Sam Abbott - intro

Hi all,

A brief intro post to get the ball rolling.

I am an infectious disease modeller by background with an undergraduate degree in Mathematics and an Msc in Mathematical Biology. I did my PhD in the use of the BCG vaccine in the UK for controlling Tuberculosis which ended up blending statistical and dynamic modelling. During my PhD I spent a year working as a data scientist in a financial technology start-up working on lending risk models.

Since 2020 I have been working on the real-time modelling of COVID-19 at the London School of Hygiene and Tropical Medicine. More recently I have been branching out into other diseases but maintaining a real-time focus.

Much of my work has featured method/tool development for common real-time modelling tasks such as estimating the effective reproduction number, understanding the relative transmissibility of novel variants, and tracking changes in case fatality ratios. As part of this work, I built a wildly used package (EpiNow2) that takes a modular approach to many of the common tasks we face (i.e chaining models together and custom analysis at the end) and is commonly used as a benchmark for novel methods (for example).

I started explicit work focussing on nowcasting in 2021 (thanks to prompts from @johannes) with the idea of learning some lessons from the work on EpiNow2 and hopefully making the basis for a next-generation set of tools. This work ended up being a prototype version of epinowcast (see the git history here) which is largely unrecognisable now.

I am currently doing active development on epinowcast including new feature development with @adrianlison. I hope to be able to build an effective case for funding future methodological development that enhances the current functionality of epinowcast in order to assist practitioners in developing better real-time analyses (more on this hopefully coming soon). A crucial part of this work will be evaluating and validating what approaches work well when and comparing methods we use as a community vs other available options (and ideally making these more available). My primary research goal is to establish an effective community of practice that can work together to improve real-time analysis (both routine surveillance and in outbreak settings) rather than the current model of adversarial development.

Iā€™m interested in hearing about new methods being developed for real-time analysis, new case studies for deploying currently available methods, problems for which current methods have no support, and opportunities for funding either myself, the epinowcast community, or others to work on similar problems and with a similar mindset.

More on me and my work here and here.

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