{"id":50656667,"url":"https://github.com/epiforecasts/bvdoutbreaksize","last_synced_at":"2026-06-11T00:00:40.673Z","repository":{"id":358939868,"uuid":"1243778099","full_name":"epiforecasts/BVDOutbreakSize","owner":"epiforecasts","description":"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.","archived":false,"fork":false,"pushed_at":"2026-06-07T23:33:08.000Z","size":1406678,"stargazers_count":10,"open_issues_count":23,"forks_count":2,"subscribers_count":1,"default_branch":"main","last_synced_at":"2026-06-08T00:23:20.496Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"https://epiforecasts.io/BVDOutbreakSize/stable/","language":"Julia","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/epiforecasts.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":".github/CODEOWNERS","security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2026-05-19T16:50:45.000Z","updated_at":"2026-06-07T19:28:50.000Z","dependencies_parsed_at":null,"dependency_job_id":null,"html_url":"https://github.com/epiforecasts/BVDOutbreakSize","commit_stats":null,"previous_names":["seabbs/bvdoutbreaksize","epiforecasts/bvdoutbreaksize"],"tags_count":47,"template":false,"template_full_name":null,"purl":"pkg:github/epiforecasts/BVDOutbreakSize","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2FBVDOutbreakSize","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2FBVDOutbreakSize/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2FBVDOutbreakSize/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2FBVDOutbreakSize/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiforecasts","download_url":"https://codeload.github.com/epiforecasts/BVDOutbreakSize/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2FBVDOutbreakSize/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34175887,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-10T02:00:07.152Z","response_time":89,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2026-06-08T00:03:32.470Z","updated_at":"2026-06-11T00:00:40.661Z","avatar_url":"https://github.com/epiforecasts.png","language":"Julia","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Estimating the current size of the 2026 DRC Bundibugyo virus outbreak\n\n**Authors:** Sam Abbott, Kath Sherratt, Samuel Brand and Sebastian Funk.\n\n[![Stable](https://img.shields.io/badge/docs-stable-blue.svg)](https://epiforecasts.io/BVDOutbreakSize/stable) [![Dev](https://img.shields.io/badge/docs-dev-blue.svg)](https://epiforecasts.io/BVDOutbreakSize/dev) [![Tests](https://github.com/epiforecasts/BVDOutbreakSize/actions/workflows/test.yml/badge.svg)](https://github.com/epiforecasts/BVDOutbreakSize/actions/workflows/test.yml) [![codecov](https://codecov.io/gh/epiforecasts/BVDOutbreakSize/branch/main/graph/badge.svg)](https://codecov.io/gh/epiforecasts/BVDOutbreakSize) [![Aqua QA](https://raw.githubusercontent.com/JuliaTesting/Aqua.jl/master/badge.svg)](https://github.com/JuliaTesting/Aqua.jl) [![Code Style: SciML](https://img.shields.io/static/v1?label=code%20style\u0026message=SciML\u0026color=9558b2\u0026labelColor=389826)](https://github.com/SciML/SciMLStyle) [![DOI](https://zenodo.org/badge/1243778099.svg)](https://doi.org/10.5281/zenodo.20312758)\n\n**Last updated:** on each rebuild. This is a live report, re-run as new\ndata arrive, so the estimates change between updates.\n\n**Data as of:** the most recent situation report. DRC counts come from the\nsituation reports of the Institut National de Santé Publique (INSP); Uganda\nimports come from WHO. The rendered report fills in the build date and the\nexact data cut-off automatically; the suspected-case and suspected-death\nstreams, which carry most of the signal, were last published earlier than\nthe laboratory-confirmed streams.\n\n**See:**\n[current outbreak size](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Summary) ·\n[one-week-ahead forecast](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#One-week-ahead-forecast-results) ·\n[estimate evolution across releases](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Estimate-evolution-across-releases) ·\n[comparison with McCabe et al.](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Comparison-with-McCabe-et-al.) ·\n[how the data streams compare](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Outbreak-size-estimated-by-each-data-stream) ·\n[limitations](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Limitations) ·\n[full joint results](https://epiforecasts.io/BVDOutbreakSize/stable/analysis#Results).\n\n**Abstract.** An outbreak of Ebola disease caused by Bundibugyo virus\n(BVD) is ongoing in the Democratic Republic of the Congo (DRC), with\ncases also detected across the border in Uganda.\nThis is a real-time joint Bayesian estimate of the current size of that\noutbreak, refreshed as new data arrive.\nMost infections are not yet reported, so the current size has to be\ninferred from the surveillance data that are available.\nThe model is a discrete-time renewal process on a daily grid that fits the\nsurveillance streams jointly in a single posterior: the DRC suspected\ncases, suspected deaths, laboratory-confirmed cases and confirmed deaths,\nand the cases and deaths exported to Uganda.\nIt estimates the latent infections, symptom onsets and deaths over time,\nthe reported and confirmed cases, and the time-varying reproduction number\nwith its growth rate and doubling time, alongside the case-fatality ratio,\nthe ascertainment of each surveillance system, and a short-term forecast of\neach stream over the coming week.\nThe DRC data come from the INSP situation reports and the Uganda exports\nfrom the WHO situation reports and Disease Outbreak News, with a genetic\nbound on the time to the most recent common ancestor and priors taken from\nthe McCabe et al. report.\n\n**Scope.** This work is motivated by adding an external view of the\ncurrent situation, based on our understanding of real-time infectious\ndisease dynamics and the infection process that gives rise to observed\nepidemic surveillance counts.\nWe are actively developing it and encourage feedback, so please get in\ntouch.\nWe fully support reuse and adaptation.\nFind out more in the\n[contributing guide](https://epiforecasts.io/BVDOutbreakSize/stable/contributing).\n\n**Use of AI.** The model code and analysis were drafted by a language\nmodel and reviewed and revised under human oversight; the named authors\nare responsible for that oversight.\n\n\u003c!-- SHARED:END --\u003e\n\n## Installing the package\n\nTo use the model and the bundled outbreak data from your own Julia\nenvironment, add the package from the repository:\n\n```julia\nusing Pkg\nPkg.add(url = \"https://github.com/epiforecasts/BVDOutbreakSize\")\n```\n\nYou can then load the model machinery and the data the report is\nfitted to:\n\n```julia\nusing BVDOutbreakSize\nobs = load_observations()\n```\n\nThis gives you the exported model components, constants and data\nloaders, enough to build your own analysis on top of the package.\nReproducing the full report (fitting the models and writing the\nresult tables and plots) can be done in a few ways, described next.\n\n## Running\n\nThere are a couple of ways to re-fit the model.\n\n### Re-fit from a clone\n\n```bash\ngit clone --recurse-submodules https://github.com/epiforecasts/BVDOutbreakSize\ncd BVDOutbreakSize\njulia --project=. -e 'using Pkg; Pkg.instantiate()'\njulia --project=. scripts/run.jl\n```\n\n`scripts/run.jl` fits the models and writes the output CSVs (the\nanalysis literate is also run as part of the docs build). Running\n`docs/examples/analysis.jl` directly instead steps through the full\nnarrative.\n\n### Re-fit without cloning\n\n`scripts/reproduce.jl` fetches the package, instantiates its\nenvironment, and runs the fit:\n\n```bash\ncurl -fsSL https://raw.githubusercontent.com/epiforecasts/BVDOutbreakSize/main/scripts/reproduce.jl | julia\n```\n\nOutputs land in `./bvd-output`; set `BVD_OUTPUT_DIR` to write them\nelsewhere, or `BVD_REF` to a release tag to reproduce a specific\nversion. The script clones into a temporary directory and runs from\nthere, so it leaves your own Julia environments untouched.\n\n### Render the docs page\n\nExecutes the literate and produces HTML at `docs/build/`:\n\n```bash\njulia --project=docs -e 'using Pkg; Pkg.develop(PackageSpec(path=pwd())); Pkg.instantiate()'\njulia --project=docs docs/make.jl\n```\n\nUpdating the observation counts for a new sitrep is a single-file\nedit of `data/observations.toml`; the literate picks the new numbers\nup automatically.\n\n## Outputs and releases\n\nEach push to `main` regenerates the model outputs as part of the\ndocumentation build and publishes them as a GitHub Release. The\n[latest release](https://github.com/epiforecasts/BVDOutbreakSize/releases/latest)\nbundles the saved result tables and plots, thinned posterior draws, a\ncopy of the input `observations.toml` that produced them, a\n`site.zip` snapshot of the rendered report site, and `analysis.html`,\na self-contained single-file copy of the report that opens offline\n([download the latest](https://github.com/epiforecasts/BVDOutbreakSize/releases/latest/download/analysis.html));\nthe same artifacts are\nwritten to the repository's `output/` directory on each build. Browse\n[all releases](https://github.com/epiforecasts/BVDOutbreakSize/releases)\nfor earlier output bundles.\nMajor versions of the report are kept as GitHub Releases.\n\nThe rendered report is published from the\n[`gh-pages` branch](https://github.com/epiforecasts/BVDOutbreakSize/tree/gh-pages),\nwhere past and development versions of the analysis page can be found.\n\n## Submodules\n\n- `external/bdbv-linelist-analysis` — Bayesian reanalysis of the 2012\n  Isiro BDBV line list (Rosello et al. 2015). Source of the\n  informative onset-to-death gamma shape and scale priors.\n\n## Citation\n\nIf you use or build on this project, please cite the works this\nrepository depends on:\n\n- **This project** — Abbott, S., Brand, S., Funk, S. (2026).\n  *BVDOutbreakSize: joint forward-generative Turing model for the\n  2026 DRC Bundibugyo outbreak.*\n  \u003chttps://github.com/epiforecasts/BVDOutbreakSize\u003e.\n  DOI: [10.5281/zenodo.20312758](https://doi.org/10.5281/zenodo.20312758).\n- **INSP situation reports** that supply the DRC suspected-case and\n  suspected-death counts and the sitrep cumulative trajectory —\n  Institut National de Santé Publique, Démocratique du Congo (2026).\n  *Situation reports on the 17th Ebola epidemic.*\n  \u003chttps://insp.cd/ebola-17eme-epidemie/\u003e. Transcribed across health\n  zones by INRB-UMIE/Ebola_DRC_2026,\n  \u003chttps://github.com/INRB-UMIE/Ebola_DRC_2026\u003e.\n- **WHO situation reports and Disease Outbreak News** that supply\n  the Uganda import-case counts and the dated detection and death\n  events for the first Uganda import —\n  World Health Organization Regional Office for Africa (2026).\n  *Ebola disease caused by Bundibugyo virus outbreak, Democratic\n  Republic of the Congo and Uganda — Weekly External Situation\n  Report 01.* Data as of 18 May 2026.\n  World Health Organization (2026). *Disease Outbreak News:\n  Ebola disease caused by Bundibugyo virus — Democratic Republic\n  of the Congo and Uganda (DON602, DON603).* Source of the first\n  Uganda import hospital-admission date (11 May 2026) and the fatal\n  import death date (14 May 2026).\n- **Imperial reports** that this work re-implements and compares\n  against, in both released versions —\n  McCabe, R., Ebbarnezh, L., Okware, S., Fotsing, R., Koua, E.,\n  Mbaka, P., Lofungola, A., van Elsland, S. L., McMenamin, M.,\n  Ferguson, N., le Polain de Waroux, O., Cori, A. (2026).\n  *Estimation of the size of the outbreak of Ebola disease caused\n  by Bundibugyo virus in DRC.* Imperial College London, 18 May 2026.\n  DOI: [10.25560/130007](https://doi.org/10.25560/130007).\n  [Report page](https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/research-themes/preparedness-and-response-to-emerging-threats/report-ebola-18-05-2026/).\n  McCabe, R. and others (2026).\n  *Estimation of the size of the Ebola outbreak caused by Bundibugyo\n  virus in DRC: May 20, 2026 update.* Imperial College London,\n  20 May 2026.\n  DOI: [10.25560/13005307](https://doi.org/10.25560/13005307).\n  [Report PDF](https://www.imperial.ac.uk/media/imperial-college/medicine/mrc-gida/Report-ebola-update-20-05-2026.pdf).\n- **Onset-to-death delay reanalysis** that this work uses for\n  delay priors — Funk, S. (2026). *bdbv-linelist-analysis:\n  Bayesian reanalysis of the 2012 Isiro Bundibugyo line list.*\n  \u003chttps://github.com/sbfnk/bdbv-linelist-analysis\u003e.\n\n## Funding\n\nThis work was funded by the National Institute for Health and Care\nResearch (NIHR) Health Protection Research Unit in Health Analytics \u0026\nModelling, a partnership between the UK Health Security Agency, Imperial\nCollege London and the London School of Hygiene \u0026 Tropical Medicine\n(grant code NIHR207404).\nThe views expressed are those of the author(s) and not necessarily those\nof the NIHR, UK Health Security Agency or the Department of Health and\nSocial Care.\n\n## Further references\n\n- Rosello et al., *Ebola virus disease in DRC, 1976–2014*, eLife 2015.\n  Original Isiro 2012 onset-to-death gamma point estimate.\n- Imai et al., *Estimating the potential total number of novel\n  coronavirus cases in Wuhan City*, Imperial COVID-19 Response Team\n  Report 1, 17 January 2020. Methodological template for Method 1.\n- Charniga et al., *Best practices for estimating and reporting\n  epidemiological delay distributions*, PLOS Computational Biology 2024.\n  Followed for the delay-distribution reporting here.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fbvdoutbreaksize","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiforecasts%2Fbvdoutbreaksize","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fbvdoutbreaksize/lists"}