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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Introduction · Persefone</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="Persefone logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href="index.html">Introduction</a><ul class="internal"><li><a class="tocitem" href="#Running-the-model"><span>Running the model</span></a></li><li><a class="tocitem" href="#Model-input"><span>Model input</span></a></li></ul></li><li><a class="tocitem" href="odd.html">Overview, Design, Details (ODD)</a></li><li><span class="tocitem">Developing</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li><a class="tocitem" href="architecture.html">Source code architecture</a></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li></ul></li><li><span class="tocitem">Core</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input, Output, and Settings</a></li></ul></li><li><span class="tocitem">Nature</span><ul><li><a class="tocitem" href="nature.html">Nature</a></li><li><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a></li><li><a class="tocitem" href="species.html">Species</a></li></ul></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="index.html">Introduction</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Introduction</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/index.md#" title="Edit source"><span class="docs-icon fa"></span><span class="docs-label is-hidden-touch">Edit source</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Introduction"><a class="docs-heading-anchor" href="#Introduction">Introduction</a><a id="Introduction-1"></a><a class="docs-heading-anchor-permalink" href="#Introduction" title="Permalink"></a></h1><p><strong>Go back to the <a href="https://persefone-model.eu">homepage</a>, or view the source code on <a href="https://git.idiv.de/persefone/persefone-model">Gitlab</a>.</strong></p><p>Persefone.jl models agricultural practice and how it impacts animal species at a landscape scale. It includes a farm submodel, a crop growth submodel, and individual-based models of multiple indicator species. Its aim is to investigate how changes in farm operations (e.g. through policy changes in the CAP) influence biodiversity.</p><p>The model is based on the <a href="https://juliadynamics.github.io/Agents.jl/stable/">Agents.jl</a> framework. It is currently in the early stages of development.</p><h2 id="Running-the-model"><a class="docs-heading-anchor" href="#Running-the-model">Running the model</a><a id="Running-the-model-1"></a><a class="docs-heading-anchor-permalink" href="#Running-the-model" title="Permalink"></a></h2><p>To run a single experiment, execute <code>run.jl</code>:</p><pre><code class="nohighlight hljs">julia run.jl -c <CONFIG></code></pre><p>Other commandline arguments are:</p><pre><code class="nohighlight hljs">usage: run.jl [-c CONFIGFILE] [-s SEED] [-o OUTDIR] [-l LOGLEVEL]
[--version] [-h]
optional arguments:
-c, --configfile CONFIGFILE
name of the configuration file
-s, --seed SEED inital random seed (type: Int64)
-o, --outdir OUTDIR location of the output directory
-l, --loglevel LOGLEVEL
verbosity: "debug", "info", or "quiet"
--version show version information and exit
-h, --help show this help message and exit</code></pre><h2 id="Model-input"><a class="docs-heading-anchor" href="#Model-input">Model input</a><a id="Model-input-1"></a><a class="docs-heading-anchor-permalink" href="#Model-input" title="Permalink"></a></h2><p>Persefone requires three input files: a configuration file and two map files. How to generate the map files is documented <a href="gis.html">elsewhere</a>. The <a href="io.html">configuration file</a> defines parameter values and looks like this (see <code>src/parameters.toml</code> for a complete list of parameters):</p><pre><code class="language-TOML hljs">### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
### This is the default configuration file for Persefone, containing all model parameters.
### The syntax is described here: https://toml.io/en/
[core]
configfile = "src/parameters.toml" # location of the configuration file
outdir = "results" # location and name of the output folder
overwrite = "ask" # overwrite the output directory? (true/false/"ask")
loglevel = "debug" # verbosity level: "debug", "info", "warn"
processors = 2 # number of processors to use on parallel runs
seed = 2 # seed value for the RNG (0 -> random value)
# dates to start and end the simulation
startdate = 2022-01-01
enddate = 2022-12-31
[world]
landcovermap = "data/landcover_jena.tif" # location of the landcover map
farmfieldsmap = "data/fields_jena.tif" # location of the field geometry map
weatherfile = "data/weather_jena.csv" # location of the weather data file
[farm]
farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)
[nature]
targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
insectmodel = ["season", "habitat", "pesticides", "weather"] # factors affecting insect growth
[crop]
cropmodel = "almass" # crop growth model to use, "almass" or "aquacrop"
cropfile = "data/crop_data_general.csv" # file with general crop parameters
growthfile = "data/almass_crop_growth_curves.csv" # file with crop growth parameters</code></pre><div class="admonition is-info"><header class="admonition-header">Parameter scanning</header><div class="admonition-body"><p>You can set any parameter to a list of different values, e.g. <code>seed = [1,2,3]</code>. Persefone will then set up and run multiple simulations, one for every possible combination of parameters that you entered (i.e. do a full-factorial simulation experiment).</p></div></div><p><em>Last updated: 2023-09-13 (commit 34f053e)</em></p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="odd.html">Overview, Design, Details (ODD) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.23 on <span class="colophon-date" title="Wednesday 13 September 2023 16:00">Wednesday 13 September 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>