moved section 'How it works' down, added TOCs

README.md

@@ -4,6 +4,33 @@ This is an example project to demonstrate Literate Programming to create [NetLog
 
 The document you are currently reading contains the [ODD protocol](#rabies-model-odd-protocol) ([Grimm et al. 2006, 2010](#references)) of a model for Rabies in red foxes. The ODD description is interleaved with code blocks showing the NetLogo code used for the described aspect (ODD+C). Using the Literate Programming tool [Yarner](https://github.com/mlange-42/yarner), these code blocks are extracted from the document and arranged into a working NetLogo model.
 
+* [How to use it](#how-to-use-it)
+* [How it works](#how-it-works)
+* [Rabies model - ODD protocol](#rabies-model-odd-protocol)
+* [References](#references)
+* [Appendix](#appendix)
+
+## How to use it
+
+**Read the ODD**
+
+The best way to understand how to use Literate Programming with Yarner to create a NetLogo model from an ODD protocol is to read the below [ODD+C of the Rabies model.](#rabies-model-odd-protocol) It contains the complete code of the model, except the UI elements.
+
+See section [How it works](#how-it-works) for how the model is extracted from this document.
+
+**Run from downloads**
+
+The [Downloads](https://git.ufz.de/oesa/literate-netlogo/-/jobs/artifacts/main/download?job=build) contain a folder `model` with files `Model.nlogo` and `Code.nls`. Open the `.nlogo` file with NetLogo.
+
+**Build from sources**
+
+1. [Install Yarner](https://mlange-42.github.io/yarner/installation.html)
+2. Clone the sources of this example:  
+   `git clone https://git.ufz.de/oesa/literate-netlogo.git`
+3. `cd` into folder `literate-netlogo`
+4. Run command `yarner` to extract the model code
+5. Open file `model/Model.nlogo` with NetLogo
+
 ## How it works
 
 Yarner scans the document for code blocks and puts them together using macros. Each code block has a name, given in its first line and prefixed with `;-`:
@@ -30,27 +57,16 @@ let y 1
 
 For a comprehensive guide and a description of all features, see the [Yarner documentation](https://mlange-42.github.io/yarner/).
 
-## How to use it
-
-**Read the ODD**
-
-The best way to understand how to use Literate Programming with Yarner to create a NetLogo model from an ODD protocol is to read the below [ODD+C of the Rabies model.](#rabies-model-odd-protocol) It contains the complete code of the model, except the UI elements.
-
-**Run from downloads**
-
-The [Downloads](https://git.ufz.de/oesa/literate-netlogo/-/jobs/artifacts/main/download?job=build) contain a folder `model` with files `Model.nlogo` and `Code.nls`. Open the `.nlogo` file with NetLogo.
-
-**Build from sources**
-
-1. [Install Yarner](https://mlange-42.github.io/yarner/installation.html)
-2. Clone the sources of this example:  
-   `git clone https://git.ufz.de/oesa/literate-netlogo.git`
-3. `cd` into folder `literate-netlogo`
-4. Run command `yarner` to extract the model code
-5. Open file `model/Model.nlogo` with NetLogo
-
 ## Rabies model - ODD protocol
 
+* [Purpose](#purpose)
+* [Entities, state variables, and scales](#entities-state-variables-and-scales)
+* [Process overview and scheduling](#process-overview-and-scheduling)
+* [Design concepts](#)
+* [Initialization](#)
+* [Input data](#)
+* [Submodels](#)
+
 ### Purpose
 
 The purpose of this model is to demonstrate how NetLogo models can be created from ODD protocols, using Literate Programming with Yarner.