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‎assignments/PoPS_calibration.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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<title>NCSU GIS 714: Geospatial Computation and Simulations</title>
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<link rel="shortcut icon" href=".././img/favicon.ico" />
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<link href="../layout.css" rel="stylesheet" type="text/css" media="screen">
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<link href="../style.css" rel="stylesheet" type="text/css" media="screen">
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</head>
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<body>
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<div id="outercontainer">
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<div id="container">
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<header>
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<div id="header-image">
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<h1>NCSU GIS 714:<br>Geospatial Computing and Simulations</h1>
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</div>
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<nav>
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<ul class="nav">
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<li><a href="../index.html">Syllabus</a></li>
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<li><a href="../schedule.html">Schedule</a></li>
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<li><a href="../logistics.html">Course logistics</a></li>
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<li><a href="../topics/index.html">Topics</a></li>
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<li><a href="../projects.html">Projects</a></li>
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</ul>
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</nav>
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</header>
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<main>
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<!-- This is a generated file. Do not edit. -->
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<h2>PoPS calibration</h2>
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Resources to download:
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<ul>
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<li><a href="http://fatra.cnr.ncsu.edu/pops/data/SOD_ABC_calibration.zip">test data</a></li>
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<li><a href="../resources/SOD_ABC_calibration.R">PoPS calibration R script</a></li>
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</ul>
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R software:
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<ul>
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<li>install rpops, follow <a href="https://github.com/ncsu-landscape-dynamics/rpops#how-to-install"> installation instructions</a></li>
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<li>install <a href="https://cran.r-project.org/web/packages/folderfun/index.html">folderfun</a> package
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</ul>
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<h3>Tasks</h3>
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Run the calibration code to derive parameters for spore rate, distance and direction strength for SOD based on 2018.
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Unzip the dataset to a folder and change the path to that folder in the R script.
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The script will output information about the progress of calibration.
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<ul>
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<li>What role does generation size and number of generations play in the calibration process?
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Change them and observe the impacts.</li>
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<li>Change the thresholds of accepting a parameter set (checks variable).
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Observe the impacts.</li>
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<li>Inspect the results of the calibration.</li>
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</ul>
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<!--
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<p>Outline:
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<ul>
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<li>Use provided test data to calibrate PoPS model</li>
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<li>Use parameters derived from calibration to validate PoPS outputs</li>
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<li>Try to answer questions below</li>
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</ul>
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<p>
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Resources to download:
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<ul>
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<li><a href="http://fatra.cnr.ncsu.edu/pops/data/calibration_validation_sample_data.zip">test data</a></li>
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<li><a href="../resources/PoPS_calibration.R">PoPS calibration R script</a></li>
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<li><a href="../resources/PoPS_validation.R">PoPS validation R script</a></li>
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</ul>
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Run each block in the provided R scripts step by step and see the associated instructions as comments in the code.
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<h3>Calibration</h3>
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Run the calibration code to derive parameters for spore rate and distance for the PoPs model.
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<ul>
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<li>What are the parameters?</li>
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<li>How many times were the spore rate and distance parameters used out of the total number of calibration iterations?</li>
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<li>What does the distribution of the two parameters look like?</li>
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</ul>
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Optional:
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<ul>
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<li>Try different numbers of iterations. Are derived parameters different?</li>
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<li>Try turning management on (line 22). Are derived parameters different?</li>
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</ul>
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<h3>Validation</h3>
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Use the parameters derived from the calibration code to run the PoPS model and
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validate the outputs using the validation code.
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<ul>
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<li>What was the average disagreement and landscape similarity?</li>
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</ul>
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Optional:
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<ul>
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<li>Try with management on (line 24). How are the total disagreement and landscape similarity affected?</li>
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<li>Try with different spore rate and distance parameters. How are total disagreement and landscape similarity affected?</li>
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<li>Try with different conditions. How are total disagreement and landscape similarity affected?
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<ul>
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<li>With mortality on - Set mortality to "TRUE" and you can change the
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conditions for time lag and mortality rate (lines 28-30)</li>
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<li>With wind direction on - Can set wind to "N", "S", "W", "E".
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Higher kappa values make the wind direction stronger (lines 33-34).</li>
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</ul>
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</li>
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</ul>
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-->
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</main>
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<footer>
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<nav>
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<ul>
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<li><a class="term-changes" href="https://moodle-courses2527.wolfware.ncsu.edu/course/view.php?id=5978">Moodle site</a></li>
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<li><a href="https://help.ncsu.edu/">Computing Help</a></li>
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<li><a href="https://geospatial.ncsu.edu/">GIST Home</a></li>
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<li><a href="https://www.ncsu.edu/policies/prr-disclaimer.php">Disclaimer</a></li>
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<li><a href="https://oit.ncsu.edu/itaccess">Accessibility</a></li>
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<li>
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<a href="https://github.com/ncsu-geoforall-lab/geospatial-simulations-course" title="Source code for web pages on GitHub">
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<img src="../img/github_logo.png" alt="GitHub Octocat logo">
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</a>
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</li>
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<li title="Copyright and license (not applicable to linked materials)">
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&copy; 2023
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<a href="https://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a>
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<a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll Lab</a>
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</li>
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</ul>
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</nav>
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</footer>
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</div>
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</div>
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</body>
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</html>

‎assignments/abm.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
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<title>NCSU GIS 714: Geospatial Computation and Simulations</title>
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<link rel="shortcut icon" href=".././img/favicon.ico" />
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<link href="../layout.css" rel="stylesheet" type="text/css" media="screen">
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<link href="../style.css" rel="stylesheet" type="text/css" media="screen">
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</head>
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<body>
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<div id="outercontainer">
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<div id="container">
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<header>
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<div id="header-image">
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<h1>NCSU GIS 714:<br>Geospatial Computing and Simulations</h1>
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</div>
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<nav>
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<ul class="nav">
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<li><a href="../index.html">Syllabus</a></li>
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<li><a href="../schedule.html">Schedule</a></li>
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<li><a href="../logistics.html">Course logistics</a></li>
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<li><a href="../topics/index.html">Topics</a></li>
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<li><a href="../projects.html">Projects</a></li>
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</ul>
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</nav>
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</header>
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<main>
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<!-- This is a generated file. Do not edit. -->
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<h2>Agent Based Modeling</h2>
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<p>
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Resources:
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<ul>
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<li><a href="http://grass.osgeo.org/grass-stable/manuals/">
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GRASS GIS overview and manual</a>
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<li><a href="http://www.grassbook.org/">GRASS book</a>
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<li><a href="https://grass.osgeo.org/grass-stable/manuals/addons/r.landscape.evol.html">r.landscape.evol</a>
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<li><a href="https://github.com/projectmesa/mesa/">MESA: agent based modeling in Python</a>
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</ul>
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<h3>Agent Based Modeling in Python using Mesa</h3>
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We will install ABM framework <a href="https://mesa.readthedocs.io/en/master/">MESA</a>,
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run some example models, and then modify and expand the fire model to reuse it as a tree disease spread model.
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<h4>Installation</h4>
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Use pip to install Mesa, note that Mesa requires Python 3:
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<pre><code>pip install mesa
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</code></pre>
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Test if successfull:
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<pre><code>mesa --help
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# alternatively ~/.local/bin/mesa --help
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</code></pre>
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Download <a href="https://github.com/projectmesa/mesa/archive/v0.8.5.zip">Mesa v0.8.5</a>, unzip and in command line go to examples folder,
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pick an example folder (for example <code>Schelling</code>) and install dependencies:
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<pre><code>pip install -r requirements.txt
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</code></pre>
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<pre><code>mesa runserver
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</code></pre>
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Inspect the code in <code>model.py</code> defining the agent rules.
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<h4>From fire to disease spread ABM</h4>
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Copy folder <code>forest_fire</code> and rename it to <code>disease_spread</code>.
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Now run the model in the same way and observe the behavior.
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Inspect the code in <code>model.py</code>, <code>agent.py</code> and <code>server.py</code>.
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<p>
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Now the task is to change and expand the forest fire model to represent a tree disease spread simulation.
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Start by renaming the categories: "On Fire" to "Infected", "Burned Out" to "Dead".
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Then independently work on these possible tasks, or come up with your own rules and behaviors:
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<ul>
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<li>Change mortality to have trees die after a specified number of steps </li>
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<li>Add stochastic behavior, for example, infect neighbor only with certain probability</li>
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<li>Increase distance how far the disease can spread
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(use <a href="https://mesa.readthedocs.io/en/master/apis/space.html#space.Grid.iter_neighbors"><code>model.grid.iter_neighbors</code></a>)</li>
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<li>Implement prevailing spread direction, can be stochastic</li>
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<li>Add another agent (use <a href="https://mesa.readthedocs.io/en/master/apis/space.html#space.MultiGrid"><code>MultiGrid</code></a>)
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who is doing random walk and spreading disease</li>
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<li>Add slider/dropdown box to the web interface to interactively explore the effects</li>
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</ul>
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Solution can be found <a href="https://github.com/ncsu-geoforall-lab/mesa-teaching-example">here</a>.
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<h3>Modeling coupled human and natural systems using MedlanD </h3>
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Things to download:
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<ul>
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<li><a href="../resources/r.landscape.evol2.py">r.landscape.evol2</a></li>
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<li><a href="../resources/r.agropast.adaptive2.py">r.agropast.adaptive2</a></li>
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<li><a href="https://drive.google.com/a/ncsu.edu/file/d/1aHTMkhhe52oXhEp1_qdunGwFSQBjZ7m_/view?usp=sharing">GRASS Location</a></li>
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<li><a href="https://drive.google.com/a/ncsu.edu/file/d/1dv7A7n6NC4_rHKnqRaSffJBEE6D6yyi9/view?usp=sharing">GRASS reclassification rules</a></li>
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</ul>
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Start GRASS in the provided Location and create new mapset.
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Unzip the reclassification rules to a directory and place there the scripts r.agropast.adaptive2.py and r.landscape.evol2.py.
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Change to the directory where the rule files and the scripts are and run the simulation for 3 iterations:
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<pre><code>python3 r.agropast.adaptive2.py -1 numpeople=30 years=3 prefx=sim costsurf=farm_catch_10yr_30ppl_cost_surface agcatch=farm_catch_10yr_30ppl grazecatch=graze_catch fodder_rules=fodder_rules.txt inlcov=init_veg infert=init_fert lc_rules=luse_reclass_rules.txt cfact_rules=cfactor_recode_rules.txt elev=DEM initbdrk=init_bdrk
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</code></pre>
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<!-- If you want to set up your own geographic locale for this, you'll also need r.catchment -->
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<!-- "https://github.com/comses/medland/blob/master/Scripts/r.catchment.py" -->
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<!-- there is also a spreadsheet with default values for agropastoral economy - get the numbers into the assignment webpage -->
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</main>
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<footer>
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<nav>
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<ul>
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<li><a class="term-changes" href="https://moodle-courses2527.wolfware.ncsu.edu/course/view.php?id=5978">Moodle site</a></li>
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<li><a href="https://help.ncsu.edu/">Computing Help</a></li>
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<li><a href="https://geospatial.ncsu.edu/">GIST Home</a></li>
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<li><a href="https://www.ncsu.edu/policies/prr-disclaimer.php">Disclaimer</a></li>
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<li><a href="https://oit.ncsu.edu/itaccess">Accessibility</a></li>
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<li>
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<a href="https://github.com/ncsu-geoforall-lab/geospatial-simulations-course" title="Source code for web pages on GitHub">
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<img src="../img/github_logo.png" alt="GitHub Octocat logo">
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</a>
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</li>
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<li title="Copyright and license (not applicable to linked materials)">
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&copy; 2023
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<a href="https://creativecommons.org/licenses/by-sa/4.0/">CC BY-SA</a>
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<a href="https://geospatial.ncsu.edu/geoforall/">NCSU GeoForAll Lab</a>
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</li>
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</ul>
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</nav>
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</footer>
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</div>
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</div>
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</body>
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</html>

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