Epidemiologist Prof Wim Delva is looking for an intern to work with him and his team on COVID-19 modelling.  If you'd like to apply, please remember to share your GitHub solutions with us on the discussion board and share your CVs with us at zindi@zindi.africa.

Project outline

The COVID-19 pandemic has impacted all aspects of society across all countries in the world. To help inform policies and decisions at the global, national and local level, various epidemiological models have been developed. However, these models cannot be blindly applied in any setting and to address any question around operational planning and planning for health care use. This project seeks to leverage an existing model for COVID-19 epidemics and extend it as appropriate for the purpose of guiding the internal healthcare and operational planning process by the Client, who is an international mining company. The modelling process includes the checking and adjusting of assumptions and model inputs, making alterations to the structure of the model, model calibration to available data for multiple settings, generation and visualization of model outputs, continuous updating of model inputs and data to calibrate the model to, and communication of the model output and its implications for decision making with the Client. Specifically, models will be developed for South Africa, Brazil, Chile, Peru, Australia, and possibly the UK.

Deliverables

The successful applicant for this internship will work with the modelling team to help produce the following deliverables:

1. Inventory of the raw observational data and the scientific publications used to inform the model structure and model parameter values.
2. Model diagrams, to aid communication and discussion of the model and its output.
3. The mathematical equations of the models
4. The code implementation of the models in the R programming language, as well as the code used to fit the models to the available data
5. Model output in the form of graphs and tables with accompanying captions.
6. A report detailing the scope of the work, methods used, results obtained and how they should be interpreted when used as input into the decision making around health care, operations and human resources.
7. Derived from this report: a scientific paper describing the work, for publication in a peer-reviewed journal.

The modelling team

The intern will be working closely with the 3 members of the modelling team.

Professor Wim Delva (team leader) trained as a medical doctor and proceeded to obtain a PhD in medical sciences with a strong focus on the epidemiology of HIV. He specialized in epidemiological modelling and applied biostatistics. He has an extensive publication track record, and thrives in environments where cutting-edge methods are applied to solve complex problems. Professor Rashid Ouifki is an Associate Professor at the University of Pretoria. He has more than 20 years of experience in mathematical modelling of infectious diseases, and is specialised in the development and analysis of differential equation models. Dr Roxanne Beauclair is data science consultant with a PhD in medical sciences from Ghent University (under the supervision of Professor Delva). She is specialised in data science applied to epidemiological research questions.

Project timeline

The project has already started. The successful intern can start ASAP.

The project is expected to be completed by the end of October 2020.