Cape Town R User Group

There will be refreshments and networking from 18h00.
Agenda
~~~~~~~~~~~~
* Meeting start at 16h30
* Jared Norman will give a talk titled From Chaos to Clarity: Creating a Resurgence Analysis Dashboard during the COVID-19 pandemic
* Meeting finish at 18h00
About the talk
Nobody was prepared for COVID-19. In March 2020, a few of us at the Modelling and Simulation Hub, Africa (MASHA) decided to focus all of our efforts into facilitating evidence-based decision-making. A key aspect of this effort was to collaborate with two other institutions and form the South African COVID-19 Modelling Consortium (SACMC) together with SACEMA and HE2RO, and chaired by the NICD.
A mathematical model was built but once we learned that the virus was mutating enough to create variants with different key features and that new variants could arise at any time, we realised that mechanistic modelling techniques would bring with them very large uncertainty. As such, we pivoted after the first wave and decided to focus on resurgence metrics which would be frequently updated. The mechanistic modelling would be included in less-regular reports. This philosophy of using whatever techniques solve the real-world problem being considered is at the core of OR.
Around this time, the World Health Organisation (WHO) had put out guidance on what actions a country should take if certain thresholds were met. This guidance was generic and we decided to apply our minds to this problem to come up with several metrics which were made linkable with actions through RAG-type categorisation.
The metrics were tracked with up-to-date data in a drake pipeline and displayed on a dashboard (for the OR literate: read “decision support tool”) alongside some forecasting analysis. The (now decommissioned) dashboard is called the SACMC Epidemic Explorer and was created in about 2 weeks using R Shiny.
To me this talk is a perfect trinity audience: The R User Group from Cape Town, The R User Group from Joburg, and the Operations Research Society of South Africa (ORSSA) Special Interest Group (SIG) on OR in Public Policy. I will frame the talk so that it is relevant to both R users and OR practitioners alike. I will discuss the design goals of this dashboard, the practicalities of building software pipelines like this during a pandemic, and how we implemented and deployed the dashboard multiple times each week for over a year.
I look forward to connecting with people after the talk.
About the presenter
Jared Norman is a researcher at the Modelling and Simulation Hub, Africa (MASHA). He has worked in the information security field defending businesses against cyber threats but pivoted to MASHA in 2019 to fight a different kind of virus. This proved to be an interesting time to shift to disease modelling as 6 months later the world would develop quite a need for it. Since joining MASHA, he has worked on several disease transmission models. He has designed, implemented and maintained application interfaces which facilitate the communication and utility of the models and has provided various improvements to code and automation within the team.