Software

R packages and other software developed by the group

EpiNow2: Estimate Real-Time Case Counts and Time-Varying Epidemiological Parameters.

Estimates the time-varying reproduction number, rate of spread, and doubling time using a range of open-source tools (Abbott et al. (2020)), and current best practices (Gostic et al. (2020)). It aims to help users avoid some of the limitations of naive implementations in a framework that is informed by community feedback and is actively supported.

covid19.nhs.data: NHS Trust Level COVID-19 Data Aggregated to a Range of Spatial Scales.

Facilitates access to data on NHS trust level COVID-19 data aggregated to a range of spatial scales.

covidregionaldata: Subnational Data for COVID-19 Epidemiology.

An interface to subnational and national level COVID-19 data sourced from both official sources, such as Public Health England in the UK, and from other COVID-19 data collections, including the World Health Organisation (WHO), European Centre for Disease Prevention and Control (ECDC), John Hopkins University (JHU), Google Open Data and others. Designed to streamline COVID-19 data extraction, cleaning, and processing from a range of data sources in an open and transparent way. This allows users to inspect and scrutinise the data, and tools used to process it, at every step. For all countries supported, data includes a daily time-series of cases. Wherever available data is also provided for deaths, hospitalisations, and tests. National level data are also supported using a range of sources.

epinowcast: Flexible Hierarchical Nowcasting.

Tools to enable flexible and efficient hierarchical nowcasting of right-truncated epidemiological time-series using a semi-mechanistic Bayesian model with support for a range of reporting and generative processes. Nowcasting, in this context, is gaining situational awareness using currently available observations and the reporting patterns of historical observations. This can be useful when tracking the spread of infectious disease in real-time: without nowcasting, changes in trends can be obfuscated by partial reporting or their detection may be delayed due to the use of simpler methods like truncation. While the package has been designed with epidemiological applications in mind, it could be applied to any set of right-truncated time-series count data.

rbi: Interface to ‘LibBi’.

Provides a complete interface to ‘LibBi’, a library for Bayesian inference (see https://libbi.org and Murray, 2015 for more information). This includes functions for manipulating ‘LibBi’ models, for reading and writing ‘LibBi’ input/output files, for converting ‘LibBi’ output to provide traces for use with the coda package, and for running ‘LibBi’ to conduct inference.

rbi.helpers: ‘rbi’ Helper Functions.

Contains a collection of helper functions to use with ‘rbi’, the R interface to ‘LibBi’, described in Murray et al. (2015). It contains functions to adapt the proposal distribution and number of particles in particle Markov-Chain Monte Carlo, as well as calculating the Deviance Information Criterion (DIC) and converting between times in ‘LibBi’ results and R time/dates.

scoringutils: Utilities for Scoring and Assessing Predictions.

scoringutils facilitates the evaluation of forecasts in a convenient framework based on data.table. It allows user to to check their forecasts and diagnose issues, to visualise forecasts and missing data, to transform data before scoring, to handle missing forecasts, to aggregate scores, and to visualise the results of the evaluation. The package mostly focuses on the evaluation of probabilistic forecasts and allows evaluating several different forecast types and input formats. Find more information about the package in the Vignettes as well as in the accompanying paper (doi:10.48550/arXiv.2205.07090).