Supporting materials for NHSEI COVID-19 Data Analytics community mini-huddle on 10 June 2020
- Slides including detailed references
- Example basic and very stylised SEIR model for COVID-19 in Microsoft Excel
A general national UK-level model for C19 from LSHTM SAGE modellers
by Davies N et al, LSHTM CMMID nCoV Working Group
COVID-19 Transmission App
Another alternative SEIR webapp with visual sliders by Gabriel Goh, Epidemic Calculator
An excellent example of an operational dashboard using SEIR dynamics that has been fit to real-time Trust & PHE data
from the East London Health & Care Partnership - WEL Financial Strategy Team,
"NEL COVID-19 Demand Modelling Dashboard"
Sub-national R0 estimates over time for the UK from Funk S et al, LSHTM CMMID nCoV Working Group, “Temporal variation in transmission during the COVID-19 outbreak – National and subnational estimates for the United Kingdom”
Various Python and R repositories exist for S(E)IR models
, including for the above examples, e.g.
- https://github.com/gabgoh/epcalc (Python)
- https://github.com/cmmid/covid-uk (R, including Rcpp with C++ style scripts and Bayesian/bootstrapped uncertainty bounds)
- https://github.com/cmmid/covidm_reports (R, with scenario modelling for various countries)
- https://github.com/ImperialCollegeLondon/covid19model/tree/master (C++, Python, and R, including stan for Bayesian uncertainty - this is a geospatial microsimulation model and requires significant RAM to run)
Emilia Vynnycky and Richard G White, An Introduction to Infectious Disease Modelling
On COVID-19 modelling and epidemiology in general, my LSHTM colleagues in the Centre for Mathematical Modelling of Infectious Diseases (CMMID) nCoV working group have a fab repo of data visualisation and modelling web apps (using RShiny) and quick research reports as manuscripts are prepped for peer review. Check it out: https://cmmid.github.io/topics/covid19/
Many thanks to Jason Pickles and Sophie Hodges from NHSE/I for inviting and coordinating to the mini-huddle. Recording is on FutureNHS. All queries and corrections welcome to julia dot shen dot 1 at lshtm dot ac dot uk