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    128 repositories

    • BVDOutbreakSize

      Public
      Joint Bayesian generative Turing model for the 2026 DRC BVD outbreak. Combines exports, deaths and reported suspected cases (with ascertainment) in a single pos…
      Julia
      •
      MIT License
      •2•11•37•3•Updated Sep 5, 2026Sep 5, 2026

    • socialmixr

      Public
      Derive social mixing matrices from survey data.
      rr-package
      rr-package
      R
      •
      Other
      •15•44•3•3•Updated Sep 4, 2026Sep 4, 2026

    • epimixr

      Public
      Epidemiological analysis using social mixing matrices
      R
      •
      MIT License
      •0•4•3•1•Updated Sep 3, 2026Sep 3, 2026

    • rbi

      Public
      Bayesian inference with state-space models using LibBi.
      R
      •8•25•1•0•Updated Sep 3, 2026Sep 3, 2026

    • EpiNow2

      Public
      Estimate Realtime Case Counts and Time-varying Epidemiological Parameters
      open-sourcerstatsstan
      open-sourcerstatsstangaussian-processesbackcalculationcovid-19reproduction-number
      R
      •
      Other
      •40•140•63•2•Updated Sep 3, 2026Sep 3, 2026

    • contactsurveys

      Public
      Download and access social contact data
      R
      •
      Other
      •3•2•1•1•Updated Sep 2, 2026Sep 2, 2026

    • distspec

      Public
      Define probability distributions with certain or uncertain parameters
      R
      •
      Other
      •0•1•2•0•Updated Sep 1, 2026Sep 1, 2026

    • epiforecasts.github.io

      Public
      Quarto website for EpiForecasts
      HTML
      •8•5•3•0•Updated Aug 31, 2026Aug 31, 2026

    • andv-linelist-analysis

      Public
      Joint estimation of incubation period, transmission timing, and R(t) for the Epuyén ANDV outbreak
      Julia
      •
      MIT License
      •2•10•13•3•Updated Aug 31, 2026Aug 31, 2026

    • slack_bot

      Public
      The source code for our friendly EpiForecasts bot
      R
      •
      Other
      •0•2•0•1•Updated Aug 28, 2026Aug 28, 2026

    • eval-by-method

      Public
      R
      •
      Other
      •0•6•7•0•Updated Aug 27, 2026Aug 27, 2026

    • EpiBranch.jl

      Public
      Branching process models for infectious disease epidemiology
      Julia
      •
      MIT License
      •1•6•27•9•Updated Aug 26, 2026Aug 26, 2026

    • cfrnow

      Public
      Real-time case fatality ratio from a line list via a Bayesian mixture-cure survival model
      R
      •
      Other
      •0•2•1•0•Updated Aug 26, 2026Aug 26, 2026

    • forecastbaselines

      Public
      forecastbaselines: R interface to ForecastBaselines.jl
      R
      •
      Other
      •0•0•1•0•Updated Aug 26, 2026Aug 26, 2026

    • ForecastEnsembles.jl

      Public
      Combining probabilistic forecasts in Julia (with an R wrapper)
      Julia
      •
      MIT License
      •0•1•3•1•Updated Aug 26, 2026Aug 26, 2026

    • epiforecasts.r-universe.dev

      Public
      epiforecasts R universe
      infrastructure
      infrastructure
      0•2•0•0•Updated Aug 25, 2026Aug 25, 2026

    • ringbp

      Public
      Simulate infectious disease transmission with contact tracing
      transmissioncontrolling-outbreaks
      transmissioncontrolling-outbreaks
      R
      •
      Other
      •12•18•17•0•Updated Aug 25, 2026Aug 25, 2026

    • scoringutils

      Public
      Utilities for Scoring and Assessing Predictions
      forecastingr-packageforecast-evaluation
      forecastingr-packageforecast-evaluation
      R
      •
      Other
      •24•64•106•14•Updated Aug 25, 2026Aug 25, 2026

    • lopensemble

      Public
      Model stacking for predictive ensembles
      forecastingensemblesstacking
      forecastingensemblesstackingcrps
      HTML
      •
      MIT License
      •3•7•5•4•Updated Aug 24, 2026Aug 24, 2026

    • qrensemble

      Public
      Function and example for quantile regression average
      R
      •
      MIT License
      •0•3•1•4•Updated Aug 24, 2026Aug 24, 2026

    • rbi.helpers

      Public
      Helper functions for inference with LibBi. Building on the rbi library.
      R
      •2•4•1•0•Updated Aug 24, 2026Aug 24, 2026

    • daily-vs-weekly-forecast-eval

      Public
      Evaluation of forecasts generated with daily and weekly inputs
      R
      •0•3•13•2•Updated Aug 21, 2026Aug 21, 2026

    • .github

      Public
      Default community files
      infrastructure
      infrastructure
      0•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • omicron-sgtf-forecast

      Public
      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 transmi…
      forecastomicroncovid-19
      forecastomicroncovid-19
      R
      •
      Other
      •4•15•0•3•Updated Aug 20, 2026Aug 20, 2026

    • inc2prev

      Public
      Estimate epidemiological quantities from repeated cross-sectional prevalence measurements
      open-sciencerstatsstan
      open-sciencerstatsstancovid-19
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •6•17•4•2•Updated Aug 20, 2026Aug 20, 2026

    • euro-hub-ensemble

      Public
      Analysis of ensemble methods to aggregate Covid-19 forecasts across Europe.
      articlecovid-19forecast-hub
      articlecovid-19forecast-hubcovid19-forecast-hub-europe
      TeX
      •
      Other
      •0•7•0•0•Updated Aug 20, 2026Aug 20, 2026

    • evalbehtransmission

      Public
      Evaluation of nowcasting and forecasting using behavioural data including CoMix and Google Mobility
      R
      •
      MIT License
      •0•0•27•2•Updated Aug 14, 2026Aug 14, 2026

    • llm-epi-composition

      Public
      Evaluating LLM ability to compose epidemic models with and without validated components
      Julia
      •0•3•0•0•Updated Aug 13, 2026Aug 13, 2026

    • eurohub-ensembles

      Public
      R
      •
      MIT License
      •2•2•0•1•Updated Aug 10, 2026Aug 10, 2026

    • mme-review

      Public
      Systematic review of multi-model ensemble evaluations in infectious disease
      TeX
      •
      MIT License
      •0•4•13•0•Updated Jul 28, 2026Jul 28, 2026
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