From 982a220b2548e2dbd99dffd2dfaf9b1826861c53 Mon Sep 17 00:00:00 2001
From: Daniel Vedder <daniel.vedder@idiv.de>
Date: Mon, 29 Jul 2024 18:02:34 +0200
Subject: [PATCH] Added "Scientific documentation" section to website
---
docs/builddocs.jl | 11 ++++++-----
docs/src/CHANGELOG.md | 1 +
docs/src/crop-models.md | 7 +++++++
docs/src/energy.md | 2 ++
docs/src/index.md | 2 +-
docs/src/management.md | 7 +++++++
docs/src/nature.md | 16 +++++++++++++---
docs/src/odd.md | 42 ++++++++++++++++++++++++++++++++++++++++-
8 files changed, 78 insertions(+), 10 deletions(-)
create mode 120000 docs/src/CHANGELOG.md
create mode 100644 docs/src/crop-models.md
create mode 100644 docs/src/management.md
diff --git a/docs/builddocs.jl b/docs/builddocs.jl
index 721baf0..53abafa 100644
--- a/docs/builddocs.jl
+++ b/docs/builddocs.jl
@@ -12,8 +12,6 @@ push!(LOAD_PATH, "../src/")
using Documenter, Persefone
-#TODO add a changelog: https://keepachangelog.com/en/1.0.0/
-
makedocs(sitename="Persefone.jl",
modules = [Persefone],
repo = Remotes.GitLab("git.idiv.de", "persefone", "persefone-model"),
@@ -26,12 +24,17 @@ makedocs(sitename="Persefone.jl",
"gui.md",
"config.md"],
#"odd.md",
+ "Scientific documentation" => [
+ "management.md",
+ "crop-models.md",
+ "skylark.md"],
"Developer guide" => [
"developing.md",
"adapting.md",
"architecture.md",
"gis.md",
- "species-dsl.md"],
+ "species-dsl.md",
+ "CHANGELOG.md"],
"Core" => [
"simulation.md",
"io.md"],
@@ -41,6 +44,4 @@ makedocs(sitename="Persefone.jl",
"species.md"],
"crops.md",
"farm.md"
- "Scientific documentation" => [
- "skylark.md"],
])
diff --git a/docs/src/CHANGELOG.md b/docs/src/CHANGELOG.md
new file mode 120000
index 0000000..699cc9e
--- /dev/null
+++ b/docs/src/CHANGELOG.md
@@ -0,0 +1 @@
+../../CHANGELOG.md
\ No newline at end of file
diff --git a/docs/src/crop-models.md b/docs/src/crop-models.md
new file mode 100644
index 0000000..10b31e4
--- /dev/null
+++ b/docs/src/crop-models.md
@@ -0,0 +1,7 @@
+# Crop models
+
+*TODO*
+
+## ALMaSS
+
+## AquaCrop
diff --git a/docs/src/energy.md b/docs/src/energy.md
index 3bac2de..cf7de33 100644
--- a/docs/src/energy.md
+++ b/docs/src/energy.md
@@ -1,5 +1,7 @@
# Dynamic Energy Budgets
+**NOTE: currently not used.**
+
Persefone's nature module uses Kooijman's Dynamic Energy Budget theory to model energy
flows within individuals.
diff --git a/docs/src/index.md b/docs/src/index.md
index 9f9a71e..7105cf1 100644
--- a/docs/src/index.md
+++ b/docs/src/index.md
@@ -14,4 +14,4 @@ changes in farm operations (e.g. through policy changes in the CAP) influence bi
The model is open-source software available on
[Gitlab](https://git.idiv.de/persefone/persefone-model).
-*This documentation was last updated on 2024-07-16 for **Persefone.jl v0.5.1** (commit [897e96c](https://git.idiv.de/persefone/persefone-model/-/commit/897e96c)).*
+*This documentation was last updated on 2024-07-29 for **Persefone.jl v0.5.1** (commit [402fa8e](https://git.idiv.de/persefone/persefone-model/-/commit/402fa8e)).*
diff --git a/docs/src/management.md b/docs/src/management.md
new file mode 100644
index 0000000..8a64c8a
--- /dev/null
+++ b/docs/src/management.md
@@ -0,0 +1,7 @@
+# Farm management
+
+*TODO*
+
+## Crop rotations and management
+
+## Environmental regulations
diff --git a/docs/src/nature.md b/docs/src/nature.md
index 86b8b70..480e457 100644
--- a/docs/src/nature.md
+++ b/docs/src/nature.md
@@ -18,10 +18,20 @@ Modules = [Persefone]
Pages = ["nature/macros.jl"]
```
+## individuals.jl
+
+This file contains life-history and other ecological functions that apply to
+all animal individuals, such reproduction, death, and movement.
+
+```@autodocs
+Modules = [Persefone]
+Pages = ["nature/individuals.jl"]
+```
+
## populations.jl
-This file contains a set of utility functions for species, including initialisation,
-reproduction, and mortality.
+This file contains functions that apply to all animal populations, such as for
+initialisation, or querying for neighbours.
```@autodocs
Modules = [Persefone]
@@ -31,7 +41,7 @@ Pages = ["nature/populations.jl"]
## insects.jl
This file contains the insect submodel, which calculates the likely insect biomass
-in a given location at a given time.
+in a given location at a given time. (**NOTE: currently not used.**)
```@autodocs
Modules = [Persefone]
diff --git a/docs/src/odd.md b/docs/src/odd.md
index 4639bd9..bfc2a65 100644
--- a/docs/src/odd.md
+++ b/docs/src/odd.md
@@ -1,3 +1,43 @@
# Overview, Design, Details (ODD)
-*TODO*
+The model description follows the ODD (Overview, Design concepts, Details) protocol (Grimm et al., [2006](https://doi.org/10.1016/j.ecolmodel.2006.04.023); [2010](https://doi.org/10.1016/j.ecolmodel.2010.08.019); [2020](https://doi.org/10.18564/jasss.4259)):
+
+
+## 1. Purpose
+
+## 2. Entities, state variables, and scales
+
+## 3. Process overview and scheduling
+
+## 4. Design concepts
+
+### 4.1 Basic principles
+
+### 4.2 Emergence
+
+### 4.3 Adaptation
+
+### 4.4 Objectives
+
+### 4.5 Learning
+
+### 4.6 Prediction
+
+### 4.7 Sensing
+
+### 4.8 Interaction
+
+### 4.9 Stochasticity
+
+### 4.10 Collectives
+
+### 4.11 Observation
+
+## 5. Initialisation
+
+## 6. Input data
+
+## 7. Submodels
+
+
+## Sources
--
GitLab