Epiforecasts

EpiNow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

scoringutils

Utilities for Scoring and Assessing Predictions

socialmixr

R package for deriving social mixing matrices from survey data.

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.

bpmodels

[No longer being developed. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models

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

covid19-uk-nowcasts-projections

Nowcasts and projections of Covid-19 in the UK

epiforecasts.github.io

Quarto website for EpiForecasts

europe-covid-forecast

stackr

Model stacking for predictive ensembles

nowcasting.example

Estimate reporting delays and use them for nowcasting

qra

Function and example for quantile regression average

epiforecasts_gantt_chart

Some basic R code for making the lab personnel gantt chart

eval-by-method

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

slack_bot

The source code for our friendly EpiForecasts bot

transformation-forecast-evaluation

uk-crowd-forecasting-challenge

delayscompare

dist.spec

Define probability distributions with certain or uncertain parameters

modelling-utility-review

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