{"id":28702941,"url":"https://github.com/epiforecasts/covid","last_synced_at":"2025-07-23T11:39:53.575Z","repository":{"id":42554424,"uuid":"249007415","full_name":"epiforecasts/covid","owner":"epiforecasts","description":"Temporal variation in transmission during the COVID-19 outbreak","archived":false,"fork":false,"pushed_at":"2022-05-18T08:44:54.000Z","size":12303818,"stargazers_count":109,"open_issues_count":8,"forks_count":30,"subscribers_count":14,"default_branch":"master","last_synced_at":"2025-06-14T13:06:01.450Z","etag":null,"topics":["covid"],"latest_commit_sha":null,"homepage":"https://epiforecasts.io/covid/","language":"TeX","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":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-03-21T15:44:20.000Z","updated_at":"2024-01-04T16:43:42.000Z","dependencies_parsed_at":"2022-08-23T23:20:47.335Z","dependency_job_id":null,"html_url":"https://github.com/epiforecasts/covid","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"purl":"pkg:github/epiforecasts/covid","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiforecasts","download_url":"https://codeload.github.com/epiforecasts/covid/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266671262,"owners_count":23966139,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-07-23T02:00:09.312Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":["covid"],"created_at":"2025-06-14T13:06:00.160Z","updated_at":"2025-07-23T11:39:53.371Z","avatar_url":"https://github.com/epiforecasts.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Temporal variation in transmission during the COVID-19 outbreak\n\nFor the underlying estimates see [here](https://github.com/epiforecasts/covid-rt-estimates). See [here](https://github.com/epiforecasts/EpiNow2) for documentation on the methodology used. See [here](https://github.com/epiforecasts/covidregionaldata) for our data back-end. \n\n## Usage\n\n### Clone the website\n\n```bash\ngit clone --depth 1 https://github.com/epiforecasts/covid.git\n```\n\n### Update results\n\nThis repository uses Azure blob storage to store results. To download these first install [`azcopy`](https://docs.microsoft.com/en-us/azure/storage/common/storage-use-azcopy-v10) (see here for a script to do this for [Linux](https://github.com/epiforecasts/covid-rt-estimates/blob/master/bin/install_azcopy.sh)) and then run the following.\n\n\n```bash\nRscript utils/update_estimates.R\n```\n\n*Warning when run for the first time this will download several GB of data. See [`covid-rt-estimates`](https://github.com/epiforecasts/covid-rt-estimates) for further support accessing estimates.*\n\n### Update the website\n\n#### Update\n\nUpdate the website with the following:\n\n```bash\nbash bin/update_website.sh\n```\n\nSee the `bin` folder for other updating scripts.\n\n## Docker\n\nThis analysis was developed in a docker container based on the `rocker/geospatial` docker image.\n\nTo build the docker image run (from the `covid` directory):\n\n```bash\ndocker build . -t covid\n```\n\nTo run the docker image run:\n\n```bash\ndocker run -d -p 8787:8787 --name covid -e USER=covid -e PASSWORD=covid covid\n```\n\nThe RStudio client can be found on port :8787 at your local machines ip. The default username:password is time_vary:time_vary, set the user with -e USER=username, and the password with - e PASSWORD=newpasswordhere. The default is to save the analysis files into the user directory.\n\nTo mount a folder (from your current working directory - here assumed to be `tmp`) in the docker container to your local system use the following in the above docker run command (as given mounts the whole `covid` directory to `tmp`).\n\n```{bash, eval = FALSE}\n--mount type=bind,source=$(pwd)/tmp,target=/home/covid\n```\n\nTo access the command line run the following:\n\n```{bash, eval = FALSE}\ndocker exec -ti covid bash\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiforecasts%2Fcovid","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid/lists"}