jointvetch

An agent-based, pattern-oriented, and GIS-based simulation of Aeschynomene virginica, or Sensitive joint-vetch, in its tidal marshland habitat of Holts Creek, VA.

Relative classpath to jars:

• /jointvetch/jointvetch/
• /jointvetch/lib/mason/jar/mason.17.jar
• /jointvetch/lib/geomason-1.5/geomason.1.5.jar
• /jointvetch/lib/jts-1.13/lib/jts-1.13.jar
• /jointvetch/lib/mason/itext-1.2.jar
• /jointvetch/lib/mason/jcommon-1.0.21.jar
• /jointvetch/lib/mason/jmf.jar
• /jointvetch/lib/mason/portfolio.jar
• /jointvetch/lib/mason/jfreechart-1.0.17.jar
• /jointvetch/lib/commons-math3-3.2/commons-math3-3.2.jar

Compiling

To compile, cd to "jointvetch," then:

javac -classpath ../lib/mason/jar/mason.17.jar:../lib/geomason-1.5/geomason.1.5.jar:../lib/jts-1.13/lib/jts-1.13.jar:../lib/mason/itext-1.2.jar:../lib/mason/jcommon-1.0.21.jar:../lib/mason/jmf.jar:../lib/mason/portfolio.jar:../lib/mason/jfreechart-1.0.17.jar:../lib/commons-math3-3.2/commons-math3-3.2.jar *.java

A possibly useful bash script

function comp() {
    echo Compiling jointvetch...
    cd /YOUR/PATH/TO/jointvetch/jointvetch
    if [ ! -e "/tmp/classes" ]
    then
        mkdir /tmp/classes
    if
    javac -classpath ../lib/mason/jar/mason.17.jar:../lib/geomason-1.5/geomason.1.5.jar:../lib/jts-1.13/lib/jts-1.13.jar:../lib/mason/itext-1.2.jar:../lib/mason/jcommon-1.0.21.jar:../lib/mason/jmf.jar:../lib/mason/portfolio.jar:../lib/mason/jfreechart-1.0.17.jar:../lib/commons-math3-3.2/commons-math3-3.2.jar -d /tmp/classes *.java
}

Running

To run, cd to "jointvetch," then:

java -classpath ../jointvetch:../lib/mason/jar/mason.17.jar:../lib/geomason-1.5/geomason.1.5.jar:../lib/jts-1.13/lib/jts-1.13.jar:../lib/mason/itext-1.2.jar:../lib/mason/jcommon-1.0.21.jar:../lib/mason/jmf.jar:../lib/mason/portfolio.jar:../lib/mason/jfreechart-1.0.17.jar:../lib/commons-math3-3.2/commons-math3-3.2.jar:.. -Xmx8g jointvetch.HoltsCreek envStochMax hydrochoryBool implantationRate adjustmentFactor

For instance:

java -classpath ../jointvetch:../lib/mason/jar/mason.17.jar:../lib/geomason-1.5/geomason.1.5.jar:../lib/jts-1.13/lib/jts-1.13.jar:../lib/mason/itext-1.2.jar:../lib/mason/jcommon-1.0.21.jar:../lib/mason/jmf.jar:../lib/mason/portfolio.jar:../lib/mason/jfreechart-1.0.17.jar:../lib/commons-math3-3.2/commons-math3-3.2.jar:.. -Xmx8g jointvetch.HoltsCreek .2 true .08 .3

A possibly useful bash script

function run() {
    if [ $# -lt 4 ]
    then
        echo Usage: run stochMax hydrochoryBool implantationRate adjustmentFactor [-verbose] [-seed seed].
    else
        echo Running jointvetch...
        cd /YOUR/PATH/TO/jointvetch/jointvetch
        java -classpath ../jointvetch:../lib/mason/jar/mason.17.jar:../lib/geomason-1.5/geomason.1.5.jar:../lib/jts-1.13/lib/jts-1.13.jar:../lib/mason/itext-1.2.jar:../lib/mason/jcommon-1.0.21.jar:../lib/mason/jmf.jar:../lib/mason/portfolio.jar:../lib/mason/jfreechart-1.0.17.jar:../lib/commons-math3-3.2/commons-math3-3.2.jar:/tmp/classes -Xmx8g jointvetch.HoltsCreek $1 $2 $3 $4 $5 $6 $7 -quiet
    fi
}
# args are: envStochMax hydrochoryBool implantationRate adjustmentFactor

R scripts

The R scripts require the following libraries to run:

• raster
• rgdal (On Ubuntu, first run "sudo apt-get install libgdal1-dev libproj-dev")