Real-time infection dynamics and forecasting

EpiNow2 estimates the time-varying reproduction number, growth rate, and doubling time using a range of open-source tools, and current best practices.

Covid-19 data

covidregionaldata is an interface to subnational and national level COVID-19 data.

covid19.nhs.data is an R package that contains a many-to-many mapping between local authority districts and NHS Acute Trusts in England.

Forecast evaluation

scoringutils is an R package to evaluate forecasts. It provides a collection of metrics and proper scoring rules that make it simple to score forecasts against the true observed values.

Social contact patterns

socialmixr is an R package to estimate contact matrices from diary data such as collected in the POLYMOD study.

epimixr is an R package to conduct epidemiological analysis using these contact matrices.

Bayesian inference using state-space models with high-performance hardware

rbi is an R interface to LibBi, or Library for Bayesian Inference. It performs fast Bayesian inference with parallelised Sequential Monte Carlo, on CPUs or GPUs.

rbi.helpers is a supporting package for rbi, especially for constructing proposal distributions and determining the number of particles.