Epiforecasts

All

102 repositories

EpiNow2
Public
Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
open-source rstats stan gaussian-processes backcalculation reproduction-number covid-19
R
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Other
•34•122•44•6•Updated Mar 12, 2025Mar 12, 2025
cityforecasts
Public
R scripts to generate city-level forecasts
R
•0•1•12•2•Updated Mar 11, 2025Mar 11, 2025
eval-by-method
Public
Thematic analysis of model performance in the European COVID-19 Forecast Hub
R
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Other
•0•3•1•3•Updated Mar 11, 2025Mar 11, 2025
scoringutils
Public
Utilities for Scoring and Assessing Predictions
forecasting r-package forecast-evaluation
R
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Other
•23•52•101•2•Updated Mar 10, 2025Mar 10, 2025
ringbp
Public
Simulate infectious disease transmission with contact tracing
transmission controlling-outbreaks
R
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Other
•10•15•12•2•Updated Mar 7, 2025Mar 7, 2025
dist.spec
Public
Define probability distributions with certain or uncertain parameters
R
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MIT License
•0•1•2•0•Updated Mar 5, 2025Mar 5, 2025
socialmixr
Public
R package for deriving social mixing matrices from survey data.
r r-package
R
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Other
•11•38•14•2•Updated Mar 3, 2025Mar 3, 2025
epiforecasts.github.io
Public
Quarto website for EpiForecasts
HTML
•6•5•8•2•Updated Mar 1, 2025Mar 1, 2025
stanedit
Public
Edit stan models from R
probabilistic-programming stan
R
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Other
•0•2•1•1•Updated Feb 24, 2025Feb 24, 2025
stackr
Public
Model stacking for predictive ensembles
forecasting ensembles stacking crps
HTML
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MIT License
•3•5•5•1•Updated Feb 24, 2025Feb 24, 2025
qrensemble
Public
Function and example for quantile regression average
R
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MIT License
•0•3•0•0•Updated Feb 24, 2025Feb 24, 2025
delayscompare
Public
R
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GNU General Public License v3.0
•0•1•0•0•Updated Feb 17, 2025Feb 17, 2025
bpmodels
Public
[RETIRED. Use the epichains package instead]. Methods for simulating and analysing the sizes and lengths of chains from branching process models
r epidemiology r-package branching-process epidemic-simulations epidemic-modelling transmission-chain-reconstruction transmission-chain outbreak-simulator epidemic-dynamics
R
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Other
•7•8•6•0•Updated Feb 5, 2025Feb 5, 2025
slack_bot
Public
The source code for our friendly EpiForecasts bot
R
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Other
•0•2•3•0•Updated Jan 29, 2025Jan 29, 2025
europe-covid-forecast
Public
R
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MIT License
•1•4•5•0•Updated Jan 12, 2025Jan 12, 2025
epiforecasts.r-universe.dev
Public
epiforecasts R universe
infrastructure
0•2•0•0•Updated Nov 13, 2024Nov 13, 2024
modelling-utility-review
Public
MIT License
•0•1•0•0•Updated Sep 27, 2024Sep 27, 2024
nowcasting.example
Public
Estimate reporting delays and use them for nowcasting
R
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MIT License
•1•3•4•0•Updated Sep 7, 2024Sep 7, 2024
epiforecasts_gantt_chart
Public
Some basic R code for making the lab personnel gantt chart
R
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MIT License
•6•2•0•0•Updated Jul 16, 2024Jul 16, 2024
uk-crowd-forecasting-challenge
Public
TeX
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MIT License
•0•2•0•0•Updated May 15, 2024May 15, 2024
covid.german.forecasts
Public
Comparing crowd sourced and model derived forecasts of Covid-19 for Germany and Poland
forecast covid-19 reproduction-number epinow2 epiexpert germany poland
TeX
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MIT License
•1•4•3•0•Updated May 15, 2024May 15, 2024
schedule
Public
EpiForecasts server job scheduling (CRON, docker, and bash)
Shell
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MIT License
•2•1•0•0•Updated Apr 17, 2024Apr 17, 2024
multi-model-information
Public
Characterising information loss due to aggregating epidemic model outputs
R
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MIT License
•0•1•0•0•Updated Mar 28, 2024Mar 28, 2024
Ebola-Expert-Elicitation
Public
Evaluation of spatial forecasts made by humans and models at the end of the 2018-20 Ebola epidemic in North-Kivu, DRC
Jupyter Notebook
•0•0•0•0•Updated Mar 14, 2024Mar 14, 2024
Ebola-Expert-Interviews
Public
Analysis of the results from interviews with experts regarding the spatial spread of Ebola in North-Kivu (2019/20)
R
•0•0•0•3•Updated Mar 13, 2024Mar 13, 2024
euro-hub-ensemble
Public
Analysis of ensemble methods to aggregate Covid-19 forecasts across Europe.
article forecast-hub covid19-forecast-hub-europe covid-19
TeX
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Other
•0•7•0•0•Updated Feb 21, 2024Feb 21, 2024
transformation-forecast-evaluation
Public
TeX
•1•2•0•0•Updated Feb 20, 2024Feb 20, 2024
ecdc-covid19-admissions
Public
Admissions forecasts for the European Forecast Hub
R
•1•0•0•0•Updated Jan 15, 2024Jan 15, 2024
inc2prev
Public
Estimate epidemiological quantities from repeated cross-sectional prevalence measurements
open-science rstats stan covid-19
HTML
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BSD 3-Clause "New" or "Revised" License
•7•17•3•2•Updated Nov 10, 2023Nov 10, 2023
covid19-uk-nowcasts-projections
Public
Nowcasts and projections of Covid-19 in the UK
R
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Other
•0•4•0•0•Updated Nov 7, 2023Nov 7, 2023