index.qmd

# Preface {.unnumbered}

The Open and Reproducible Science in R sub-module of the [MSc in International Health and Tropical Medicine](https://www.tropicalmedicine.ox.ac.uk/study-with-us/msc-ihtm) 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](https://r-project.org) *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](https://posit.co/products/open-source/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.