Discover epiforecasts/rt-breakpoints Open Source project

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R
License
MIT License
Created about 4 years ago
Updated about 4 years ago

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Estimate Rt using breakpoints with EpiNow2

EpiNow2

Estimate Realtime Case Counts and Time-varying Epidemiological Parameters

112

covid

Temporal variation in transmission during the COVID-19 outbreak

TeX

109

scoringutils

Utilities for Scoring and Assessing Predictions

socialmixr

R package for deriving social mixing matrices from survey data.

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

HTML

covid-rt-estimates

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

NCoVUtils

Utility functions for the 2019-NCoV outbreak

inc2prev

Estimate epidemiological quantities from repeated cross-sectional prevalence measurements

HTML

ringbp

Simulate infectious disease transmission with contact tracing

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.

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

covid19.nhs.data

Trust-level COVID-19 hospitalisations in England

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.

covid-us-forecasts

Forecasting Covid-19 in the US

HTML

epinowcast

Hierarchical nowcasting of right censored epidemological counts

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

euro-hub-ensemble

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

TeX

EpiSoon

Forecasting the effective reproduction number over short timescales

HTML

RtD3

Rt visualisation in D3

JavaScript

covid19.sgene.utla.rt

Local area reproduction numbers and S-gene target failure.

covid19_uk_local

UK local Covid-19 analysis

covid-global-archive

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

epiforecasts.github.io

Quarto website for EpiForecasts

HTML

simplified-forecaster-evaluation

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

TeX

stackr

Model stacking for predictive ensembles

HTML

covid-regional-archive

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

covid.german.forecasts

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

TeX

europe-covid-forecast

idbrms

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

qra

Function and example for quantile regression average

covid19-forecast-hub-europe-research

TeX

covid19.lfd.england

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

exploreringbp

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

covid19-hospital-activity

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

HTML

covid19-uk-nowcasts-projections

Nowcasts and projections of Covid-19 in the UK

covid-uk-upload

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

covid19_ct_pillar2

transformation-forecast-evaluation

TeX

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

covid-regional-2-archive

as covid-regional, different countries

crowdforecastr

covidforecastanalysis

Code for evaluating COVID-19 forecasts

HTML

covid-rt-estimates-batch

Python

backcalc

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

HTML

eval-germany-sp-nowcasting

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

epiforecasts.r-universe.dev

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

eval-omicron-for-case-forecasting

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

Shell

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"

ctdist

Inferring changes in the distribution of Ct values over time

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.

uk-crowd-forecasting-challenge

TeX

slack_bot

The source code for our friendly EpiForecasts bot

jekyll-epiforecasts-website

central website

HTML

GM-PL-forecast-evaluation

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

rcomb

Exploring the sensitivity or R estimation

crowd-evaluation

Evaluation for our crowd forecasts

HTML

covid_schools

covid19.forecasts.uk

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

covid19_immunity

Covid-19 immunity estimates

multi-model-information

Characterising information loss due to aggregating epidemic model outputs

dist.spec

Define probability distributions with certain or uncertain parameters

marburg.parameters

Preliminary estimation of delays from data on Marburg in Equatorial Guinea

EpiCastR

R package for spatial forecasting of infectious disease outbreaks

evaluate-delta-for-forecasting

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

nowcasting.example

Estimate reporting delays and use them for nowcasting

EpiForecastsUtils

covid-rt-brazil-subregional

Subregional estimates of Rt for Covid-19 in Brazil

CovidAgeGroupForecast

ons_severity_estimates

actions-dashboard

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

delayscompare

epiforecasts/rt-breakpoints

epiforecasts

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