> For the complete documentation index, see [llms.txt](https://epispot.gitbook.io/manual/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://epispot.gitbook.io/manual/master.md).

# The epispot manual

**This manual is currently in development. Unlinked sections have not been created yet.**

This is the official manual to the epispot package. It includes background information on the mathematical modeling of infectious diseases, the motivation behind the epispot package, a complete guide to using epispot and understanding its documentation, and a full explanation of the epispot development process. As epispot grows, this manual is subject to change and will be versioned on the [GitHub repo](https://github.com/epispot/manual/releases). This current version of the manual is maintained at <https://github.com/epispot/manual> and ported to both HTML and PDF formats via GitBook.

## Table of Contents

1. [Compartmental Models in Epidemiology](/manual/ch1.md)
   * 1.1 [Basic Disease Models](/manual/ch1.md#1-1-basic-disease-models)
   * 1.2 [Related Modeling Techniques](/manual/ch1.md#1-2-related-modeling-techniques)
     * 1.2.1 [Agent-based Modeling](/manual/ch1.md#1-2-1-agent-based-modeling)
     * 1.2.2 [Compartmental Models](/manual/ch1.md#1-2-2-compartmental-models)
   * 1.3 [The SIR Model](/manual/ch1.md#1-3-the-sir-model)
     * 1.3.1 [Motivation](/manual/ch1.md#1-3-1-motivation)
     * 1.3.2 [Definitions](/manual/ch1.md#1-3-2-definitions)
     * 1.3.3 [Derivation](/manual/ch1.md#1-3-3-derivation)
     * 1.3.4 [In Practice](/manual/ch1.md#1-3-4-in-practice)
2. [The Structure of epispot](/manual/ch2.md)
   * 2.1 [Visualizing Compartmental Models](/manual/ch2.md#2-1-visualizing-compartmental-models)
     * 2.1.1 [The SIR Model](/manual/ch2.md#2-1-1-the-sir-model)
     * 2.1.2 [Expanding Models](/manual/ch2.md#2-1-2-expanding-models)
     * 2.1.3 [More Complex Models](/manual/ch2.md#2-1-3-more-complex-models)
   * 2.2 [Epispot's Layer Combination Rules](/manual/ch2.md#2-2-epispots-layer-combination-rules)
   * 2.3 [Compiling Models with epispot](/manual/ch2.md#2-3-compiling-models-with-epispot)
     * 2.3.1 [The Basics: Pre-compiled Models](/manual/ch2.md#2-3-1-the-basics-pre-compiled-models)
     * 2.3.2 [Playing with the Model](/manual/ch2.md#2-3-2-playing-with-the-model)
     * 2.3.3 [Compiling the SIHRD Model](/manual/ch2.md#2-3-3-compiling-the-sihrd-model)
3. [Contributing Guidelines](/manual/ch3.md)
   * 3.1 [Introduction](/manual/ch3.md#3-1-introduction)
   * 3.2 [Installation](/manual/ch3.md#3-2-installation)
     * 3.2.1 [Cloning from VCS](/manual/ch3.md#3-2-1-cloning-from-vcs)
     * 3.2.2 [Environment Setup](/manual/ch3.md#3-2-2-environment-setup)
     * 3.2.3 [Building from source](/manual/ch3.md#3-2-3-building-from-source)
   * 3.3 [Structure](/manual/ch3.md#3-3-structure)
     * 3.3.1 [Repository Structure](/manual/ch3.md#3-3-1-repository-structure)
     * 3.3.2 [Package Structure](/manual/ch3.md#3-3-2-package-structure)
   * 3.4 Development
     * 3.4.1 Testing & Code Coverage
     * 3.4.2 Documentation
     * 3.4.3 Security
     * 3.4.4 VCS Notes
   * 3.5 Contributing to this Manual
4. Credits
   * 4.1 Open-Source Policy
   * 4.2 Licensing
   * 4.3 Citations
   * 4.4 Idea & Inspiration
   * 4.5 Dependencies
   * 4.6 External Code Management Tools