Epiforecasts

EpiNow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

scoringutils

Utilities for Scoring and Assessing Predictions

covidregionaldata

An interface to subnational and national level COVID-19 data. For all countries supported, this includes a daily time-series of cases. Wherever available we also provide data on deaths, hospitalisations, and tests. National level data is also supported using a range of data sources as well as linelist data and links to intervention data sets.

socialmixr

R package for deriving social mixing matrices from survey data.

EpiNow

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

inc2prev

Estimate epidemiological quantities from repeated cross-sectional prevalence measurements

ringbp

Simulate infectious disease transmission with contact tracing

forecast.vocs

Contains models and tools to produce short-term forecasts for both case and sequence notifications assuming circulation of either one or two variants. Tools are also provided to allow the evaluation of the use of sequence data for short-term forecasts in both real-world settings and in user generated scenarios.

EpiSoon

Forecasting the effective reproduction number over short timescales

euro-hub-ensemble

Analysis of ensemble methods to aggregate Covid-19 forecasts across Europe.

covid.german.forecasts

Comparing crowd sourced and model derived forecasts of Covid-19 for Germany and Poland

epiforecasts.github.io

Quarto website for EpiForecasts

europe-covid-forecast

stackr

Model stacking for predictive ensembles

covid-uk-upload

Collation and upload of epidemiological estimates of COVID-19 in the UK

covid19-uk-nowcasts-projections

Nowcasts and projections of Covid-19 in the UK

qra

Function and example for quantile regression average

marburg.parameters

Preliminary estimation of delays from data on Marburg in Equatorial Guinea

slack_bot

The source code for our friendly EpiForecasts bot

transformation-forecast-evaluation

uk-crowd-forecasting-challenge

delayscompare

epidemia

epidemia package

eval-by-method

Thematic analysis of model performance in the European COVID-19 Forecast Hub

multi-model-information

Characterising information loss due to aggregating epidemic model outputs

schedule

EpiForecasts server job scheduling (CRON, docker, and bash)

Ebola-Expert-Elicitation

Evaluation of spatial forecasts made by humans and models at the end of the 2018-20 Ebola epidemic in North-Kivu, DRC

Ebola-Expert-Interviews

Analysis of the results from interviews with experts regarding the spatial spread of Ebola in North-Kivu (2019/20)

ecdc-covid19-admissions

Admissions forecasts for the European Forecast Hub

stackr-archived