Added "Scientific documentation" section to website

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"],
                   ])

docs/src/CHANGELOG.md

+../../CHANGELOG.md
\ No newline at end of file

docs/src/crop-models.md

+# Crop models
+
+*TODO*
+
+## ALMaSS
+
+## AquaCrop

docs/src/energy.md

 # Dynamic Energy Budgets
 
+**NOTE: currently not used.**
+
 Persefone's nature module uses Kooijman's Dynamic Energy Budget theory to model energy
 flows within individuals.
 

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)).*

docs/src/management.md

+# Farm management
+
+*TODO*
+
+## Crop rotations and management
+
+## Environmental regulations

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]

docs/src/odd.md

 # 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