diff --git a/docs/build/index.html b/docs/build/index.html
index 401c98b2e20f7cfc3c27c5cfe6b1da39264da25b..f78acaf812d3a7ed9c8b25be9f3ff6782a21816b 100644
--- a/docs/build/index.html
+++ b/docs/build/index.html
@@ -1,2 +1,42 @@
<!DOCTYPE html>
-<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Introduction · Persefone</title><meta name="title" content="Introduction · Persefone"/><meta property="og:title" content="Introduction · Persefone"/><meta property="twitter:title" content="Introduction · Persefone"/><meta name="description" content="Documentation for Persefone."/><meta property="og:description" content="Documentation for Persefone."/><meta property="twitter:description" content="Documentation for Persefone."/><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.050/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/6.4.2/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link 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src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="Persefone logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone</a></span></div><button class="docs-search-query input is-rounded is-small is-clickable my-2 mx-auto py-1 px-2" id="documenter-search-query">Search docs (Ctrl + /)</button><ul class="docs-menu"><li class="is-active"><a class="tocitem" href="index.html">Introduction</a></li><li><span class="tocitem">User guide</span><ul><li><a class="tocitem" href="using.html">The Persefone.jl Package</a></li><li><a class="tocitem" href="gui.html">Graphical User Interface</a></li><li><a class="tocitem" href="config.html">Configuration</a></li></ul></li><li><span class="tocitem">Developer guide</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li><a class="tocitem" href="architecture.html">Source code architecture</a></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li></ul></li><li><span class="tocitem">Core</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input and Output</a></li></ul></li><li><span class="tocitem">Nature</span><ul><li><a class="tocitem" href="nature.html">Nature</a></li><li><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a></li><li><a class="tocitem" href="species.html">Species</a></li></ul></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><a class="docs-sidebar-button docs-navbar-link fa-solid fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="index.html">Introduction</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Introduction</a></li></ul></nav><div class="docs-right"><a class="docs-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/index.md" title="Edit source"><span class="docs-icon fa-solid"></span></a><a class="docs-settings-button docs-navbar-link 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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>Last updated: 2023-10-27 (commit b27fb1b)</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="auto">Automatic (OS)</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.1.2 on <span class="colophon-date" title="Tuesday 31 October 2023 18:07">Tuesday 31 October 2023</span>. Using Julia version 1.9.3.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>Introduction · Persefone</title><script data-outdated-warner src="assets/warner.js"></script><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.045/juliamono.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.4/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.24/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL="."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="assets/documenter.js"></script><script src="siteinfo.js"></script><script src="../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><a class="docs-logo" href="index.html"><img src="assets/logo.png" alt="Persefone logo"/></a><div class="docs-package-name"><span class="docs-autofit"><a href="index.html">Persefone</a></span></div><form class="docs-search" action="search.html"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li class="is-active"><a class="tocitem" href="index.html">Introduction</a><ul class="internal"><li><a class="tocitem" href="#Running-the-model"><span>Running the model</span></a></li><li><a class="tocitem" href="#Model-input"><span>Model input</span></a></li></ul></li><li><a class="tocitem" href="odd.html">Overview, Design, Details (ODD)</a></li><li><span class="tocitem">Developing</span><ul><li><a class="tocitem" href="developing.html">Developing Persefone</a></li><li><a class="tocitem" href="adapting.html">Adapting Persefone</a></li><li><a class="tocitem" href="architecture.html">Source code architecture</a></li><li><a class="tocitem" href="gis.html">Maps and weather data</a></li><li><a class="tocitem" href="species-dsl.html">Defining new species</a></li></ul></li><li><span class="tocitem">Core</span><ul><li><a class="tocitem" href="simulation.html">Simulation</a></li><li><a class="tocitem" href="io.html">Input, Output, and Settings</a></li></ul></li><li><span class="tocitem">Nature</span><ul><li><a class="tocitem" href="nature.html">Nature</a></li><li><a class="tocitem" href="energy.html">Dynamic Energy Budgets</a></li><li><a class="tocitem" href="species.html">Species</a></li></ul></li><li><a class="tocitem" href="crops.html">Crop submodel</a></li><li><a class="tocitem" href="farm.html">Farm submodel</a></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href="index.html">Introduction</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href="index.html">Introduction</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://git.idiv.de/xo30xoqa/persephone/-/blob/master//docs/src/index.md#" title="Edit source"><span class="docs-icon fa"></span><span class="docs-label is-hidden-touch">Edit source</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="Introduction"><a class="docs-heading-anchor" href="#Introduction">Introduction</a><a id="Introduction-1"></a><a class="docs-heading-anchor-permalink" href="#Introduction" title="Permalink"></a></h1><p>Persefone is an agent-based, socio-economic-ecological model of agricultural landscapes in Europe under the Common Agricultural Policy (CAP).</p><p>It's aim is to investigate how policy affects farmer decision-making, and how this in turn affects various animal species. It includes a farm submodel, a crop-growth submodel, and an ecological submodels.</p><h2 id="Running-the-model"><a class="docs-heading-anchor" href="#Running-the-model">Running the model</a><a id="Running-the-model-1"></a><a class="docs-heading-anchor-permalink" href="#Running-the-model" title="Permalink"></a></h2><p>To run a single experiment, execute <code>run.jl</code>:</p><pre><code class="nohighlight hljs">julia run.jl -c <CONFIG></code></pre><p>Other commandline arguments are:</p><pre><code class="nohighlight hljs">usage: run.jl [-c CONFIGFILE] [-s SEED] [-o OUTDIR] [-l LOGLEVEL]
+ [--version] [-h]
+
+optional arguments:
+ -c, --configfile CONFIGFILE
+ name of the configuration file
+ -s, --seed SEED inital random seed (type: Int64)
+ -o, --outdir OUTDIR location of the output directory
+ -l, --loglevel LOGLEVEL
+ verbosity: "debug", "info", or "quiet"
+ --version show version information and exit
+ -h, --help show this help message and exit</code></pre><h2 id="Model-input"><a class="docs-heading-anchor" href="#Model-input">Model input</a><a id="Model-input-1"></a><a class="docs-heading-anchor-permalink" href="#Model-input" title="Permalink"></a></h2><p>Persefone requires three input files: a configuration file and two map files. How to generate the map files is documented <a href="gis.html">elsewhere</a>. The <a href="io.html">configuration file</a> defines parameter values and looks like this (see <code>src/parameters.toml</code> for a complete list of parameters):</p><pre><code class="language-TOML hljs">### Persefone - a socio-economic-ecological model of European agricultural landscapes.
+###
+### This is the default configuration file for Persefone, containing all model parameters.
+### The syntax is described here: https://toml.io/en/
+
+[core]
+configfile = "src/parameters.toml" # location of the configuration file
+outdir = "results" # location and name of the output folder
+overwrite = "ask" # overwrite the output directory? (true/false/"ask")
+loglevel = "debug" # verbosity level: "debug", "info", "warn"
+processors = 2 # number of processors to use on parallel runs
+seed = 2 # seed value for the RNG (0 -> random value)
+# dates to start and end the simulation
+startdate = 2022-01-01
+enddate = 2022-12-31
+
+[world]
+landcovermap = "data/landcover_jena.tif" # location of the landcover map
+farmfieldsmap = "data/fields_jena.tif" # location of the field geometry map
+
+[farm]
+farmmodel = "FieldManager" # which version of the farm model to use (not yet implemented)
+
+[nature]
+targetspecies = ["Wolpertinger", "Wyvern"] # list of target species to simulate
+popoutfreq = "daily" # output frequency population-level data, daily/monthly/yearly/end/never
+indoutfreq = "end" # output frequency individual-level data, daily/monthly/yearly/end/never
+
+[crop]
+cropmodel = "linear" # crop growth model to use, "linear" or "aquacrop" (not yet implemented)</code></pre><div class="admonition is-info"><header class="admonition-header">Parameter scanning</header><div class="admonition-body"><p>You can set any parameter to a list of different values, e.g. <code>seed = [1,2,3]</code>. Persefone will then set up and run multiple simulations, one for every possible combination of parameters that you entered (i.e. do a full-factorial simulation experiment).</p></div></div><p><em>Last updated: 2023-07-27 (commit 1e6e7d6)</em></p></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="odd.html">Overview, Design, Details (ODD) »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.23 on <span class="colophon-date" title="Thursday 27 July 2023 10:12">Thursday 27 July 2023</span>. Using Julia version 1.9.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
diff --git a/docs/src/architecture.md b/docs/src/architecture.md
index 1889fd89ccb36d3829b2d6fd8f3c7640a9d5d51b..1712124a2e15628dfec9361eb1e5a059f5d63cf0 100644
--- a/docs/src/architecture.md
+++ b/docs/src/architecture.md
@@ -33,7 +33,7 @@ the `Animal`s in the model landscape.
### The `model` object
A cursory reading of the source code will quickly show that most functions take an
-`AgentBasedModel` object as one of their arguments. This is the key data structure
+`SimulationModel` object as one of their arguments. This is the key data structure
of [Agents.jl](https://juliadynamics.github.io/Agents.jl/stable/tutorial/#.-The-model-1),
and holds all state that is in any way relevant to a simulation run. (Persefone has
a strict "no global state" policy to avoid state-dependent bugs and allow parallelisation.)
diff --git a/test/io_tests.jl b/test/io_tests.jl
index 734ee7844566ddf2eb6cc01cd421204d9d253084..de75781afc8f997b64f75fec715c6d677ae26ce2 100644
--- a/test/io_tests.jl
+++ b/test/io_tests.jl
@@ -7,7 +7,7 @@
settings = Ps.getsettings(TESTPARAMETERS)
properties = Dict{Symbol,Any}(:settings=>settings)
space = GridSpace((10,10), periodic=false)
- model = AgentBasedModel(Animal, space, properties=properties, warn=false)
+ model = SimulationModel(Animal, space, properties=properties, warn=false)
@test @param(core.configfile) == basename(TESTPARAMETERS)
@test @param(core.startdate) == Date(2022, 2, 1)
diff --git a/test/runtests.jl b/test/runtests.jl
index 4636903dfea5c7034e079cbae9f42b5eec5c95fc..c761eeb1b3f79f7424d5f4c9ca8fc9dbcd6a8f1e 100644
--- a/test/runtests.jl
+++ b/test/runtests.jl
@@ -6,7 +6,6 @@
using Pkg
Pkg.activate("..")
-using Agents
using Dates
using DataFrames
using Logging
@@ -24,7 +23,7 @@ const TESTSETTINGS = Ps.getsettings(TESTPARAMETERS)
"""
inittestmodel(smallmap=true)
-Initialise an AgentBasedModel for testing purposes.
+Initialise an SimulationModel for testing purposes.
`smallmap`: use a hypothetical small landscape rather than a real one?
"""
@@ -35,24 +34,26 @@ function inittestmodel(smallmap=true)
landscape = Ps.initlandscape(TESTSETTINGS["world.landcovermap"],
TESTSETTINGS["world.farmfieldsmap"])
end
- space = GridSpace(size(landscape), periodic=false)
weather = Ps.initweather(TESTSETTINGS["world.weatherfile"],
TESTSETTINGS["core.startdate"],
TESTSETTINGS["core.enddate"])
crops = Ps.readcropparameters(TESTSETTINGS["crop.cropfile"],
TESTSETTINGS["crop.growthfile"])
- properties = Dict{Symbol,Any}(:date=>TESTSETTINGS["core.startdate"],
- :landscape=>landscape,
- :weather=>weather,
- :crops=>crops,
- :events=>Vector{FarmEvent}(),
- :migrants=>Vector{Pair{Animal, Date}}(),
- :logger=>global_logger(),
- :dataoutputs=>Vector{DataOutput}(),
- :datatables=>Dict{String,DataFrame}(),
- :settings=>TESTSETTINGS)
- return AgentBasedModel(Union{Farmer,Animal,FarmPlot}, space, properties=properties,
- rng=StableRNG(TESTSETTINGS["core.seed"]), warn=false)
+ model = SimulationModel(TESTSETTINGS,
+ StableRNG(TESTSETTINGS["core.seed"]),
+ global_logger(),
+ Vector{DataOutput}(),
+ Dict{String, DataFrame}(),
+ TESTSETTINGS["core.startdate"],
+ landscape,
+ weather,
+ crops,
+ Vector{Farmer}(),
+ Vector{FarmPlot}(),
+ Vector{Union{Animals,Nothing}}(),
+ Vector{Pair{Animal, Date}}(),
+ Vector{FarmEvent}())
+ model
end
"""