Epiforecasts
Researchers at the London School of Hygiene & Tropical Medicine doing research to forecast infectious diseases and perform real-time analyses.
London
Pinned Repositories
covid
Temporal variation in transmission during the COVID-19 outbreak
covid-rt-estimates
National and subnational estimates of the time-varying reproduction number for Covid-19
covid19.nhs.data
Trust-level COVID-19 hospitalisations in England
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.
EpiNow
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
NCoVUtils
Utility functions for the 2019-NCoV outbreak
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.
scoringutils
Utilities for Scoring and Assessing Predictions
socialmixr
R package for deriving social mixing matrices from survey data.
Epiforecasts's Repositories
epiforecasts/EpiNow2
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
epiforecasts/scoringutils
Utilities for Scoring and Assessing Predictions
epiforecasts/socialmixr
R package for deriving social mixing matrices from survey data.
epiforecasts/inc2prev
Estimate epidemiological quantities from repeated cross-sectional prevalence measurements
epiforecasts/ringbp
Simulate infectious disease transmission with contact tracing
epiforecasts/bpmodels
[RETIRED. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models
epiforecasts/EpiSoon
Forecasting the effective reproduction number over short timescales
epiforecasts/euro-hub-ensemble
Analysis of ensemble methods to aggregate Covid-19 forecasts across Europe.
epiforecasts/epiforecasts.github.io
Quarto website for EpiForecasts
epiforecasts/stackr
Model stacking for predictive ensembles
epiforecasts/covid.german.forecasts
Comparing crowd sourced and model derived forecasts of Covid-19 for Germany and Poland
epiforecasts/covid19-uk-nowcasts-projections
Nowcasts and projections of Covid-19 in the UK
epiforecasts/europe-covid-forecast
epiforecasts/nowcasting.example
Estimate reporting delays and use them for nowcasting
epiforecasts/qrensemble
Function and example for quantile regression average
epiforecasts/epiforecasts.r-universe.dev
epiforecasts R universe
epiforecasts/epiforecasts_gantt_chart
Some basic R code for making the lab personnel gantt chart
epiforecasts/eval-by-method
Thematic analysis of model performance in the European COVID-19 Forecast Hub
epiforecasts/slack_bot
The source code for our friendly EpiForecasts bot
epiforecasts/stanedit
Edit stan models from R
epiforecasts/transformation-forecast-evaluation
epiforecasts/uk-crowd-forecasting-challenge
epiforecasts/delayscompare
epiforecasts/dist.spec
Define probability distributions with certain or uncertain parameters
epiforecasts/modelling-utility-review
epiforecasts/multi-model-information
Characterising information loss due to aggregating epidemic model outputs
epiforecasts/schedule
EpiForecasts server job scheduling (CRON, docker, and bash)
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
epiforecasts/Ebola-Expert-Interviews
Analysis of the results from interviews with experts regarding the spatial spread of Ebola in North-Kivu (2019/20)
epiforecasts/ecdc-covid19-admissions
Admissions forecasts for the European Forecast Hub