The epispot manual

v0.1.0.4-beta-3.3.2 for epispot v2.1.1

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. 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

   • 1.1 Basic Disease Models

   • 1.2 Related Modeling Techniques

     • 1.2.1 Agent-based Modeling

     • 1.2.2 Compartmental Models

   • 1.3 The SIR Model

     • 1.3.1 Motivation

     • 1.3.2 Definitions

     • 1.3.3 Derivation

     • 1.3.4 In Practice

2. The Structure of epispot

   • 2.1 Visualizing Compartmental Models

     • 2.1.1 The SIR Model

     • 2.1.2 Expanding Models

     • 2.1.3 More Complex Models

   • 2.2 Epispot's Layer Combination Rules

   • 2.3 Compiling Models with epispot

     • 2.3.1 The Basics: Pre-compiled Models

     • 2.3.2 Playing with the Model

     • 2.3.3 Compiling the SIHRD Model

3. Contributing Guidelines

   • 3.1 Introduction

   • 3.2 Installation

     • 3.2.1 Cloning from VCS

     • 3.2.2 Environment Setup

     • 3.2.3 Building from source

   • 3.3 Structure

     • 3.3.1 Repository Structure

     • 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