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\vspace*{0.1cm}\par\noindent
\today
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\textbf{ v0.6.0 }
\textbf{ v0.7.0 }
\end{center}
\end{titlingpage}
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Configuration · Persefone.jl</title><meta name="title" content="Configuration · Persefone.jl"/><meta property="og:title" content="Configuration · Persefone.jl"/><meta property="twitter:title" content="Configuration · Persefone.jl"/><meta name="description" content="Documentation for Persefone.jl."/><meta property="og:description" content="Documentation for Persefone.jl."/><meta property="twitter:description" content="Documentation for Persefone.jl."/><script data-outdated-warner src="assets/warner.js"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" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="search_index.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/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-frappe.css" data-theme-name="catppuccin-frappe"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-latte.css" data-theme-name="catppuccin-latte"/><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.jl logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone.jl</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 class="is-active"><a class="tocitem" href="config.html">Configuration</a></li></ul></li><li><span class="tocitem">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</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><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</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"><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">User guide</a></li><li class="is-active"><a href="config.html">Configuration</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="config.html">Configuration</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/config.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="Configuration"><a class="docs-heading-anchor" href="#Configuration">Configuration</a><a id="Configuration-1"></a><a class="docs-heading-anchor-permalink" href="#Configuration" title="Permalink"></a></h1><p>Persefone requires three <a href="io.html">input</a> files: a configuration file and two map files. How to generate the map files is documented <a href="gis.html">elsewhere</a>. The configuration file defines parameter values and looks like this (see <code>src/parameters.toml</code> for the default):</p><pre><code class="language-TOML hljs">### Persefone.jl - a model of agricultural landscapes and ecosystems in Europe.
###
### This is the default configuration file for Persefone, containing all model parameters.
### The syntax is described here: https://toml.io/en/
[core]
configfile = &quot;src/parameters.toml&quot; # location of the configuration file
outdir = &quot;results&quot; # location and name of the output folder
overwrite = &quot;ask&quot; # overwrite the output directory? (true/false/&quot;ask&quot;)
logoutput = &quot;both&quot; # log output to screen/file/both
csvoutput = true # save collected data in CSV files
visualise = true # generate result graphs
storedata = true # keep collected data in memory
loglevel = &quot;debug&quot; # verbosity level: &quot;debug&quot;, &quot;info&quot;, &quot;warn&quot;
processors = 2 # number of processors to use on parallel runs
seed = 2 # seed value for the RNG (0 -&gt; random value)
startdate = 2022-01-01 # first day of the simulation
enddate = 2022-12-31 # last day of the simulation
[world]
landcovermap = &quot;data/regions/jena/landcover.tif&quot; # location of the landcover map
farmfieldsmap = &quot;data/regions/jena/fields.tif&quot; # location of the field geometry map
weatherfile = &quot;data/regions/jena/weather.csv&quot; # location of the weather data file
[farm]
farmmodel = &quot;FieldManager&quot; # which version of the farm model to use (not yet implemented)
[nature]
targetspecies = [&quot;Wolpertinger&quot;, &quot;Wyvern&quot;] # list of target species to simulate
popoutfreq = &quot;daily&quot; # output frequency population-level data, daily/monthly/yearly/end/never
indoutfreq = &quot;end&quot; # output frequency individual-level data, daily/monthly/yearly/end/never
insectmodel = [&quot;season&quot;, &quot;habitat&quot;, &quot;pesticides&quot;, &quot;weather&quot;] # factors affecting insect growth
[crop]
cropmodel = &quot;almass&quot; # crop growth model to use, &quot;almass&quot; or &quot;aquacrop&quot;
cropfile = &quot;data/crops/almass/crop_data_general.csv&quot; # file with general crop parameters
growthfile = &quot;data/crops/almass/almass_crop_growth_curves.csv&quot; # file with crop growth parameters </code></pre><div class="admonition is-info"><header class="admonition-header">Parameter scanning</header><div class="admonition-body"><p>You can set any parameter to a list of different values, e.g. <code>seed = [1,2,3]</code>. Persefone will then set up and run multiple simulations, one for every possible combination of parameters that you entered (i.e. do a full-factorial simulation experiment).</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="gui.html">« Graphical User Interface</a><a class="docs-footer-nextpage" href="management.html">Farm management »</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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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<!DOCTYPE html>
<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Crop models · Persefone.jl</title><meta name="title" content="Crop models · Persefone.jl"/><meta property="og:title" content="Crop models · Persefone.jl"/><meta property="twitter:title" content="Crop models · Persefone.jl"/><meta name="description" content="Documentation for Persefone.jl."/><meta property="og:description" content="Documentation for Persefone.jl."/><meta property="twitter:description" content="Documentation for Persefone.jl."/><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" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.8/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="search_index.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/catppuccin-mocha.css" data-theme-name="catppuccin-mocha"/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/catppuccin-macchiato.css" data-theme-name="catppuccin-macchiato"/><link class="docs-theme-link" rel="stylesheet" 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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><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</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 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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">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</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><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li class="is-active"><a class="tocitem" href="crops.html">Crop submodel</a><ul class="internal"><li><a class="tocitem" href="#farmplot.jl"><span>farmplot.jl</span></a></li><li><a class="tocitem" href="#crops.jl"><span>crops.jl</span></a></li></ul></li><li><a class="tocitem" href="farm.html">Farm submodel</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"><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">Software API</a></li><li class="is-active"><a href="crops.html">Crop submodel</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="crops.html">Crop submodel</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/crops.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="Crop-submodel"><a class="docs-heading-anchor" href="#Crop-submodel">Crop submodel</a><a id="Crop-submodel-1"></a><a class="docs-heading-anchor-permalink" href="#Crop-submodel" title="Permalink"></a></h1><p>Eventually, the plan is to have Persefone include a reimplementation of the AquaCrop model, a well-established crop growth model developed by the FAO. Until then, we are using the crop growth submodel used in <a href="https://doi.org/10.1016/S0304-3800(03)00173-X">ALMaSS</a>.</p><h2 id="farmplot.jl"><a class="docs-heading-anchor" href="#farmplot.jl">farmplot.jl</a><a id="farmplot.jl-1"></a><a class="docs-heading-anchor-permalink" href="#farmplot.jl" title="Permalink"></a></h2><p>This file is responsible for the farm plots, i.e. the indidivual fields that farmers manage.</p><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.FarmPlot" href="#Persefone.FarmPlot"><code>Persefone.FarmPlot</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">FarmPlot</code></pre><p>A struct representing a single field, on which a crop can be grown.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L6-L10">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.averagefieldsize-Tuple{SimulationModel}" href="#Persefone.averagefieldsize-Tuple{SimulationModel}"><code>Persefone.averagefieldsize</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">averagefieldsize(model)</code></pre><p>Calculate the average field size in hectares for the model landscape.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L105-L109">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.cropcover-Tuple{Tuple{Int64, Int64}, SimulationModel}" href="#Persefone.cropcover-Tuple{Tuple{Int64, Int64}, SimulationModel}"><code>Persefone.cropcover</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">cropcover(model, position)</code></pre><p>Return the crop cover of the crop at this position, or nothing if there is no crop here (utility wrapper).</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L148-L153">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.cropheight-Tuple{Tuple{Int64, Int64}, SimulationModel}" href="#Persefone.cropheight-Tuple{Tuple{Int64, Int64}, SimulationModel}"><code>Persefone.cropheight</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">cropheight(model, position)</code></pre><p>Return the height of the crop at this position, or nothing if there is no crop here (utility wrapper).</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L137-L142">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.cropname-Tuple{Tuple{Int64, Int64}, SimulationModel}" href="#Persefone.cropname-Tuple{Tuple{Int64, Int64}, SimulationModel}"><code>Persefone.cropname</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">cropname(model, position)</code></pre><p>Return the name of the crop at this position, or an empty string if there is no crop here (utility wrapper).</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L126-L131">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.croptype-Tuple{Tuple{Int64, Int64}, SimulationModel}" href="#Persefone.croptype-Tuple{Tuple{Int64, Int64}, SimulationModel}"><code>Persefone.croptype</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">croptype(model, position)</code></pre><p>Return the crop at this position, or nothing if there is no crop here (utility wrapper).</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L116-L120">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.harvest!-Tuple{FarmPlot, SimulationModel}" href="#Persefone.harvest!-Tuple{FarmPlot, SimulationModel}"><code>Persefone.harvest!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">harvest!(farmplot, model)</code></pre><p>Harvest the crop of this farmplot.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L57-L61">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.isgrassland-Tuple{FarmPlot, SimulationModel}" href="#Persefone.isgrassland-Tuple{FarmPlot, SimulationModel}"><code>Persefone.isgrassland</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">isgrassland(farmplot, model)</code></pre><p>Classify a farmplot as grassland or not (i.e., is the landcover of &gt;80% of its pixels grass?)</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L88-L92">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.sow!-Tuple{FarmPlot, SimulationModel, String}" href="#Persefone.sow!-Tuple{FarmPlot, SimulationModel, String}"><code>Persefone.sow!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">sow!(farmplot, model, cropname)</code></pre><p>Sow the specified crop on the farmplot.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L41-L45">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.stepagent!-Tuple{FarmPlot, SimulationModel}" href="#Persefone.stepagent!-Tuple{FarmPlot, SimulationModel}"><code>Persefone.stepagent!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">stepagent!(farmplot, model)</code></pre><p>Update a farm plot by one day.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L32-L36">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.@harvest-Tuple{}" href="#Persefone.@harvest-Tuple{}"><code>Persefone.@harvest</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">@harvest()</code></pre><p>Harvest the current field. Requires the variables <code>field</code> and <code>model</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L77-L81">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.@sow-Tuple{Any}" href="#Persefone.@sow-Tuple{Any}"><code>Persefone.@sow</code></a> — <span class="docstring-category">Macro</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">@sow(cropname)</code></pre><p>Sow the named crop on the current field. Requires the variables <code>field</code> and <code>model</code>.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/crop/farmplot.jl#L68-L72">source</a></section></article><h2 id="crops.jl"><a class="docs-heading-anchor" href="#crops.jl">crops.jl</a><a id="crops.jl-1"></a><a class="docs-heading-anchor-permalink" href="#crops.jl" title="Permalink"></a></h2><p>This includes the types and functions needed for all crop growth model, which are also referenced by the other submodels.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="species.html">« Species models</a><a class="docs-footer-nextpage" href="farm.html">Farm 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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. 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submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</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"><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="developing.html">Developing Persefone</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="developing.html">Developing 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/developing.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="Developing-Persefone"><a class="docs-heading-anchor" href="#Developing-Persefone">Developing Persefone</a><a id="Developing-Persefone-1"></a><a class="docs-heading-anchor-permalink" href="#Developing-Persefone" title="Permalink"></a></h1><h2 id="Setting-up"><a class="docs-heading-anchor" href="#Setting-up">Setting up</a><a id="Setting-up-1"></a><a class="docs-heading-anchor-permalink" href="#Setting-up" title="Permalink"></a></h2><p>If you haven&#39;t worked with Julia before, here are detailed instructions for how to set up your development environment. The main development is currently done on Linux (and as the primary execution platform will be an HPC, Linux compatibility is important), but developing on Windows works too.</p><h3 id="Visual-Studio-Code-on-Windows"><a class="docs-heading-anchor" href="#Visual-Studio-Code-on-Windows">Visual Studio Code on Windows</a><a id="Visual-Studio-Code-on-Windows-1"></a><a class="docs-heading-anchor-permalink" href="#Visual-Studio-Code-on-Windows" title="Permalink"></a></h3><ol><li><p>Download and install <a href="https://julialang.org/downloads/">Julia</a>, <a href="https://git-scm.com/download/win">git</a> and <a href="https://code.visualstudio.com/">Visual Studio Code</a>.</p></li><li><p>Install the <a href="https://www.julia-vscode.org/">Julia extension for VS Code</a>: In VS Code, open the extensions pane (<code>Ctrl+Shift+X</code>). Search for and install Julia Language Support.</p></li><li><p>Clone the <a href="https://git.idiv.de/persefone/persefone-model.git">Gitlab repository</a>: In VS Code, open the source control pane (<code>Ctrl+Shift+G</code>). Click on <code>Clone</code> and enter the repo URL. Then select a folder on your computer to download the files into, and let VS Code open the project once it has been cloned.</p></li><li><p>Start a Julia REPL: In VS Code, bring up the command palette (<code>Ctrl+Shift+P</code>). Execute the command <code>Julia: Start REPL</code>. Then install all dependencies of Persefone by running <code>using Pkg; Pkg.activate(&quot;.&quot;); Pkg.instantiate()</code>. (This will take some time.)</p></li><li><p>Open the file <code>run.jl</code> and click <code>Execute</code> (triangular button in the top right). The source code will compile (this can take a lot of time the first time you do it) and run a default simulation.</p></li><li><p>Further steps: You may want to familiarise yourself with how to use <a href="https://code.visualstudio.com/docs/sourcecontrol/overview">git with VS Code</a>. You may also want to clone the Persefone Desktop <a href="https://git.idiv.de/persefone/persefone-desktop.git">repository</a> (repeat steps 3 to 5).</p></li></ol><h3 id="Emacs-on-Linux"><a class="docs-heading-anchor" href="#Emacs-on-Linux">Emacs on Linux</a><a id="Emacs-on-Linux-1"></a><a class="docs-heading-anchor-permalink" href="#Emacs-on-Linux" title="Permalink"></a></h3><p><em>You can of course also use VS Code on Linux. In that case, follow the instructions above.</em></p><p>Make sure you have git and Julia installed. Git should be in your distro&#39;s repos (e.g. <code>sudo apt install git</code>). To install Julia, <a href="https://julialang.org/downloads/">download</a> the binary and unpack it. For greater ease of use, copy the unpacked files to <code>/usr/local/lib/julia</code> (or similar) and create a symlink to the executable: <code>sudo ln -s /usr/local/lib/julia/bin/julia /usr/local/bin/julia</code>. Then go the to folder that you want to use for development and run <code>git clone https://git.idiv.de/persefone/persefone-model.git .</code> in your terminal.</p><p>There are a couple of addons that make working with Julia much nicer in Emacs:</p><ol><li><p><code>julia-mode</code> gives syntax highlighting. Install with <code>M-x package-install julia-mode</code>.</p></li><li><p><a href="https://github.com/gcv/julia-snail"><code>julia-snail</code></a> provides IDE-like features, especially a fully-functional REPL and the ability to evaluate code straight from inside a buffer. Note that the installation can be somewhat tricky. You first need to manually install all the dependencies of its dependency <a href="https://github.com/akermu/emacs-libvterm">vterm</a>, then install vterm itself with <code>M-x package-install vterm</code>, <em>before</em> you can do <code>M-x package-install julia-snail</code>. Then add it to your <code>init.el</code> with <code>(require &#39;julia-snail)</code> and <code>(add-hook &#39;julia-mode-hook #&#39;julia-snail-mode)</code>.</p></li><li><p><a href="http://company-mode.github.io/"><code>company-mode</code></a> integrates with Snail to give code completion. Install with <code>M-x package-install company</code>, then add <code>(add-hook &#39;julia-mode-hook #&#39;company-mode)</code> and <code>(global-set-key (kbd &quot;C-&lt;tab&gt;&quot;) &#39;company-complete)</code> to your <code>init.el</code>.</p></li><li><p><a href="https://magit.vc/"><code>magit</code></a> is a great git interface for Emacs. Install with <code>M-x package-install magit</code> and add <code>(global-set-key (kbd &quot;C-x g&quot;) &#39;magit-status)</code> to your <code>init.el</code>.</p></li></ol><h2 id="Development-workflow"><a class="docs-heading-anchor" href="#Development-workflow">Development workflow</a><a id="Development-workflow-1"></a><a class="docs-heading-anchor-permalink" href="#Development-workflow" title="Permalink"></a></h2><ol><li><p>Pull the current version from the master branch on Gitlab: <a href="https://git.idiv.de/persefone/persefone-model">https://git.idiv.de/persefone/persefone-model</a>.</p></li><li><p>If you are working on a new feature, create a new branch to avoid breaking the <code>master</code> branch. (The <code>master</code> branch on Github should always be in a runnable and error-free state.)</p></li><li><p>Implement your changes.</p></li><li><p>Run an example simulation and the test suite to make sure everything works without crashing (<code>make run</code> and <code>make test</code> on Linux, or execute <code>run.jl</code> and <code>test/runtests.jl</code> manually.)</p></li><li><p>Commit your work frequently, and try to keep each commit small. Don&#39;t forget to add relevant tests to the test suite.</p></li><li><p>Once your satisfied with your work, do another pull/merge from the <code>master</code> branch in case somebody else changed the branch in the meantime. Then merge your work into <code>master</code> and push to the Gitlab server.</p></li><li><p>Repeat :-)</p></li></ol><p>The Gitlab <a href="https://git.idiv.de/persefone/persefone-model/-/boards/373">issue tracker</a> can be used to create, discuss, and assign tasks, as well as to monitor progress towards milestones/releases. Once we have a first release, we will start using <a href="https://semver.org/">semantic versioning</a> and a <a href="https://keepachangelog.com/en/1.0.0/">changelog</a>.</p><h2 id="Important-libraries"><a class="docs-heading-anchor" href="#Important-libraries">Important libraries</a><a id="Important-libraries-1"></a><a class="docs-heading-anchor-permalink" href="#Important-libraries" title="Permalink"></a></h2><h3 id="Revise.jl"><a class="docs-heading-anchor" href="#Revise.jl">Revise.jl</a><a id="Revise.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Revise.jl" title="Permalink"></a></h3><p><a href="https://timholy.github.io/Revise.jl/stable/"><code>Revise.jl</code></a> allows one to reload code without restarting the Julia interpreter. Get it with <code>Pkg.add(&quot;Revise&quot;)</code>, then add <code>using Revise</code> to <code>.julia/config/startup.jl</code> to have it automatically available.</p><h3 id="Test"><a class="docs-heading-anchor" href="#Test">Test</a><a id="Test-1"></a><a class="docs-heading-anchor-permalink" href="#Test" title="Permalink"></a></h3><p>Persefone uses the inbuilt Julia <a href="https://docs.julialang.org/en/v1/stdlib/Test/">testing framework</a>. All new functions should have appropriate tests written for them in the appropriate file in the <code>test</code> directory. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/test/runtests.jl"><code>test/runtests.jl</code></a> for details.) There are three ways to run the test suite: in the terminal, executing <code>make test</code> or <code>cd test; julia runtests.jl</code>; or in the Julia REPL, <code>Pkg.activate(&quot;.&quot;); Pkg.test()</code>.</p><h3 id="Documenter.jl"><a class="docs-heading-anchor" href="#Documenter.jl">Documenter.jl</a><a id="Documenter.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Documenter.jl" title="Permalink"></a></h3><p>The HTML documentation is generated using <a href="https://documenter.juliadocs.org">Documenter.jl</a>. Therefore, all new functions should have docstrings attached. New files need to be integrated into the relevant documentation source files in <code>docs/src</code>, and if necessary into <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/docs/builddocs.jl"><code>docs/builddocs.jl</code></a>. To build the documentation, run <code>make docs</code>, or <code>cd docs; julia builddocs.jl</code> (if using the latter, don&#39;t forget to update the date and commit in <code>docs/src/index.md</code>).</p><h3 id="Graphics-and-user-interface"><a class="docs-heading-anchor" href="#Graphics-and-user-interface">Graphics and user interface</a><a id="Graphics-and-user-interface-1"></a><a class="docs-heading-anchor-permalink" href="#Graphics-and-user-interface" title="Permalink"></a></h3><p>Persefone uses <a href="https://makie.org/">Makie</a> as a plotting library to generate its output graphics. Additionally, Persefone Desktop uses <a href="https://github.com/JuliaGraphics/QML.jl">QML.jl</a> to create its graphical user interface.</p><h3 id="Unitful.jl"><a class="docs-heading-anchor" href="#Unitful.jl">Unitful.jl</a><a id="Unitful.jl-1"></a><a class="docs-heading-anchor-permalink" href="#Unitful.jl" title="Permalink"></a></h3><p>Throughout the source code, variables can be tagged with their appropriate units using the <a href="https://painterqubits.github.io/Unitful.jl/stable/">Unitful.jl</a> library. This makes the code easier to understand, and also allows automatic unit conversion:</p><pre><code class="language-julia hljs">julia&gt; 1ha == 10000m²
true
julia&gt; 2km |&gt; m
2000 m
julia&gt; 2km / 10m
200.0</code></pre><p>Within Persefone, the following units and dimensions have been imported for direct usage: <code>cm</code>, <code>m</code>, <code>km</code>, <code>m²</code>, <code>ha</code>, <code>km²</code>, <code>mg</code>, <code>g</code>, <code>kg</code>, <code>Length</code>, <code>Area</code>, <code>Mass</code>.</p><h3 id="Dates"><a class="docs-heading-anchor" href="#Dates">Dates</a><a id="Dates-1"></a><a class="docs-heading-anchor-permalink" href="#Dates" title="Permalink"></a></h3><p>Persefone expands the default <a href="https://docs.julialang.org/en/v1/stdlib/Dates/">Dates</a> library with the <a href="simulation.html#Persefone.AnnualDate"><code>AnnualDate</code></a> type, which can be used to store dates that recur every year (e.g. migration or harvest). <code>AnnualDates</code> can be compared and added/subtracted just as normal dates. Use <a href="@ref"><code>thisyear()</code></a> to convert an <code>AnnualDate</code> to a <code>Date</code>.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="skylark.html">« Skylark</a><a class="docs-footer-nextpage" href="adapting.html">Adapting Persefone »</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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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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">Software API</a></li><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-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/farm.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="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, the aim is to create a full socio-economic farm decision model for Persefone. However, for the time being, we will restrict ourselves to a simple model that executes typical farm operations and crop rotations.</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-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.BasicFarmer" href="#Persefone.BasicFarmer"><code>Persefone.BasicFarmer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">BasicFarmer</code></pre><p>The BasicFarmer type simply applies a set crop rotation to his fields and keeps track of income.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L37-L41">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.Farmer" href="#Persefone.Farmer"><code>Persefone.Farmer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><p>This is the agent type for the farm ABM.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L9">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.findsetasides-Tuple{Persefone.BasicFarmer, SimulationModel}" href="#Persefone.findsetasides-Tuple{Persefone.BasicFarmer, SimulationModel}"><code>Persefone.findsetasides</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">findsetasides(farmer, model)</code></pre><p>Return a vector of field IDs that this farmer should keep fallow to satisfy the configured set-aside rules.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L108-L113">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.initbasicfarms!-Tuple{SimulationModel}" href="#Persefone.initbasicfarms!-Tuple{SimulationModel}"><code>Persefone.initbasicfarms!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">initbasicfarms!(model)</code></pre><p>Initialise the basic farm model. All fields are controlled by a single farmer actor and are assigned as grassland, set-aside, or arable land with a crop rotation.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L80-L85">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.initfarms!-Tuple{SimulationModel}" href="#Persefone.initfarms!-Tuple{SimulationModel}"><code>Persefone.initfarms!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">initfarms!(model)</code></pre><p>Initialise the model with a set of farm agents, depending on the configured farm model.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L15-L19">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="Persefone.stepagent!-Tuple{Persefone.BasicFarmer, SimulationModel}" href="#Persefone.stepagent!-Tuple{Persefone.BasicFarmer, SimulationModel}"><code>Persefone.stepagent!</code></a> — <span class="docstring-category">Method</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">stepagent!(farmer, model)</code></pre><p>Update a farmer by one day. Cycle through all fields and see what management is needed.</p></div><a class="docs-sourcelink" target="_blank" href="https://git.idiv.de/persefone/persefone-model/-/tree/b1802d1f4c7de3584a62fd93cfe9eb20421c1cd7/src/farm/farm.jl#L51-L55">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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</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>Maps and weather data · Persefone.jl</title><meta name="title" content="Maps and weather data · Persefone.jl"/><meta property="og:title" content="Maps and weather data · Persefone.jl"/><meta property="twitter:title" content="Maps and weather data · Persefone.jl"/><meta name="description" content="Documentation for Persefone.jl."/><meta property="og:description" content="Documentation for Persefone.jl."/><meta property="twitter:description" content="Documentation for Persefone.jl."/><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 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href="index.html">Persefone.jl</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">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</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 class="is-active"><a class="tocitem" href="gis.html">Maps and weather data</a><ul class="internal"><li><a class="tocitem" href="#Land-cover-maps"><span>Land cover maps</span></a></li><li><a class="tocitem" href="#Field-ID-maps"><span>Field ID maps</span></a></li><li><a class="tocitem" href="#Soil-data"><span>Soil data</span></a></li><li><a class="tocitem" href="#Weather-data"><span>Weather data</span></a></li></ul></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li><li><a class="tocitem" href="CHANGELOG.html">Changelog</a></li></ul></li><li><span class="tocitem">Software API</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li><li><a class="tocitem" href="nature.html">Nature submodel</a></li><li><a class="tocitem" href="species.html">Species models</a></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</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"><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="gis.html">Maps and weather data</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="gis.html">Maps and weather data</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/gis.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="Maps-and-weather-data"><a class="docs-heading-anchor" href="#Maps-and-weather-data">Maps and weather data</a><a id="Maps-and-weather-data-1"></a><a class="docs-heading-anchor-permalink" href="#Maps-and-weather-data" title="Permalink"></a></h1><p>Persefone.jl requires three map input files: one for land cover, one for for field geometries, and one for soil types. Additionally, a weather input file is needed. This documents describe how to obtain and process the data needed for each of these.</p><p>There is a QGIS project file at <code>data/regions/auxiliary/persefone.qgz</code>, which can be used get an overview of the existing region input files and add new ones. All region data files are stored using the following convention:</p><pre><code class="nohighlight hljs">data/regions/&lt;regionname&gt;/
-&gt; &lt;regionname&gt;.geojson
-&gt; landcover.tif
-&gt; fields.tif
-&gt; soil.tif
-&gt; weather.csv</code></pre><p>Where <code>&lt;regionname&gt;</code> is currently one of <code>bodensee</code>, <code>eichsfeld</code>, <code>hohenlohe</code>, <code>jena</code>, <code>oberrhein</code>, or <code>thueringer_becken</code>.</p><h2 id="Land-cover-maps"><a class="docs-heading-anchor" href="#Land-cover-maps">Land cover maps</a><a id="Land-cover-maps-1"></a><a class="docs-heading-anchor-permalink" href="#Land-cover-maps" title="Permalink"></a></h2><p>Land cover maps for Germany at 10m resolution can be obtained from <a href="https://data.mundialis.de/geonetwork/srv/eng/catalog.search#/metadata/9246503f-6adf-460b-a31e-73a649182d07">Mundialis</a>. These are generated annually from Sentinel data and comprise the following land cover classes:</p><pre><code class="nohighlight hljs">10: forest
20: low vegetation
30: water
40: built-up
50: bare soil
60: agriculture</code></pre><p>To create a Persefone map input file, you need to crop the national Mundialis map to the extent that you want to simulate (suggestion: edge lengths between 10-20 km are a reasonable size).</p><p>To do so, download the Mundialis map and import it into QGIS. Then create a new vector layer and create a rectangle feature to delimit the extent of your region. You can save this as a GEOJSON file to the region folder for future reference. Then go to <code>Raster -&gt; Extraction -&gt; Clip Raster by Extent</code>. Select the Mundialis map as the input layer, set the clipping extent by choosing your region vector layer under <code>Calculate from Layer</code> and specify the output file name before clicking <code>Run</code>. This will generate a TIF file that you can pass to Persefone as the <code>landcovermap</code> parameter.</p><h2 id="Field-ID-maps"><a class="docs-heading-anchor" href="#Field-ID-maps">Field ID maps</a><a id="Field-ID-maps-1"></a><a class="docs-heading-anchor-permalink" href="#Field-ID-maps" title="Permalink"></a></h2><p>In addition to the land cover data explained above, Persefone also needs information about agricultural field boundaries in order to assign these to the farming agents. Unfortunately, getting this is rather more complicated.</p><p>In the EU, every country runs a Land Parcel Information System (LPIS) to administer CAP payments. In Germany, this is called InVeKoS and is run by the Länder. For example, you can view and download the InVeKoS data for <a href="https://thueringenviewer.thueringen.de/thviewer/invekos.html">Thüringen</a> or <a href="https://metadaten.geoportal-bw.de/geonetwork/srv/eng/catalog.search#/metadata/03873032-80e7-41ec-bb3e-3d34231617e4">Baden-Württemberg</a>. This gives you a vector layer which can be loaded into QGIS. However, it needs to be converted to a raster layer and cropped to your region extent before it can be used in Persefone.</p><p>The first thing to do is to make sure that the vector layer has a numeric (!) field with a unique identifier for each field block (check the attribute table). The Thüringen data has the FBI (&quot;Feldblockident&quot;) field, but this is a string value and therefore not usable by the rasteriser. So, we set the vector layer to edit mode, open the field calculator, enter the information for a new field (call it &quot;FID&quot; and set it to a 32-bit integer), and enter <code>@row_number</code> in the expression field. Then save the layer and close the calculator.</p><p>Secondly, you need to filter out all non-field/non-grassland plot types. (LPIS also has data on forests and various landscape elements that are not relevant to our use case.) Assuming you&#39;re working with the Thüringen InVeKoS data (other data sets may have a different structure), right-click on the layer name in QGIS&#39; layer overview and click on &quot;Filter...&quot;. Then, enter this expression in the query builder: <code>&quot;BNK&quot; = &#39;AL&#39; OR &quot;BNK&quot; = &#39;GL&#39;</code> and click &quot;OK&quot;. This will select only field and grassland plots.</p><p>Next, open the rasteriser (<code>Raster -&gt; Conversion -&gt; Rasterize</code>). Select your FID field as the &quot;Field to use for a burn-in value&quot;, and your land cover map (as created above - this ensures the two layers match) as the output extent. Make sure the &quot;fixed value to burn&quot; is &quot;Not set&quot;. Then choose &quot;Georeferenced units&quot; as the &quot;Out raster size units&quot; and set horizontal and vertical resolution to 10.0. In the advanced parameters, set the output data type to <code>UInt32</code>. Finally, enter an output file name and run. The resulting TIF file can be passed to Persefone as the <code>farmfieldmap</code> parameter.</p><h2 id="Soil-data"><a class="docs-heading-anchor" href="#Soil-data">Soil data</a><a id="Soil-data-1"></a><a class="docs-heading-anchor-permalink" href="#Soil-data" title="Permalink"></a></h2><p>Soil data for Germany is provided by the Bundesanstalt für Geowissenschaften und Rohstoffe in form of the <a href="https://bodenatlas.bgr.de/">Bodenatlas</a>. This provides a (coarse, but for our purposes sufficient) map of the distribution of the basic soil types such as clay, silt, sand, and loam.</p><p>To create the Persefone input file, you first need to rasterise the data. See the instructions above - choose <code>BODENART</code> as the field for the burn-in value. (Note: rastering the whole map produces a 20GB file! This can later be deleted again.) Then you need to align and crop it to the extent you require, using the dialog at <code>Raster -&gt; Align Rasters...</code>. Select your landcover map as the reference layer and the extent layer, then choose your national soil map as the input. (Don&#39;t forget to define the output file name using <code>Configure Raster...</code>, this is a bit hidden.) The created output file can then be used for the <code>soilmap</code> parameter. Its integer values map onto the <code>SoilType</code> enum as follows:</p><pre><code class="nohighlight hljs">1: Abbauflächen -&gt; nosoil
2: Gewässer -&gt; nosoil
3: Lehmsande (ls) -&gt; loamy_sand
4: Lehmschluffe (lu) -&gt; silt_loam
5: Moore -&gt; nosoil
6: Normallehme (ll) -&gt; loam
7: Reinsande (ss) -&gt; sand
8: Sandlehme (sl) -&gt; sandy_loam
9: Schluffsande (us) -&gt; sandy_loam
10: Schlufftone (ut) -&gt; silty_clay
11: Siedlung -&gt; nosoil
12: Tonlehme (tl) -&gt; clay_loam
13: Tonschluffe (tu) -&gt; silty_clay_loam
14: Watt -&gt; nosoil</code></pre><p><img src="assets/soil_types_english.png" alt="Soil types triangle"/></p><p><em>Names of soil types are based on the relative composition of clay, silt, and sand. Note that the typology used in the Bodenatlas does not map perfectly on to this international classification. Image source: <a href="https://www.australianenvironmentaleducation.com.au/education-resources/what-is-soil/">Australian Environmental Education</a></em></p><h2 id="Weather-data"><a class="docs-heading-anchor" href="#Weather-data">Weather data</a><a id="Weather-data-1"></a><a class="docs-heading-anchor-permalink" href="#Weather-data" title="Permalink"></a></h2><p>Currently, Persefone uses historical weather data from the closest 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 <a href="https://www.dwd.de/DE/leistungen/cdc/cdc_ueberblick-klimadaten.html?nn=16102">German weather service (DWD)</a>.</p><p>The description of these data sets and the list of weather stations can be found in the Persefone repository, in the <code>docs</code> 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. The currently included regions have the following station codes:</p><ul><li><strong>Region Jena:</strong> station number 02444 (&quot;Jena (Sternwarte)&quot;)</li><li><strong>Region Eichsfeld:</strong> station number 02925 (&quot;Leinefelde&quot;) </li><li><strong>Region Thüringer Becken:</strong> station number 00896 (&quot;Dachwig&quot;)</li><li><strong>Region Hohenlohe:</strong> station number 03761 (&quot;Oehringen&quot;)</li><li><strong>Region Bodensee:</strong> station number 06263 (&quot;Singen&quot;)</li><li><strong>Region Nördlicher Oberrhein:</strong> station number 05275 (&quot;Waghäusel-Kirrlach&quot;)</li></ul><p>The script <code>data/regions/auxiliary/extract_weather_data.R</code> can be used to download and process the data into the format needed by Persefone. This uses the <a href="https://bookdown.org/brry/rdwd/"><code>rdwd</code></a> package. To use it, simply specify the desired <code>region</code>, adding its ID to the <code>stationid</code> list if necessary. The produced CSV file can be copied into the respective region folder.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="architecture.html">« Source code architecture</a><a class="docs-footer-nextpage" href="species-dsl.html">Defining new 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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</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"><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">User guide</a></li><li class="is-active"><a href="gui.html">Graphical User Interface</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="gui.html">Graphical User Interface</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/gui.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="Graphical-User-Interface"><a class="docs-heading-anchor" href="#Graphical-User-Interface">Graphical User Interface</a><a id="Graphical-User-Interface-1"></a><a class="docs-heading-anchor-permalink" href="#Graphical-User-Interface" title="Permalink"></a></h1><p>Due to the computational demands of simulating many individuals at high temporal and spatial resolution, Persefone.jl is primarily designed to be run non-interactively on an HPC. However, to allow interactive exploratory simulations to be conducted while learning or developing the model, a graphical user interface is available as an additional package: <a href="https://git.idiv.de/persefone/persefone-desktop">Persefone Desktop</a>.</p><h2 id="Quick-start"><a class="docs-heading-anchor" href="#Quick-start">Quick start</a><a id="Quick-start-1"></a><a class="docs-heading-anchor-permalink" href="#Quick-start" title="Permalink"></a></h2><p><em>Follow these instructions if you simply want to try out the software as a user. If you want to play around with the source code, see the next section.</em></p><ol><li>Download the <a href="https://julialang.org/downloads/">Julia programming language</a> and install it on </li></ol><p>your computer.</p><ol><li>Start Julia. This should launch a commandline interface/REPL.</li><li>Execute the following commands (copy-and-paste should work):</li></ol><pre><code class="language-julia hljs">using Pkg
Pkg.add(url=&quot;https://git.idiv.de/persefone/persefone-model.git&quot;)
Pkg.add(url=&quot;https://git.idiv.de/persefone/persefone-desktop.git&quot;)
using PersefoneDesktop
ENV[&quot;QSG_RENDER_LOOP&quot;] = &quot;basic&quot; # only needed on Windows
launch()</code></pre><h2 id="Running-from-the-repo"><a class="docs-heading-anchor" href="#Running-from-the-repo">Running from the repo</a><a id="Running-from-the-repo-1"></a><a class="docs-heading-anchor-permalink" href="#Running-from-the-repo" title="Permalink"></a></h2><p><em>Follow these instructions if you want to get to grips with the source code. For more detailed installation instructions, see <a href="developing.html">here</a>.</em></p><p><strong>To install:</strong> Install <a href="https://julialang.org/downloads/">Julia</a> and download/clone the <a href="https://git.idiv.de/persefone/persefone-desktop">repository</a>. Open a Julia REPL in the downloaded folder and execute the following to install all dependencies:</p><pre><code class="language-julia hljs">using Pkg
Pkg.activate(&quot;.&quot;)
Pkg.instantiate()</code></pre><p><strong>To run:</strong> Run <code>desktop.jl</code>. Alternatively, open a Julia REPL in this folder and run:</p><pre><code class="language-julia hljs">using Pkg
Pkg.activate(&quot;.&quot;)
using PersefoneDesktop
launch()</code></pre><p><em>Note:</em> Due to the necessary pre-compilation done by Julia, installing and launching the application can take quite a long time. (Start-up time with <code>desktop.jl</code> is currently about 2 minutes.) We will reduce this as much as possible in future releases.</p><h2 id="User-interface"><a class="docs-heading-anchor" href="#User-interface">User interface</a><a id="User-interface-1"></a><a class="docs-heading-anchor-permalink" href="#User-interface" title="Permalink"></a></h2><p><img src="assets/screenshot.png" alt="Persefone.jl Desktop screenshot"/></p><p>The main window component is the <strong>map view</strong>. This displays a land cover map of the simulated region: dark green are forests, light green grassland, yellow fields, red built-up areas and blue water. On it, little circles show the position of individual animals, with different species denoted by different colours.</p><h3 id="Control-bar"><a class="docs-heading-anchor" href="#Control-bar">Control bar</a><a id="Control-bar-1"></a><a class="docs-heading-anchor-permalink" href="#Control-bar" title="Permalink"></a></h3><ul><li><p><strong>Back button:</strong> Rewind the simulation by one day.</p></li><li><p><strong>Step button:</strong> Advance the simulation by one day.</p></li><li><p><strong>Run button:</strong> Run the simulation until the button is pressed again or the end date is reached.</p></li><li><p><strong>Progress bar:</strong> Shows the percentage of time elapsed between the start and end dates of the simulation.</p></li><li><p><strong>Speed slider:</strong> Set the time delay between each simulation step when running.</p></li><li><p><strong>Date:</strong> Shows the simulation date currently displayed on the map.</p></li></ul><h3 id="Menu-bar"><a class="docs-heading-anchor" href="#Menu-bar">Menu bar</a><a id="Menu-bar-1"></a><a class="docs-heading-anchor-permalink" href="#Menu-bar" title="Permalink"></a></h3><p><strong>Simulation:</strong></p><ul><li><p><strong>New simulation:</strong> Reset the model and start over.</p></li><li><p><strong>Configure simulation:</strong> Change the model settings (<em>not yet implemented</em>).</p></li><li><p><strong>Load saved state:</strong> Load a model object file saved by a previous simulation run.</p></li><li><p><strong>Save current state:</strong> Save a model object file for later use.</p></li><li><p><strong>Quit:</strong> Close the application.</p></li></ul><p><strong>Data:</strong></p><ul><li><p><strong>Show population graph:</strong> Show a window with a graph of population sizes over time in the current model run.</p></li><li><p><strong>Save simulation output:</strong> Save the model output data to file (saves both raw CSV data and generated graphics).</p></li></ul><p><strong>Help:</strong></p><ul><li><p><strong>Documentation:</strong> Open the Persefone.jl online documentation in a browser.</p></li><li><p><strong>Website:</strong> Open the main Persefone.jl website in a browser.</p></li><li><p><strong>About:</strong> Show a window with core information about the application.</p></li></ul></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="using.html">« The Persefone.jl Package</a><a class="docs-footer-nextpage" href="config.html">Configuration »</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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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all docstrings"></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><a href="https://persefone-model.eu"><img src="assets/persefonejl_logo_v3_splash.png" alt="Persefone.jl splash screen"/></a></p><p><a href="https://persefone-model.eu">Persefone.jl</a> models agricultural practice and how it impacts animal species at a landscape scale. It includes a farm submodel, a crop growth submodel, and individual-based models of multiple indicator species. Its aim is to investigate how changes in farm operations (e.g. through policy changes in the CAP) influence biodiversity.</p><p>The model is open-source software available on <a href="https://git.idiv.de/persefone/persefone-model">Gitlab</a>.</p><p><em>This documentation was last updated on 2025-03-18 for <strong>Persefone.jl v0.7.0</strong> (commit <a href="https://git.idiv.de/persefone/persefone-model/-/commit/b1802d1">b1802d1</a>).</em></p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="using.html">The Persefone.jl Package »</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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. 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href="index.html">Persefone.jl</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">Scientific documentation</span><ul><li><a class="tocitem" href="management.html">Farm management</a></li><li><a class="tocitem" href="crop-models.html">Crop models</a></li><li><a class="tocitem" href="skylark.html">Skylark</a></li></ul></li><li><span class="tocitem">Developer guide</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting 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Purpose</a><a id="1.-Purpose-1"></a><a class="docs-heading-anchor-permalink" href="#1.-Purpose" title="Permalink"></a></h2><h2 id="2.-Entities,-state-variables,-and-scales"><a class="docs-heading-anchor" href="#2.-Entities,-state-variables,-and-scales">2. Entities, state variables, and scales</a><a id="2.-Entities,-state-variables,-and-scales-1"></a><a class="docs-heading-anchor-permalink" href="#2.-Entities,-state-variables,-and-scales" title="Permalink"></a></h2><h2 id="3.-Process-overview-and-scheduling"><a class="docs-heading-anchor" href="#3.-Process-overview-and-scheduling">3. Process overview and scheduling</a><a id="3.-Process-overview-and-scheduling-1"></a><a class="docs-heading-anchor-permalink" href="#3.-Process-overview-and-scheduling" title="Permalink"></a></h2><h2 id="4.-Design-concepts"><a class="docs-heading-anchor" href="#4.-Design-concepts">4. Design concepts</a><a id="4.-Design-concepts-1"></a><a class="docs-heading-anchor-permalink" href="#4.-Design-concepts" title="Permalink"></a></h2><h3 id="4.1-Basic-principles"><a class="docs-heading-anchor" href="#4.1-Basic-principles">4.1 Basic principles</a><a id="4.1-Basic-principles-1"></a><a class="docs-heading-anchor-permalink" href="#4.1-Basic-principles" title="Permalink"></a></h3><h3 id="4.2-Emergence"><a class="docs-heading-anchor" href="#4.2-Emergence">4.2 Emergence</a><a id="4.2-Emergence-1"></a><a class="docs-heading-anchor-permalink" href="#4.2-Emergence" title="Permalink"></a></h3><h3 id="4.3-Adaptation"><a class="docs-heading-anchor" href="#4.3-Adaptation">4.3 Adaptation</a><a id="4.3-Adaptation-1"></a><a class="docs-heading-anchor-permalink" href="#4.3-Adaptation" title="Permalink"></a></h3><h3 id="4.4-Objectives"><a class="docs-heading-anchor" href="#4.4-Objectives">4.4 Objectives</a><a id="4.4-Objectives-1"></a><a class="docs-heading-anchor-permalink" href="#4.4-Objectives" title="Permalink"></a></h3><h3 id="4.5-Learning"><a class="docs-heading-anchor" href="#4.5-Learning">4.5 Learning</a><a id="4.5-Learning-1"></a><a class="docs-heading-anchor-permalink" href="#4.5-Learning" title="Permalink"></a></h3><h3 id="4.6-Prediction"><a class="docs-heading-anchor" href="#4.6-Prediction">4.6 Prediction</a><a id="4.6-Prediction-1"></a><a class="docs-heading-anchor-permalink" href="#4.6-Prediction" title="Permalink"></a></h3><h3 id="4.7-Sensing"><a class="docs-heading-anchor" href="#4.7-Sensing">4.7 Sensing</a><a id="4.7-Sensing-1"></a><a class="docs-heading-anchor-permalink" href="#4.7-Sensing" title="Permalink"></a></h3><h3 id="4.8-Interaction"><a class="docs-heading-anchor" href="#4.8-Interaction">4.8 Interaction</a><a id="4.8-Interaction-1"></a><a class="docs-heading-anchor-permalink" href="#4.8-Interaction" title="Permalink"></a></h3><h3 id="4.9-Stochasticity"><a class="docs-heading-anchor" href="#4.9-Stochasticity">4.9 Stochasticity</a><a id="4.9-Stochasticity-1"></a><a class="docs-heading-anchor-permalink" href="#4.9-Stochasticity" title="Permalink"></a></h3><h3 id="4.10-Collectives"><a class="docs-heading-anchor" href="#4.10-Collectives">4.10 Collectives</a><a id="4.10-Collectives-1"></a><a class="docs-heading-anchor-permalink" href="#4.10-Collectives" title="Permalink"></a></h3><h3 id="4.11-Observation"><a class="docs-heading-anchor" href="#4.11-Observation">4.11 Observation</a><a id="4.11-Observation-1"></a><a class="docs-heading-anchor-permalink" href="#4.11-Observation" title="Permalink"></a></h3><h2 id="5.-Initialisation"><a class="docs-heading-anchor" href="#5.-Initialisation">5. Initialisation</a><a id="5.-Initialisation-1"></a><a class="docs-heading-anchor-permalink" href="#5.-Initialisation" title="Permalink"></a></h2><h2 id="6.-Input-data"><a class="docs-heading-anchor" href="#6.-Input-data">6. Input data</a><a id="6.-Input-data-1"></a><a class="docs-heading-anchor-permalink" href="#6.-Input-data" title="Permalink"></a></h2><h2 id="7.-Submodels"><a class="docs-heading-anchor" href="#7.-Submodels">7. Submodels</a><a id="7.-Submodels-1"></a><a class="docs-heading-anchor-permalink" href="#7.-Submodels" title="Permalink"></a></h2><h2 id="8.-References"><a class="docs-heading-anchor" href="#8.-References">8. References</a><a id="8.-References-1"></a><a class="docs-heading-anchor-permalink" href="#8.-References" title="Permalink"></a></h2></article><nav class="docs-footer"><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="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.9.0 on <span class="colophon-date" title="Tuesday 18 March 2025 14:39">Tuesday 18 March 2025</span>. 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