Reproducible Data Science for Public Health

A practical guide for researchers

Authors
Affiliations

Hélène Langet

Swiss Tropical and Public Health Institute

Jean Augustin DiΓ©gane Tine

Cheikh Anta Diop University of Dakar

Samwel Lwambura

Ifakara Health Institute

Fenella Beynon

Swiss Tropical and Public Health Institute

Silvia Cicconi

Swiss Tropical and Public Health Institute

Gillian Levine

Swiss Tropical and Public Health Institute

Published

May 3, 2024

Preface

Data science and artificial intelligence have the potential to generate fundamentally new insights on global health policies in Africa, but the full realization of this potential depends on the availability of a critical mass of highly trained health data scientists on the continent.

Background

This electronic book was originally created by HΓ©lΓ¨ne Langet, Fenella Beynon, Silvia Cicconi and Gillian Levine from the Swiss Tropical & Public Health Institute (Swiss TPH) and Samwel Lwambura from the Ifakara Health Institute (IHI) to accompany the Data Science for Public Health workshop which was held in Dar-es-Salaam from Monday,September 26th to Wednesday, September 28th 2022. The goal of this workshop was to enable IHI researchers to strengthen their expertise in the area and to lay the foundations for the development of a data science curriculum that is adapted to IHI’s needs.

The content of this electronic book is currently being updated and restructured. This revision aims to incorporate some of the latest technical developments and to refine explanations of key reproducible research and data science concepts to better suit the needs of a graduate-level public health audience.

License

This book is licensed under a Attribution 4.0 International (CC BY 4.0).

You are free to:

  • Share β€” copy and redistribute the material in any medium or format
  • Adapt β€” remix, transform, and build upon the material for any purpose, even commercially.

Under the following terms:

  • Attribution β€” You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
  • No additional restrictions β€” You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits.

Update History

  • September 25, 2022: First edition.
  • November 1st, 2022: Updated resources.
  • Q2 2024: planned release of the second edition, reflecting insights gained from teaching at Swiss TPH.

Acknowledgement

This work was funded by the Leading House Africa (LHA) which promotes and fosters bilateral collaboration with partner institutions in Africa.

This work was not led in isolation and is the product of interdisciplinary discussions with the following research and public health professionals in Switzerland and in Sub-Saharan Africa:

  • Ms Moniek Bresser, Dr Aurelio Di Pasquale, Prof Manuel Hetzel, Dr Marek Kwiatkowski, Dr Fabian SchΓ€r from Swiss TPH (Switzerland)
  • M. Ibrahim Mtebene, Dr Abdallah Mkopi, Dr Grace Mhalu, and Dr Robert Moshiro from IHI, Charles Festo, Hajirani Msuya and Martine Masonda from IHI (Tanzania)
  • M. Francis Njiri from University of Nairobi (UoN, Kenya)