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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Adapting Persefone · Persefone</title><meta name="title" content="Adapting Persefone · Persefone"/><meta property="og:title" content="Adapting Persefone · Persefone"/><meta property="twitter:title" content="Adapting Persefone · Persefone"/><meta name="description" content="Documentation for Persefone."/><meta property="og:description" content="Documentation for Persefone."/><meta property="twitter:description" content="Documentation for Persefone."/><script data-outdated-warner src="assets/warner.js"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/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" 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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><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li><a class="tocitem" href="index.html">Introduction</a></li><li><span class="tocitem">User guide</span><ul><li><a class="tocitem" href="using.html">The Persefone.jl Package</a></li><li><a class="tocitem" href="gui.html">Graphical User Interface</a></li><li><a class="tocitem" href="config.html">Configuration</a></li></ul></li><li><span class="tocitem">Developer guide</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li class="is-active"><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 and Output</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"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Developer guide</a></li><li class="is-active"><a href="adapting.html">Adapting Persefone</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="adapting.html">Adapting Persefone</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model/-/tree/master/docs/src/adapting.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Adapting-Persefone"><a class="docs-heading-anchor" href="#Adapting-Persefone">Adapting Persefone</a><a id="Adapting-Persefone-1"></a><a class="docs-heading-anchor-permalink" href="#Adapting-Persefone" title="Permalink"></a></h1><p>A key development goal of Persefone is to be <a href="https://doi.org/10.1515/itit-2019-0040">FAIR</a>: <em>findable, accessible, interoperable, and reusable</em>. We aim to build a model that is both easy to use and easy to adapt to new situations.</p><p>There are multiple ways to adapt Persefone for a new modelling study:</p><h3 id="Changing-the-parameters"><a class="docs-heading-anchor" href="#Changing-the-parameters">Changing the parameters</a><a id="Changing-the-parameters-1"></a><a class="docs-heading-anchor-permalink" href="#Changing-the-parameters" title="Permalink"></a></h3><p>The simplest way to adapt Persefone is simply by changing the parameters. Copy <code>src/parameters.toml</code> to a new location, adjust it to your needs, and run the model using <code>julia run.jl -c <configfile></code>.</p><h3 id="Changing-the-region"><a class="docs-heading-anchor" href="#Changing-the-region">Changing the region</a><a id="Changing-the-region-1"></a><a class="docs-heading-anchor-permalink" href="#Changing-the-region" title="Permalink"></a></h3><p>To apply Persefone to a new region, you need to create new input maps of land cover and farmplots. How to do so is described <a href="gis.html">here</a>.</p><p><em>You may also need to change aspects of the <code>farm</code> submodel. This is not yet implemented.</em></p><h3 id="Adding-new-animal-species"><a class="docs-heading-anchor" href="#Adding-new-animal-species">Adding new animal species</a><a id="Adding-new-animal-species-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-animal-species" title="Permalink"></a></h3><p>To implement a new species to the <code>nature</code> submodel, add a new file to the <code>src/nature/species</code> directory and <code>include</code> it in <code>src/Persefone.jl</code>, as well as adding the name of the species to the <code>nature.targetspecies</code> parameter. In the new file, implement the species using the <a href="nature.html#Persefone.@species-Tuple{Any, Any}"><code>@species</code></a> syntax as described <a href="species-dsl.html">here</a>.</p><h3 id="Adding-new-crop-species"><a class="docs-heading-anchor" href="#Adding-new-crop-species">Adding new crop species</a><a id="Adding-new-crop-species-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-crop-species" title="Permalink"></a></h3><p><em>Crop growth is not yet implemented.</em></p><h3 id="Adding-new-farmer-behaviour"><a class="docs-heading-anchor" href="#Adding-new-farmer-behaviour">Adding new farmer behaviour</a><a id="Adding-new-farmer-behaviour-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-new-farmer-behaviour" title="Permalink"></a></h3><p><em>Farmer behaviour is not yet implemented.</em></p><h3 id="Adding-a-new-submodel"><a class="docs-heading-anchor" href="#Adding-a-new-submodel">Adding a new submodel</a><a id="Adding-a-new-submodel-1"></a><a class="docs-heading-anchor-permalink" href="#Adding-a-new-submodel" title="Permalink"></a></h3><p>To add a new submodel in addition to the existing ones (<code>nature</code>, <code>crop</code>, and <code>farm</code>), you need to familiarise yourself with the <a href="architecture.html">software architecture</a>. In particular, you need to understand how initialisation and scheduling works in <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/simulation.jl"><code>src/core/simulation.jl</code></a>, and what information is stored in the <code>model</code> object.</p><p>If you want to add a new agent type, use Agents.jl's <a href="https://juliadynamics.github.io/Agents.jl/stable/tutorial/#Agents.@agent"><code>@agent</code></a> macro. (But be aware that Persefone already has three agent types and you may encounter <a href="https://juliadynamics.github.io/Agents.jl/stable/performance_tips/#Avoid-Unions-of-many-different-agent-types-(temporary!)-1">performance problems</a>.) Having implemented the new agent type, add it to the <code>model</code> objects type definition and scheduler, and write an initialisation function and a <code>stepagent!</code> function. (See <a href="simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}"><code>Persefone.initmodel</code></a> and <a href="simulation.html#Persefone.stepsimulation!-Tuple{Agents.AgentBasedModel}"><code>stepsimulation!</code></a> for details.)</p><h3 id="Linking-to-another-model"><a class="docs-heading-anchor" href="#Linking-to-another-model">Linking to another model</a><a id="Linking-to-another-model-1"></a><a class="docs-heading-anchor-permalink" href="#Linking-to-another-model" title="Permalink"></a></h3><p>Persefone can also be used as a software library and be called from another application. For this purpose, it is set up as a <a href="https://pkgdocs.julialang.org/v1/">Julia package</a>, with a <a href="https://docs.julialang.org/en/v1/manual/modules/">module</a> exporting various model functions, types, and macros (see <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/Persephone.jl"><code>src/Persefone.jl</code></a>). Of particular interest are the functions <a href="simulation.html#Persefone.simulate"><code>simulate</code></a> (set up and run a complete simulation based on a config file), <a href="simulation.html#Persefone.initialise"><code>initialise</code></a> (create one or more <code>model</code> objects from a config file), <a href="simulation.html#Persefone.simulate!-Tuple{Agents.AgentBasedModel}"><code>simulate!</code></a> (do a simulation run with an existing <code>model</code> object), and <a href="simulation.html#Persefone.stepsimulation!-Tuple{Agents.AgentBasedModel}"><code>stepsimulation!</code></a> (update a <code>model</code> object by one time step).</p><p>To interface with Julia from another language, see the Julia docs <a href="https://docs.julialang.org/en/v1/manual/calling-c-and-fortran-code/">here</a> and <a href="https://docs.julialang.org/en/v1/manual/embedding/">here</a>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="developing.html">« Developing Persefone</a><a class="docs-footer-nextpage" href="architecture.html">Source code architecture »</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><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Tuesday 31 October 2023 18:07">Tuesday 31 October 2023</span>. 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