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{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2025-03-18T14:39:16","documenter_version":"1.9.0"}}
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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.jl</title><meta name="title" content="Adapting Persefone · Persefone.jl"/><meta property="og:title" content="Adapting Persefone · Persefone.jl"/><meta property="twitter:title" content="Adapting Persefone · 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script data-outdated-warner src="assets/warner.js"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" 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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><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 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><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="adapting.html">Adapting Persefone</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="adapting.html">Adapting Persefone</a></li></ul></nav><div class="docs-right"><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model" title="View the repository"><span class="docs-icon fa-brands"></span><span class="docs-label is-hidden-touch">Repository</span></a><a class="docs-navbar-link" href="https://git.idiv.de/persefone/persefone-model/-/tree/master/docs/src/adapting.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link fa-solid fa-gear" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-article-toggle-button fa-solid fa-chevron-up" id="documenter-article-toggle-button" href="javascript:;" title="Collapse all docstrings"></a></div></header><article class="content" id="documenter-page"><h1 id="Adapting-Persefone"><a class="docs-heading-anchor" href="#Adapting-Persefone">Adapting Persefone</a><a id="Adapting-Persefone-1"></a><a class="docs-heading-anchor-permalink" href="#Adapting-Persefone" title="Permalink"></a></h1><p>A key development goal of Persefone is to be <a href="https://doi.org/10.1515/itit-2019-0040">FAIR</a>: <em>findable, accessible, interoperable, and reusable</em>. We aim to build a model that is both easy to use and easy to adapt to new situations.</p><p>There are multiple ways to adapt Persefone for a new modelling study:</p><h3 id="Changing-the-parameters"><a class="docs-heading-anchor" href="#Changing-the-parameters">Changing the parameters</a><a id="Changing-the-parameters-1"></a><a class="docs-heading-anchor-permalink" href="#Changing-the-parameters" title="Permalink"></a></h3><p>The simplest way to adapt Persefone is simply by changing the parameters. Copy <code>src/parameters.toml</code> to a new location, adjust it to your needs, and run the model using <code>julia run.jl -c &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, create a subtype of <a href="simulation.html#Persefone.ModelAgent"><code>ModelAgent</code></a>, implement a <a href="@ref"><code>stepagent!</code></a> function for it and add it to <a href="simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}"><code>Persefone.initmodel</code></a>.</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-Tuple{}"><code>simulate</code></a> (set up and run a complete simulation based on a config file), <a href="simulation.html#Persefone.initialise-Tuple{}"><code>initialise</code></a> (create one or more <code>model</code> objects from a config file), <a href="simulation.html#Persefone.simulate!-Tuple{SimulationModel}"><code>simulate!</code></a> (do a simulation run with an existing <code>model</code> object), and <a href="simulation.html#Persefone.stepsimulation!-Tuple{SimulationModel}"><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="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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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Source code architecture · Persefone.jl</title><meta name="title" content="Source code architecture · Persefone.jl"/><meta property="og:title" content="Source code architecture · Persefone.jl"/><meta property="twitter:title" content="Source code architecture · 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="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><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 class="is-active"><a class="tocitem" href="architecture.html">Source code architecture</a><ul class="internal"><li class="toplevel"><a class="tocitem" href="#Model-components"><span>Model components</span></a></li><li class="toplevel"><a class="tocitem" href="#Important-implementation-details"><span>Important implementation details</span></a></li></ul></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">Developer guide</a></li><li class="is-active"><a href="architecture.html">Source code architecture</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="architecture.html">Source code architecture</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/architecture.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="Source-code-architecture"><a class="docs-heading-anchor" href="#Source-code-architecture">Source code architecture</a><a id="Source-code-architecture-1"></a><a class="docs-heading-anchor-permalink" href="#Source-code-architecture" title="Permalink"></a></h1><h1 id="Model-components"><a class="docs-heading-anchor" href="#Model-components">Model components</a><a id="Model-components-1"></a><a class="docs-heading-anchor-permalink" href="#Model-components" title="Permalink"></a></h1><p><img src="assets/architecture.png" alt="&quot;model architecture&quot;"/></p><p>Persefone is divided into four components, three of which are semi-independent submodels:</p><ol><li><p><code>core</code> and <code>world</code>: These two directories provide the foundation of the model software, which sets up and executes simulation runs. It also reads all input files (the configuration file, landscape maps, and weather data), and provides data output functionality.</p></li><li><p><code>nature</code>: This is an individual-based model of species in agricultural landscapes. It defines the <a href="nature.html#Persefone.Animal"><code>Animal</code></a> agent type, and a set of macros that can be used to rapidly create new species. It also includes ecological process functions that are useful for all species.</p></li><li><p><code>farm</code>: This is an agent-based model of farmer decision making. It is not yet implemented, but will provide the <a href="farm.html#Persefone.Farmer"><code>Farmer</code></a> agent type.</p></li><li><p><code>crop</code>: This is a mathematical growth model for various crops. It is not yet implemented, but already provides the agent type <a href="crops.html#Persefone.FarmPlot"><code>FarmPlot</code></a>, representing one field and its associated extent and crop type.</p></li></ol><p>Conceptually, <code>core</code> provides functionality that is needed by all of the submodels. Decisions made by <code>Farmer</code>s affect the <code>FarmPlot</code>s they own, and (directly or indirectly) the <code>Animal</code>s in the model landscape.</p><h1 id="Important-implementation-details"><a class="docs-heading-anchor" href="#Important-implementation-details">Important implementation details</a><a id="Important-implementation-details-1"></a><a class="docs-heading-anchor-permalink" href="#Important-implementation-details" title="Permalink"></a></h1><p><img src="assets/model_object.png" alt="&quot;the model object&quot;"/></p><h3 id="The-model-object"><a class="docs-heading-anchor" href="#The-model-object">The <code>model</code> object</a><a id="The-model-object-1"></a><a class="docs-heading-anchor-permalink" href="#The-model-object" title="Permalink"></a></h3><p>A cursory reading of the source code will quickly show that most functions take an <code>SimulationModel</code> object as one of their arguments. The concrete type for this is <a href="simulation.html#Persefone.AgricultureModel"><code>AgricultureModel</code></a>, a struct that holds all state that is in any way relevant to a simulation run. (Persefone has a strict &quot;no global state&quot; policy to avoid state-dependent bugs and allow parallelisation.) The model object gives access to all agent instances. It also stores the configuration (<code>model.settings</code>), the landscape (<code>model.landscape</code>, a matrix of <a href="simulation.html#Persefone.Pixel"><code>Pixel</code></a> objects that store the local land cover, amongst other things), and the current simulation date (<code>model.date</code>). (See <a href="simulation.html#Persefone.initmodel-Tuple{Dict{String, Any}}"><code>Persefone.initmodel</code></a> for details.)</p><h3 id="Model-configuration/the-@param-macro"><a class="docs-heading-anchor" href="#Model-configuration/the-@param-macro">Model configuration/the <code>@param</code> macro</a><a id="Model-configuration/the-@param-macro-1"></a><a class="docs-heading-anchor-permalink" href="#Model-configuration/the-@param-macro" title="Permalink"></a></h3><p>The model is configured via a <a href="https://toml.io/en/">TOML</a> file, the default version of which is at <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/parameters.toml"><code>src/parameters.toml</code></a>. An individual run can be configured using a user-defined configuration file, commandline arguments, or function calls (when Persefone is used as a package rather than an application). During a model run, the <a href="io.html#Persefone.@param-Tuple{Any}"><code>@param</code></a> macro can be used to access parameter values. Note that parameter names are prepended with the name of the component they are associated with. For example, the <code>outdir</code> parameter belongs to the <code>[core]</code> section of the TOML file, and must therefore be referenced as <code>@param(core.outdir)</code>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/input.jl"><code>src/core/input.jl</code></a> for details.)</p><div class="admonition is-info"><header class="admonition-header">@param and other macros</header><div class="admonition-body"><p>As <code>@param(parameter)</code> expands to <code>model.settings[&quot;parameter&quot;]</code>, it can obviously only be used in a context where the <code>model</code> object is actually available. (This is the case for most functions in Persefone, but not for all.) Similarly, many of the <code>nature</code> macros depend on specific variables being available where they are called, and can therefore only be used in specific contexts (this is indicated in their documentation).</p></div></div><h3 id="Output-data"><a class="docs-heading-anchor" href="#Output-data">Output data</a><a id="Output-data-1"></a><a class="docs-heading-anchor-permalink" href="#Output-data" title="Permalink"></a></h3><p>Persefone can output model data into text files with a specified frequency (daily, monthly, yearly, or at the simulation end). Submodels can use <a href="io.html#Persefone.newdataoutput!"><code>Persefone.newdataoutput!</code></a> to plug into this system. For an example of how to use this, see <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/nature/ecologicaldata.jl"><code>src/nature/ecologicaldata.jl</code></a>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/output.jl"><code>src/core/output.jl</code></a> for details.)</p><h3 id="Farm-events"><a class="docs-heading-anchor" href="#Farm-events">Farm events</a><a id="Farm-events-1"></a><a class="docs-heading-anchor-permalink" href="#Farm-events" title="Permalink"></a></h3><p>The <a href="simulation.html#Persefone.FarmEvent"><code>FarmEvent</code></a> struct is used to communicate farming-related events between submodels. An event can be triggered with <a href="simulation.html#Persefone.createevent!"><code>createevent!</code></a> and affects all pixels within a <a href="crops.html#Persefone.FarmPlot"><code>FarmPlot</code></a>. (See <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/landscape.jl"><code>src/core/landscape.jl</code></a> for details.)</p><h3 id="Random-numbers-and-logging"><a class="docs-heading-anchor" href="#Random-numbers-and-logging">Random numbers and logging</a><a id="Random-numbers-and-logging-1"></a><a class="docs-heading-anchor-permalink" href="#Random-numbers-and-logging" title="Permalink"></a></h3><p>By default in Julia, the <a href="https://docs.julialang.org/en/v1/stdlib/Random/">random number generator</a> (RNG) and the <a href="https://docs.julialang.org/en/v1/stdlib/Logging/#Logging.global_logger">system logger</a> are two globally accessible variables. As Persefone needs to avoid all global data (since this would interfere with reproducibility in parallel runs), the <code>model</code> object stores a local logger and a local RNG. The local logger generally does not change the way the model uses <a href="https://docs.julialang.org/en/v1/stdlib/Logging/">log statements</a>, it is only relevant for some functions in <a href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master/src/core/simulation.jl"><code>src/core/simulation.jl</code></a>.</p><div class="admonition is-info"><header class="admonition-header">Using the model RNG</header><div class="admonition-body"><p>Whenever you need to use a <a href="https://docs.julialang.org/en/v1/stdlib/Random/#Base.rand">random number</a>, you must use the <code>model.rng</code>. The easiest way to do this is with the <a href="simulation.html#Persefone.@rand-Tuple"><code>@rand</code></a> and <a href="simulation.html#Persefone.@shuffle!-Tuple{Any}"><code>@shuffle!</code></a> macros. (Note that these, too, require access to the <code>model</code> object.)</p></div></div></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="adapting.html">« Adapting Persefone</a><a class="docs-footer-nextpage" href="gis.html">Maps and weather data »</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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<!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" 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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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