Projects in Awesome Lists by epiforecasts

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.

covid-19 data open-science r6 regional-data rstats

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-rt-estimates

National and subnational estimates of the time-varying reproduction number for Covid-19

country covid-19 epinow2 open-source reproduction-number subnational-estimates

Last synced: 14 Jun 2025

https://github.com/epiforecasts/epinow

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

Last synced: 31 Jan 2026

https://github.com/epiforecasts/inc2prev

Estimate epidemiological quantities from repeated cross-sectional prevalence measurements

covid-19 open-science rstats stan

Last synced: 01 Feb 2026

https://github.com/epiforecasts/ringbp

Simulate infectious disease transmission with contact tracing

controlling-outbreaks transmission

Last synced: 13 Oct 2025

https://github.com/epiforecasts/omicron-sgtf-forecast

In this work, we use S-gene target failure (SGTF) as a proxy of variant status combined with reported case counts to explore the evidence for changes in transmission advantage over time for the Omicron variant. If present this could indicate the impact of immune escape, bias in SGTF data or differences in the populations within which the variants are circulating. We also report estimates for growth rates by variant and overall, case counts overall and by variant for a 14 day forecast window assuming constant future growth, the date at which Omicron will become dominant in England and in each NHS region, and the estimated cumulative percentage of the population with a reported Omicron case.

covid-19 forecast omicron

Last synced: 09 Oct 2025

https://github.com/epiforecasts/wuhanseedingvstransmission

The transmissibility of novel Coronavirus in the early stages of the 2019-20 outbreak in Wuhan: Exploring initial point-source exposure sizes and durations using scenario analysis

ncov ncov-data-visual rstats rstats-package

Last synced: 14 Jun 2025

https://github.com/epiforecasts/bvdoutbreaksize

Joint Bayesian generative Turing model for the 2026 DRC BVD outbreak. Combines exports, deaths and reported suspected cases (with ascertainment) in a single posterior. Includes a no-onward-transmission deaths lower bound.

Last synced: 11 Jun 2026

https://github.com/epiforecasts/covid-us-forecasts

Forecasting Covid-19 in the US

coronavirus covid-19 forecasting united-states

Last synced: 31 Jan 2026

https://github.com/epiforecasts/covid19.nhs.data

Trust-level COVID-19 hospitalisations in England

covid19 hospitalisations local-authority nhs openscience r-package uk

Last synced: 14 Jun 2025

https://github.com/epiforecasts/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.

r-package

Last synced: 14 Jun 2025

https://github.com/epiforecasts/euro-hub-ensemble

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

article covid-19 covid19-forecast-hub-europe forecast-hub

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid19.sgene.utla.rt

Local area reproduction numbers and S-gene target failure.

covid-19 open-science reproduction-number

Last synced: 01 Jul 2025

https://github.com/epiforecasts/episoon

Forecasting the effective reproduction number over short timescales

case-forecasts forecasts

Last synced: 07 Feb 2026

https://github.com/epiforecasts/bpmodels

[RETIRED. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models

branching-process epidemic-dynamics epidemic-modelling epidemic-simulations epidemiology epiverse outbreak-simulator r r-package transmission-chain transmission-chain-reconstruction

Last synced: 14 Jun 2025

https://github.com/epiforecasts/rtd3

Rt visualisation in D3

Last synced: 19 Jul 2025

https://github.com/epiforecasts/lopensemble

Model stacking for predictive ensembles

crps ensembles forecasting stacking

Last synced: 01 Feb 2026

https://github.com/epiforecasts/epiforecasts.github.io

Quarto website for EpiForecasts

Last synced: 07 Feb 2026

https://github.com/epiforecasts/simplified-forecaster-evaluation

Evaluation of a simplified forecasting model designed to emulate the performance of the ECDC forecasting hub.

covid-19 ensemble evaluation forecast-hub forecasting github-actions

Last synced: 07 Mar 2026

https://github.com/epiforecasts/eval-by-method

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

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid.german.forecasts

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

covid-19 epiexpert epinow2 forecast germany poland reproduction-number

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid19-hospital-activity

Short-term forecasts of Trust-level COVID-19 hospital admissions in England.

Last synced: 06 Feb 2026

https://github.com/epiforecasts/covid-regional-archive

This a submodule of epiforecasts/covid - see that repo for further information.

Last synced: 12 Feb 2026

https://github.com/epiforecasts/europe-covid-forecast

Last synced: 23 Oct 2025

https://github.com/epiforecasts/mme-review

Systematic review of multi-model ensemble evaluations in infectious disease

Last synced: 17 Feb 2026

https://github.com/epiforecasts/covid19-uk-nowcasts-projections

Nowcasts and projections of Covid-19 in the UK

Last synced: 17 Feb 2026

https://github.com/epiforecasts/covid19_uk_local

UK local Covid-19 analysis

Last synced: 22 Jun 2025

https://github.com/epiforecasts/covid19.lfd.england

SARS-CoV-2 prevalence in at LTLA level and in educational institutions in England according to LFD testing.

Last synced: 14 Jun 2025

https://github.com/epiforecasts/exploreringbp

Exploring the feasibility of controlling 2019-nCoV outbreaks by isolation of cases and contacts

2019-ncov interactive open-research rstats shiny

Last synced: 14 Jun 2025

https://github.com/epiforecasts/idbrms

Population-level infectious disease modelling as an extension of brms.

brms infectious-disease-models opensource r-package

Last synced: 14 Jun 2025

https://github.com/epiforecasts/eval-germany-sp-nowcasting

Evaluating Semi-Parametric Nowcasts of COVID-19 Hospital Admissions in Germany

cmdstanr covid-19 epinowcast germany hospitalisations nowcasting targets

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-uk-upload

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

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid19-forecast-hub-europe-research

Last synced: 20 Feb 2026

https://github.com/epiforecasts/qrensemble

Function and example for quantile regression average

Last synced: 24 Feb 2026

https://github.com/epiforecasts/covid-global-archive

This is a submodule of epiforecasts/covid - see that repo for information

Last synced: 01 Feb 2026

https://github.com/epiforecasts/rt-comparison-uk-public

Evaluating the use of the reproduction number as an epidemiological tool, using spatio-temporal trends of the Covid-19 outbreak in England.

covid-19 epinow2 open-source reproduction-number rt-comparison-uk united-kingdom

Last synced: 14 Jun 2025

https://github.com/epiforecasts/uk-crowd-forecasting-challenge

Last synced: 02 Feb 2026

https://github.com/epiforecasts/covid19.slovakia.mass.testing

Data and code accompanying the preprint "The effectiveness of population-wide screening in reducing SARS-CoV-2 infection prevalence in Slovakia"

Last synced: 18 Jul 2025

https://github.com/epiforecasts/covid19_ct_pillar2

Last synced: 14 Jun 2025

https://github.com/epiforecasts/stanedit

Edit stan models from R

probabilistic-programming stan

Last synced: 05 Oct 2025

https://github.com/epiforecasts/nowcasting.example

Estimate reporting delays and use them for nowcasting

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-regional-2-archive

as covid-regional, different countries

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-global

This is a submodule of epiforecasts/covid - see that repo for information. See https://github.com/epiforecasts/covid-global-archive for an archive

Last synced: 14 Jun 2025

https://github.com/epiforecasts/transformation-forecast-evaluation

Last synced: 30 Jan 2026

https://github.com/epiforecasts/eval-omicron-for-case-forecasting

Joint forecasting of case counts and sequence (or SGTF) data across countries reporting data to GISAID

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-rt-estimates-batch

Last synced: 14 Jun 2025

https://github.com/epiforecasts/crowdforecastr

r-package

Last synced: 14 Jun 2025

https://github.com/epiforecasts/ctdist

Inferring changes in the distribution of Ct values over time

Last synced: 05 Oct 2025

https://github.com/epiforecasts/llm-epi-composition

Evaluating LLM ability to compose epidemic models with and without validated components

Last synced: 21 Jan 2026

https://github.com/epiforecasts/backcalc

Evaluating approaches to backcalculating cases counts by date of infection from cases counts by date of report

Last synced: 29 Jan 2026

https://github.com/epiforecasts/slack_bot

The source code for our friendly EpiForecasts bot

Last synced: 25 Feb 2026

https://github.com/epiforecasts/covidforecastanalysis

Code for evaluating COVID-19 forecasts

Last synced: 30 Jan 2026

https://github.com/epiforecasts/epiforecasts.r-universe.dev

epiforecasts R universe

infrastructure

Last synced: 31 Jan 2026

https://github.com/epiforecasts/crowd-evaluation

Evaluation for our crowd forecasts

Last synced: 02 Feb 2026

https://github.com/epiforecasts/covid19.forecasts.uk

Data and code accompanying the preprint "Short-term forecasts to inform the response to the Covid-19 epidemic in the UK"

Last synced: 14 Jun 2025

https://github.com/epiforecasts/multi-model-information

Characterising information loss due to aggregating epidemic model outputs

Last synced: 14 Jun 2025

https://github.com/epiforecasts/cityforecasts

R scripts to generate city-level forecasts

Last synced: 16 Oct 2025

https://github.com/epiforecasts/delayscompare

Last synced: 14 Jun 2025

https://github.com/epiforecasts/dist.spec

Define probability distributions with certain or uncertain parameters

Last synced: 14 Jun 2025

https://github.com/epiforecasts/daily-vs-weekly-forecast-eval

Evaluation of forecasts generated with daily and weekly inputs

Last synced: 30 Jul 2025

https://github.com/epiforecasts/covid19_immunity

Covid-19 immunity estimates

Last synced: 10 Jul 2025

https://github.com/epiforecasts/rcomb

Exploring the sensitivity or R estimation

Last synced: 30 Jan 2026

https://github.com/epiforecasts/actions-dashboard

A simple dashboard to visualise the status for all workflows used in this GitHub organisation

Last synced: 31 Jan 2026

https://github.com/epiforecasts/epicastr

R package for spatial forecasting of infectious disease outbreaks

Last synced: 14 Jun 2025

https://github.com/epiforecasts/schedule

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

Last synced: 03 Sep 2025

https://github.com/epiforecasts/covid_schools

Last synced: 14 Jun 2025

https://github.com/epiforecasts/epiforecastsutils

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covidagegroupforecast

Last synced: 08 Aug 2025

https://github.com/epiforecasts/evaluate-delta-for-forecasting

Evaluating the impact of modelling strain dynamics on short-term COVID-19 forecast performance

Last synced: 14 Jun 2025

https://github.com/epiforecasts/gm-pl-forecast-evaluation

(Unofficial) evaluation of the forecasts submitted to the German Forecast Hub

Last synced: 14 Jun 2025

https://github.com/epiforecasts/rt-breakpoints

Estimate Rt using breakpoints with EpiNow2

Last synced: 14 Jun 2025

https://github.com/epiforecasts/covid-rt-brazil-subregional

Subregional estimates of Rt for Covid-19 in Brazil

brazil covid-19 epinow2 reproduction-number rstats

Last synced: 14 Jun 2025

https://github.com/epiforecasts/ons_severity_estimates

Last synced: 14 Jun 2025

https://github.com/epiforecasts/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

Last synced: 14 Jun 2025

https://github.com/epiforecasts/.github

Default community files

infrastructure

Last synced: 01 Feb 2026