Open and Reproducible Science in R

Technical Handbook

Preface

The Open and Reproducible Science in R sub-module of the MSc in International Health and Tropical Medicine is designed to equip students with the knowledge and skills necessary to conduct both academic research and more importantly real-world data analysis that is transparent, reproducible, and in line with the principles of open science.

This technical handbook serves as the go-to guide for MSc IHTM students to the various tools, technologies, and processes that they will be learning and using within the module.

Organisation

This handbook is divided into three sections:

1. Tools

This section cover topics on the various tools and technologies that are to be used and/or introduced in the module. The R language and environment for statistical computing and graphics is primary of these as the module is specific to R. All other tools and technologies are either built specific for use with R (e.g. RStudio which is the IDE of choice for the module and for this handbook) or are general tools that enhance the userR experience and/or supports known and accepted best practices for open and reproducible science using R.

2. Practices

This section covers topics on recommended best practices for optimal usage and maintenance of R and RStudio.

3. Processes

This section covers topics on scientific/data analysis workflows with a focus on steps in initiating and setting up and participating and contributing to such projects within an open and reproducible framework.

How to use

Even though all efforts have been made to order the chapters in a way that is coherent and logical, this handbook is designed such that chapters are standalone topics in of themselves and uses cross-referencing between chapters to make links to the various learning topics/concepts. As such, the best use of this handbook is to use each chapter as a reference for more in-depth discussion of a topic discussed in class rather than a book to read from start to finish.