pre>
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| 5. build program
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| <pre> make</pre>
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| 6. install (requires root access)
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| <pre> sudo make install</pre>
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| 7. remove files no longer needed after installation
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| <pre> make clean
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| cd ..
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| rm -rf JAGS-<version> </pre>
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|
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|
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| =====Specific Code for JAGS version 2.1.0=====
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| <pre>
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| wget http://www-ice.iarc.fr/~martyn/software/jags/JAGS-2.1.0.tar.gz
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| tar xvfz JAGS-2.1.0.tar.gz
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| cd JAGS-2.1.0/
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| ./configure --prefix=/usr
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| make
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| sudo make install
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| make clean
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| cd ..
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| rm -rf JAGS-2.1.0
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| </pre>
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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, to use mysql with Open Database Connection actor, ''may'' need to download jar file for jdbc java connection
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|
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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 -zxf mysql-connector-java-5.1.13.tar.gz
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| cp mysql-connector-java-5.1.13/mysql-connector-java-5.1.13-bin.jar Kepler-2.0/
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| </pre>
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