Repository template for student modelling projects (repo_template)

This repository provides a template for setting up a reproducible work flow for a modelling project. The template is intended primarily for use by students who are undertaking projects that use compartmental models. The template consists of the following files:

• repo_template.Rproj - an R project file, which can be used to easily access the repository materials in R studio
• report.Rmd - an example report that reads in required functions and parameters and shows how to use these to produce tables and plots
• functions.R - function definitions for example models (SIR and SIS) and running these models
• parameters.xlsx - a spreadsheet with parameter definitions that can be used for both creating parameter tables and passing parameter values to models

Required software

• R - a statistical programming language (download links for Windows, Linux, and MacOS)
• R Studio - a user interface for R that is needed for report generation (download link)

Required packages

• deSolve - used for numerical integration of differential equations
• ggplot2 - used for plotting
• readxl - used for reading in Excel files
• knitr - used for formatting tables