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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Defining new species · Persefone</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" 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type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="index.html">Introduction</a></li><li><a class="tocitem" href="odd.html">Overview, Design, Details (ODD)</a></li><li><span class="tocitem">Developing</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li><a class="tocitem" href="architecture.html">Source code architecture</a></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li class="is-active"><a class="tocitem" href="species-dsl.html">Defining new species</a><ul class="internal"><li><a class="tocitem" href="#The-Persefone-species-DSL"><span>The Persefone species DSL</span></a></li><li><a class="tocitem" href="#Implementation-details"><span>Implementation details</span></a></li></ul></li></ul></li><li><span class="tocitem">Core</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input, Output, and Settings</a></li></ul></li><li><span class="tocitem">Nature</span><ul><li><a class="tocitem" href="nature.html">Nature</a></li><li><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a></li><li><a class="tocitem" href="species.html">Species</a></li></ul></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li><a class="is-disabled">Developing</a></li><li class="is-active"><a href="species-dsl.html">Defining new species</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="species-dsl.html">Defining new species</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/species-dsl.md#" title="Edit source"><span class="docs-icon fa"></span><span class="docs-label is-hidden-touch">Edit source</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Defining-new-species"><a class="docs-heading-anchor" href="#Defining-new-species">Defining new species</a><a id="Defining-new-species-1"></a><a class="docs-heading-anchor-permalink" href="#Defining-new-species" title="Permalink"></a></h1><h2 id="The-Persefone-species-DSL"><a class="docs-heading-anchor" href="#The-Persefone-species-DSL">The Persefone species DSL</a><a id="The-Persefone-species-DSL-1"></a><a class="docs-heading-anchor-permalink" href="#The-Persefone-species-DSL" title="Permalink"></a></h2><p>In order to make implementing new species as easy as possible, Persefone includes a <a href="https://doi.org/10.1016/j.ecoinf.2015.02.005">domain-specific language</a> (DSL) built from a collection of macros and functions.</p><p>Here is an example of what this looks like, using a hypothetical mermaid species:</p><pre><code class="language-julia hljs">@species Mermaid begin
ageofmaturity = 2
pesticidemortality = 1.0
@initialise(@habitat(@landcover() == water), pairs=true)
@phase life begin
@debug "$(animalid(animal)) is swimming happily in its pond."
@respond pesticide @kill(@trait(pesticidemortality), "poisoning")
@respond harvest @setphase(drought)
@debug "Animal: $animal"
if @trait(sex) == female && @countanimals() < 3 &&
@trait(age) >= @trait(ageofmaturity) && @landcover() == water
@reproduce()
end
end
@phase drought begin
n = sum(1 for a in @neighbours(0))
@debug "$(animalid(animal)) is experiencing drought with $n neighbour(s)."
@respond sowing @setphase(life)
end
end</code></pre><p>The two most important macros are <a href="nature.html#Persefone.@species-Tuple{Any, Any}"><code>@species</code></a> and <a href="nature.html#Persefone.@phase-Tuple{Any, Any}"><code>@phase</code></a>, followed by <a href="nature.html#Persefone.@initialise-Tuple{Any, Vararg{Any}}"><code>@initialise</code></a>, <a href="nature.html#Persefone.@trait-Tuple{Any}"><code>@trait</code></a>, <a href="nature.html#Persefone.@respond-Tuple{Any, Any}"><code>@respond</code></a>, and <a href="nature.html#Persefone.@habitat-Tuple{Any}"><code>@habitat</code></a>. Other macros provide convenience wrappers for common functions. (See <code>src/nature/nature.jl</code> for details.)</p><p>The top-level macro is <a href="nature.html#Persefone.@species-Tuple{Any, Any}"><code>@species</code></a>. This takes two arguments: a species name and a definition block (enclosed in <code>begin</code> and <code>end</code> tags). At the start of the definition block, species-specific variables can be defined that should be available throughout a species' lifetime. Code in this section has access to the <code>model</code> object and can thus reference the current model state. In this section, the user also has to call the <a href="nature.html#Persefone.@initialise-Tuple{Any, Vararg{Any}}"><code>@initialise</code></a> macro. This wraps the <a href="@ref"><code>initpopulation</code></a> function, and takes a habitat descriptor (see <a href="nature.html#Persefone.@habitat-Tuple{Any}"><code>@habitat</code></a> below) and several options to specify how the species' population should be distributed in the landscape during model initialisation.</p><p>Following this section, each species must define one or more <a href="nature.html#Persefone.@phase-Tuple{Any, Any}"><code>@phase</code></a> blocks. The concept behind this is that species show different behaviours at different phases of their lifecycle. Each <code>@phase</code> block defines the behaviour in one of these phases. (Technically, it defines a function that will be called daily, so long as the species' <code>phase</code> variable is set to the name of this phase.) Code in this section has access to the <code>model</code> object as well as an <code>animal</code> object, which is the currently active animal agent. Properties of the <code>animal</code> agent, regardless of whether they were defined by the user or by Persefone, can be accessed using the <a href="nature.html#Persefone.@trait-Tuple{Any}"><code>@trait</code></a> macro. Within a phase block, <a href="nature.html#Persefone.@respond-Tuple{Any, Any}"><code>@respond</code></a> can be used to define the species' response to a <a href="@ref"><code>FarmEvent</code></a> that affects the species' current location, while a variety of other macros provide wrappers to ecological process functions from <code>src/nature/populations.jl</code>.</p><p>Another important macro is <a href="nature.html#Persefone.@habitat-Tuple{Any}"><code>@habitat</code></a>. This defines a "habitat descriptor", i.e. a predicate function that tests whether or not a given landscape pixel is suitable for a specified purpose. Such habitat descriptors are used as arguments to various functions, for example for population initialisation or movement. The argument to <code>@habitat</code> consists of a logical expression, which has access to the animal's current position (the <code>pos</code> tuple variable) and the <code>model</code>. Various macros are available to easily reference information about the current location, such as <a href="nature.html#Persefone.@landcover-Tuple{}"><code>@landcover</code></a> or <a href="nature.html#Persefone.@distancetoedge-Tuple{}"><code>@distancetoedge</code></a>.</p><h2 id="Implementation-details"><a class="docs-heading-anchor" href="#Implementation-details">Implementation details</a><a id="Implementation-details-1"></a><a class="docs-heading-anchor-permalink" href="#Implementation-details" title="Permalink"></a></h2><p>Due to a known <a href="https://juliadynamics.github.io/Agents.jl/stable/performance_tips/#Avoid-Unions-of-many-different-agent-types-(temporary!)-1">performance problem</a> with multi-agent models, the underlying implementation of species is rather complicated (see <code>src/nature/nature.jl</code> for details.)</p><p>Rather than creating a new type/struct for each species, all <a href="@ref">Animal</a> agents have the same type. Instead, they are differentiated by a <code>traits</code> dict, which stores both species-specific parameters and run-time variables. Note that due to a redefinition of the <code>getproperty()/setproperty!()</code> methods, variables from the trait dict can be accessed and modified just like normal struct fields (i.e. although <code>phase</code> is defined in the dict, not the struct, <code>animal.phase = "newphase"</code> works just fine - one does not have to use <code>animal.traits["phase"] = "newphase"</code>.)</p><p>Under the hood, the <a href="nature.html#Persefone.@species-Tuple{Any, Any}"><code>@species</code></a> macro generates a function (with the name of the species), which in turn creates the trait dict when called. Thus, adding a new animal agent to the model involves instantiating an <a href="nature.html#Persefone.Animal"><code>Animal</code></a> object, then calling the relevant species function and attaching the returned dict to the agent object.</p><p>Similarly, the <a href="nature.html#Persefone.@phase-Tuple{Any, Any}"><code>@phase</code></a> macro too works by defining a new function, which is stored in the species' trait dict. These functions take an animal object and the model object as input, and define what the species does during its daily update.</p><p>Once again, <a href="nature.html#Persefone.@habitat-Tuple{Any}"><code>@habitat</code></a> creates a function that takes <code>model</code> and <code>pos</code> as input and returns a boolean response. Functions that require a habitat descriptor thus take in this (anonymous) function and call it internally.</p><p>Finally, the <a href="nature.html#Persefone.@initialise-Tuple{Any, Vararg{Any}}"><code>@initialise</code></a> macro is a wrapper around <a href="@ref"><code>initpopulation</code></a>, which (yet again) creates a function that specifies how a species' population is to be initialised at the beginning of a simulation run. This function is stored in the species trait dict and accessed during model setup.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="gis.html">« Maps and weather data</a><a class="docs-footer-nextpage" href="simulation.html">Simulation »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.23 on <span class="colophon-date" title="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. 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