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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><script data-outdated-warner src="assets/warner.js"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><a class="tocitem" href="index.html">Introduction</a></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 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">GIS 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><a class="is-disabled">Developing</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-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/adapting.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="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 &lt;configfile&gt;</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&#39;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="@ref"><code>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></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="Thursday 20 July 2023 16:01">Thursday 20 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Adapting Persefone · 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><a class="tocitem" href="index.html">Introduction</a></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 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, 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><a class="is-disabled">Developing</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-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/adapting.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="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 &lt;configfile&gt;</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&#39;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="@ref"><code>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></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="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Dynamic Energy Budgets · 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><a class="tocitem" href="index.html">Introduction</a></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 class="is-active"><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a><ul class="internal"><li><a class="tocitem" href="#energy.jl"><span>energy.jl</span></a></li></ul></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><a class="is-disabled">Nature</a></li><li class="is-active"><a href="energy.html">Dynamic Energy Budgets</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="energy.html">Dynamic Energy Budgets</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/energy.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="Dynamic-Energy-Budgets"><a class="docs-heading-anchor" href="#Dynamic-Energy-Budgets">Dynamic Energy Budgets</a><a id="Dynamic-Energy-Budgets-1"></a><a class="docs-heading-anchor-permalink" href="#Dynamic-Energy-Budgets" title="Permalink"></a></h1><p>Persefone&#39;s nature module uses Kooijman&#39;s Dynamic Energy Budget theory to model energy flows within individuals.</p><p><img src="assets/deb.png" alt="&quot;The standard model of the Dynamic Energy Budget theory&quot;"/></p><p><em>The standard model of the Dynamic Energy Budget theory. (Fig. 1 from Sousa et al. (2010).)</em></p><ul><li><p><a href="https://doi.org/10.1098/rstb.2010.0166">Sousa et al. (2010)</a>. Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428.</p></li><li><p><a href="https://www.researchgate.net/profile/Edgar-Meza-3/post/Is_there_a_toxicokinetic_model_for_daphnia_magna_or_other_zooplankton/attachment/59d62cf579197b807798b396/AS%3A348547653357569%401460111644286/download/Dynamic+Energy+Budget+theory+-+Kooijman.pdf">Kooijman, S. A. L. M. (2009)</a>. Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press.</p></li><li><p><a href="https://doi.org/10.1111/2041-210x.12002">Sibly et al. (2013)</a>. Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161.</p></li></ul><h2 id="energy.jl"><a class="docs-heading-anchor" href="#energy.jl">energy.jl</a><a id="energy.jl-1"></a><a class="docs-heading-anchor-permalink" href="#energy.jl" title="Permalink"></a></h2><article class="docstring"><header><a class="docstring-binding" id="Persefone.DEBparameters" href="#Persefone.DEBparameters"><code>Persefone.DEBparameters</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">DEBparameters</code></pre><p>An immutable struct to save the parameter list for a species&#39; Dynamic Energy Budget model. (See Sousa et al., 2010.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L9-L14">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.EnergyBudget" href="#Persefone.EnergyBudget"><code>Persefone.EnergyBudget</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">EnergyBudget</code></pre><p>This struct represents an individual&#39;s energy balance, as conceptualised by the Dynamic Energy Budget theory. Upon assimilation, energy is first stored as biomass in a reserve buffer, before being used for maintenance, growth, and reproduction. (Note that this is a simplified model form which ignores maturity as a separate buffer.)</p><p><strong>Sources:</strong></p><ul><li>Malishev &amp; Kramer-Schadt (2021). Movement, models, and metabolism: Individual-based energy budget models as next-generation extensions for predicting animal movement outcomes across scales. Ecological Modelling, 441, 109413. https://doi.org/10.1016/j.ecolmodel.2020.109413</li><li>Marques et al. (2018). The AmP project: Comparing species on the basis of dynamic energy budget parameters. PLOS Computational Biology,14(5), e1006100. https://doi.org/10.1371/journal.pcbi.1006100</li><li>Sibly et al. (2013). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161. https://doi.org/10.1111/2041-210x.12002</li><li>Sousa et al. (2010). Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428. https://doi.org/10.1098/rstb.2010.0166</li><li>Kooijman, S. A. L. M. (2009). Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press. https://www.researchgate.net/profile/Edgar-Meza-3/post/Is<em>there</em>a<em>toxicokinetic</em>model<em>for</em>daphnia<em>magna</em>or<em>other</em>zooplankton/attachment/59d62cf579197b807798b396/AS%3A348547653357569%401460111644286/download/Dynamic+Energy+Budget+theory+-+Kooijman.pdf</li><li><em>see also:</em> Brown et al. (2004). Toward a metabolic theory of ecology. Ecology, 85(7), 1771–1789. https://doi.org/10.1890/03-9000</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L30-L46">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.feed!-Tuple{Float64, Persefone.EnergyBudget}" href="#Persefone.feed!-Tuple{Float64, Persefone.EnergyBudget}"><code>Persefone.feed!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">feed!(quantity, energybudget)</code></pre><p>Consume a given quantity of food. Expands the energy reserve by an amount determined by the assimilation rate. Returns <code>true</code> if successful, <code>false</code> if the reserve is already full.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L207-L213">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.growthrate-Tuple{Persefone.EnergyBudget}" href="#Persefone.growthrate-Tuple{Persefone.EnergyBudget}"><code>Persefone.growthrate</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">growthrate(energybudget)</code></pre><p>Calculate the specific growth rate r. (Internal function.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L115-L120">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.investmentratio-Tuple{Persefone.EnergyBudget}" href="#Persefone.investmentratio-Tuple{Persefone.EnergyBudget}"><code>Persefone.investmentratio</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">investmentratio(energybudget)</code></pre><p>Calculate the investment ratio g. (Internal function.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L99-L104">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.maturitymaintenance-Tuple{Persefone.EnergyBudget}" href="#Persefone.maturitymaintenance-Tuple{Persefone.EnergyBudget}"><code>Persefone.maturitymaintenance</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">maturitymaintenance(energybudget)</code></pre><p>Calculate the specific maturity maintenance k_J. (Internal function.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L71-L76">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.mobilisation-Tuple{Persefone.EnergyBudget}" href="#Persefone.mobilisation-Tuple{Persefone.EnergyBudget}"><code>Persefone.mobilisation</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">mobilisation(energybudget)</code></pre><p>Calculate the mobilisation rate J_EC. (Internal function.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L136-L141">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.reproduce!-Tuple{Persefone.EnergyBudget}" href="#Persefone.reproduce!-Tuple{Persefone.EnergyBudget}"><code>Persefone.reproduce!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">reproduce!(energybudget)</code></pre><p>If there is sufficient energy in the <code>offspring</code> buffer of an adult, produce an embryo/egg, reducing the parent energy in the process. Returns the embryo&#39;s energy budget, or <code>nothing</code> if the conditions are not met.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L234-L240">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.scaledreservedensity-Tuple{Persefone.EnergyBudget}" href="#Persefone.scaledreservedensity-Tuple{Persefone.EnergyBudget}"><code>Persefone.scaledreservedensity</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">scaledreservedensity(energybudget)</code></pre><p>Calculate the scaled reserve density e. (Internal function.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L85-L90">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.update!-Tuple{Persefone.EnergyBudget}" href="#Persefone.update!-Tuple{Persefone.EnergyBudget}"><code>Persefone.update!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">update!(energybudget)</code></pre><p>Carry out a daily update of the energy budget. Mobilises reserves and allocates these to maintenance (prioritised), growth, and reproduction.</p><p>Return <code>true</code> if the individual has enough energy to survive, or <code>false</code> if the reserve is empty and it starves.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L154-L162">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.volumetriclength-Tuple{Persefone.EnergyBudget}" href="#Persefone.volumetriclength-Tuple{Persefone.EnergyBudget}"><code>Persefone.volumetriclength</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">volumetriclength(energybudget)</code></pre><p>Calculate the structural length in cm based on an individual&#39;s weight (assuming a density of 1 g/cm³ to calculate volume, see Kooijman 2009).</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/nature/energy.jl#L58-L63">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="nature.html">« Nature</a><a class="docs-footer-nextpage" href="species.html">Species »</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="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. 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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Farm submodel · 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><a class="tocitem" href="index.html">Introduction</a></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">GIS 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 class="is-active"><a class="tocitem" href="farm.html">Farm submodel</a><ul class="internal"><li><a class="tocitem" href="#farm.jl"><span>farm.jl</span></a></li></ul></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="farm.html">Farm submodel</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="farm.html">Farm submodel</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/farm.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="Farm-submodel"><a class="docs-heading-anchor" href="#Farm-submodel">Farm submodel</a><a id="Farm-submodel-1"></a><a class="docs-heading-anchor-permalink" href="#Farm-submodel" title="Permalink"></a></h1><p>Eventually, Persefone will include multiple farm-decision submodels. At the moment, we are only working with a very basic mock-up.</p><h2 id="farm.jl"><a class="docs-heading-anchor" href="#farm.jl">farm.jl</a><a id="farm.jl-1"></a><a class="docs-heading-anchor-permalink" href="#farm.jl" title="Permalink"></a></h2><p>This file is responsible for managing the farm module(s).</p><article class="docstring"><header><a class="docstring-binding" id="Persefone.Farmer" href="#Persefone.Farmer"><code>Persefone.Farmer</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Farmer</code></pre><p>This is the agent type for the farm ABM. (Not yet implemented.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L6-L10">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.initfarms!-Tuple{Agents.AgentBasedModel}" href="#Persefone.initfarms!-Tuple{Agents.AgentBasedModel}"><code>Persefone.initfarms!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">initfarms!(model)</code></pre><p>Initialise the model with a set of farm agents.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L24-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.stepagent!-Tuple{Farmer, Agents.AgentBasedModel}" href="#Persefone.stepagent!-Tuple{Farmer, Agents.AgentBasedModel}"><code>Persefone.stepagent!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">stepagent!(farmer, model)</code></pre><p>Update a farmer by one day.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L15-L19">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="crops.html">« Crop submodel</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="Thursday 20 July 2023 16:01">Thursday 20 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Farm submodel · 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><a class="tocitem" href="index.html">Introduction</a></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 class="is-active"><a class="tocitem" href="farm.html">Farm submodel</a><ul class="internal"><li><a class="tocitem" href="#farm.jl"><span>farm.jl</span></a></li></ul></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="farm.html">Farm submodel</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="farm.html">Farm submodel</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/farm.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="Farm-submodel"><a class="docs-heading-anchor" href="#Farm-submodel">Farm submodel</a><a id="Farm-submodel-1"></a><a class="docs-heading-anchor-permalink" href="#Farm-submodel" title="Permalink"></a></h1><p>Eventually, Persefone will include multiple farm-decision submodels. At the moment, we are only working with a very basic mock-up.</p><h2 id="farm.jl"><a class="docs-heading-anchor" href="#farm.jl">farm.jl</a><a id="farm.jl-1"></a><a class="docs-heading-anchor-permalink" href="#farm.jl" title="Permalink"></a></h2><p>This file is responsible for managing the farm module(s).</p><article class="docstring"><header><a class="docstring-binding" id="Persefone.Farmer" href="#Persefone.Farmer"><code>Persefone.Farmer</code></a> — <span class="docstring-category">Type</span></header><section><div><pre><code class="language-julia hljs">Farmer</code></pre><p>This is the agent type for the farm ABM. (Not yet implemented.)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L6-L10">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.initfarms!-Tuple{Agents.AgentBasedModel}" href="#Persefone.initfarms!-Tuple{Agents.AgentBasedModel}"><code>Persefone.initfarms!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">initfarms!(model)</code></pre><p>Initialise the model with a set of farm agents.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L24-L28">source</a></section></article><article class="docstring"><header><a class="docstring-binding" id="Persefone.stepagent!-Tuple{Farmer, Agents.AgentBasedModel}" href="#Persefone.stepagent!-Tuple{Farmer, Agents.AgentBasedModel}"><code>Persefone.stepagent!</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">stepagent!(farmer, model)</code></pre><p>Update a farmer by one day.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//src/farm/farm.jl#L15-L19">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="crops.html">« Crop submodel</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="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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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">GIS 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>Persefone is an agent-based, socio-economic-ecological model of agricultural landscapes in Europe under the Common Agricultural Policy (CAP).</p><p>It&#39;s aim is to investigate how policy affects farmer decision-making, and how this in turn affects various animal species. It includes a farm submodel, a crop-growth submodel, and an ecological submodels.</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 &lt;CONFIG&gt;</code></pre><p>Other commandline arguments are:</p><pre><code class="nohighlight hljs">usage: run.jl [-c CONFIGFILE] [-s SEED] [-o OUTDIR] [-l LOGLEVEL] <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" 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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>Persefone is an agent-based, socio-economic-ecological model of agricultural landscapes in Europe under the Common Agricultural Policy (CAP).</p><p>It&#39;s aim is to investigate how policy affects farmer decision-making, and how this in turn affects various animal species. It includes a farm submodel, a crop-growth submodel, and an ecological submodels.</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 &lt;CONFIG&gt;</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] [--version] [-h]
optional arguments: optional arguments:
...@@ -39,4 +39,4 @@ popoutfreq = &quot;daily&quot; # output frequency population-level data, daily/m ...@@ -39,4 +39,4 @@ popoutfreq = &quot;daily&quot; # output frequency population-level data, daily/m
indoutfreq = &quot;end&quot; # output frequency individual-level data, daily/monthly/yearly/end/never indoutfreq = &quot;end&quot; # output frequency individual-level data, daily/monthly/yearly/end/never
[crop] [crop]
cropmodel = &quot;linear&quot; # crop growth model to use, &quot;linear&quot; or &quot;aquacrop&quot; (not yet implemented)</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: 2023-07-20 (commit 0fd9917)</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="Thursday 20 July 2023 16:01">Thursday 20 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> cropmodel = &quot;linear&quot; # crop growth model to use, &quot;linear&quot; or &quot;aquacrop&quot; (not yet implemented)</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: 2023-07-27 (commit 1e6e7d6)</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="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Species · 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 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href="species.html">Species</a><ul class="internal"><li><a class="tocitem" href="#Skylark"><span>Skylark</span></a></li></ul></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><a class="is-disabled">Nature</a></li><li class="is-active"><a href="species.html">Species</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="species.html">Species</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/species.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="Species"><a class="docs-heading-anchor" href="#Species">Species</a><a id="Species-1"></a><a class="docs-heading-anchor-permalink" href="#Species" title="Permalink"></a></h1><p>The ecological submodel in Persefone simulates a range of species in agricultural landscapes.</p><h2 id="Skylark"><a class="docs-heading-anchor" href="#Skylark">Skylark</a><a id="Skylark-1"></a><a class="docs-heading-anchor-permalink" href="#Skylark" title="Permalink"></a></h2></article><nav class="docs-footer"><a class="docs-footer-prevpage" 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July 2023 16:01">Thursday 20 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html> <html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Species · 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 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href="nature.html">Nature</a></li><li><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a></li><li class="is-active"><a class="tocitem" href="species.html">Species</a><ul class="internal"><li><a class="tocitem" href="#Skylark"><span>Skylark</span></a></li></ul></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><a class="is-disabled">Nature</a></li><li class="is-active"><a href="species.html">Species</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="species.html">Species</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/species.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="Species"><a class="docs-heading-anchor" href="#Species">Species</a><a id="Species-1"></a><a class="docs-heading-anchor-permalink" href="#Species" title="Permalink"></a></h1><p>The ecological submodel in Persefone simulates a range of species in agricultural landscapes.</p><h2 id="Skylark"><a class="docs-heading-anchor" href="#Skylark">Skylark</a><a id="Skylark-1"></a><a class="docs-heading-anchor-permalink" href="#Skylark" title="Permalink"></a></h2></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="energy.html">« Dynamic Energy Budgets</a><a class="docs-footer-nextpage" href="crops.html">Crop submodel »</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 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# Dynamic Energy Budgets
Persefone's nature module uses Kooijman's Dynamic Energy Budget theory to model energy
flows within individuals.
!["The standard model of the Dynamic Energy Budget theory"](assets/deb.png)
*The standard model of the Dynamic Energy Budget theory. (Fig. 1 from Sousa et al. (2010).)*
- [Sousa et al. (2010)](https://doi.org/10.1098/rstb.2010.0166). Dynamic energy budget theory restores coherence in biology. Philosophical Transactions of the Royal Society B: Biological Sciences, 365(1557), 3413–3428.
- [Kooijman, S. A. L. M. (2009)](https://www.researchgate.net/profile/Edgar-Meza-3/post/Is_there_a_toxicokinetic_model_for_daphnia_magna_or_other_zooplankton/attachment/59d62cf579197b807798b396/AS%3A348547653357569%401460111644286/download/Dynamic+Energy+Budget+theory+-+Kooijman.pdf). Dynamic energy and mass budgets in biological systems (3rd ed). Cambridge University Press.
- [Sibly et al. (2013)](https://doi.org/10.1111/2041-210x.12002). Representing the acquisition and use of energy by individuals in agent-based models of animal populations. Methods in Ecology and Evolution, 4(2), 151–161.
## energy.jl
```@autodocs
Modules = [Persefone]
Pages = ["nature/energy.jl"]
```
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# GIS data # Maps and weather data
Persefone currently requires two separate map input files: one for land cover, Persefone currently requires two separate map input files: one for land cover,
the other for field geometry. This documents describe how to obtain and process the other for field geometry. Additionally, a weather input file is needed.
the data needed for each of these. This documents describe how to obtain and process the data needed for each
of these.
## Land cover maps ## Land cover maps
...@@ -71,3 +72,59 @@ the advanced parameters, set the output data type to `UInt32`. Finally, enter an ...@@ -71,3 +72,59 @@ the advanced parameters, set the output data type to `UInt32`. Finally, enter an
output file name and run. The resulting TIF file can be passed to Persefone output file name and run. The resulting TIF file can be passed to Persefone
as the `farmfieldmap` parameter. as the `farmfieldmap` parameter.
## Weather data
Currently, Persefone uses historical weather data from the closes weather station
as its weather input. (In future, this may be changed to a more detailed raster
input, which could then also provide future weather predictions under climate change.)
Weather data can be downloaded from the [German weather service (DWD)](https://www.dwd.de/DE/leistungen/cdc/cdc_ueberblick-klimadaten.html?nn=16102).
The relevant data are in the folder [`daily/kl/historical`](https://opendata.dwd.de/climate_environment/CDC/observations_germany/climate/daily/kl/historical/).
The description of this data set and the list of weather stations can be found in the
Persefone repository, in the `docs` folder (or downloaded from the link above).
Using the list of weather stations, select the one closest to the area of study.
Note that not all stations were continuously in operation; make sure that the selected
station covers the years of interest.
- **Region Jena:** station number 02444 ("Jena (Sternwarte)")
- **Region Eichsfeld:**
- **Region Thüringer Becken:**
- **Region Hohenlohe:**
- **Region Bodensee:**
- **Region Nördlicher Oberrhein:**
From the link above, download the ZIP file associated with the station number.
Check the included meta-data if there is any important missing data, or other relevant
information (e.g. the station moved position).
Then use `data/extract_weather_data.R` to process the data into the format needed
by Persefone:
```R
library(tidyverse)
## replace this with the correct file name
weatherfile = "produkt_klima_tag_18210101_20221231_02444.txt"
data = read.table(weatherfile, sep=";", header=T)
weather = data %>%
## drop values before 2000 to save space
filter(MESS_DATUM>=20000101) %>%
## select relevant variables and convert place-holder values to NA
select(MESS_DATUM, FM, RSK, SDK, VPM, TMK, TXK, TNK) %>%
mutate(date=MESS_DATUM, MESS_DATUM=NULL,
mean_windspeed=na_if(FM, -999), FM=NULL,
precipitation=na_if(RSK, -999), RSK=NULL,
sunshine_hours=na_if(SDK, -999), SDK=NULL,
mean_vapour_pressure=na_if(VPM, -999), VPM=NULL,
mean_temperature=na_if(TMK, -999), TMK=NULL,
max_temperature=na_if(TXK, -999), TXK=NULL,
min_temperature=na_if(TNK, -999), TNK=NULL)
## replace with the desired file name
write.csv(weather, file="weather_jena.csv", row.names=FALSE)
```
*Note: for calculating the reference evapotranspiration ET_0 (needed for the AquaCrop model),
use the [FAO Penman-Monteith equation](https://www.fao.org/3/X0490E/x0490e06.htm#equation).*
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