{"id":28702859,"url":"https://github.com/epiforecasts/covid19.lfd.england","last_synced_at":"2025-06-14T13:05:36.786Z","repository":{"id":43114694,"uuid":"344465136","full_name":"epiforecasts/covid19.lfd.england","owner":"epiforecasts","description":"SARS-CoV-2 prevalence in at LTLA level and in educational institutions in England according to LFD testing.","archived":false,"fork":false,"pushed_at":"2022-06-09T11:40:43.000Z","size":53644,"stargazers_count":3,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-06-08T03:44:03.663Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","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.Rmd","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":"2021-03-04T12:22:38.000Z","updated_at":"2022-03-03T15:54:36.000Z","dependencies_parsed_at":"2022-08-19T14:42:31.647Z","dependency_job_id":null,"html_url":"https://github.com/epiforecasts/covid19.lfd.england","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/epiforecasts/covid19.lfd.england","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.lfd.england","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.lfd.england/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.lfd.england/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.lfd.england/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiforecasts","download_url":"https://codeload.github.com/epiforecasts/covid19.lfd.england/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.lfd.england/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":259820811,"owners_count":22916548,"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","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":"2025-06-14T13:05:36.016Z","updated_at":"2025-06-14T13:05:36.778Z","avatar_url":"https://github.com/epiforecasts.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, echo = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"README-\"\n)\nTitle \u003c- \"LFD prevalence in England\"\n```\n\n# LFD prevalence in England\n\nThis data visualises the latest LFD positivy data published as part of the [Weekly statistics for NHS Test and Trace](https://www.gov.uk/government/collections/nhs-test-and-trace-statistics-england-weekly-reports).\n\n### Latest LFD positive prevalence at LTLA level\n\n![](figure/lfd_last_10_weeks.svg)\n\n![](figure/lfd_last_10_weeks_regions.svg)\n\n![](figure/lfd_last_10_weeks_maps.svg)\n\n### Latest LFD positive prevalence in educational settings\n\nApproximate periods during which schools were closed are shaded dark.\n\n![](figure/lfd_testing.svg)\n\n# LFD mass testing in English schools - additional evidence of high test specificity\n\nThis repository also contains the data and code for our note:\n\nFunk S, Flasche S,  _`r Title`_. Available at \u003chttps://cmmid.github.io/topics/covid19/mass-testing-schools.html\u003e.\n\n### How to download or install\n\nThe code is installed as an R package, `covid19.lfd.education`, from GitHub with:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\nremotes::install_github(\"sbfnk/covid19.lfd.england\")\n```\n\nTo re-create the results, run the script in `inst/scripts/lfd.r`:\n\n```{r lfd, eval = FALSE}\nsource(system.file(package = \"covid19.lfd.england\",\n                   file.path(\"scripts\", \"lfd.r\")))\nres\n```\n\nTo make changes, just create a copy of `lfd.r` locally and edit this:\n\n```{r lfd_copy, eval = FALSE}\nfile.copy(system.file(package = \"covid19.lfd.england\",\n                      file.path(\"scripts\", \"lfd.r\"),\n                      \"my_code_dir/lfd.r\"))\n```\n\nDocumentation for the `estimate_min_specificity` function, which is used to estimate the lower bound of specificity, can be found using `?estimate_min_specificity`.\n\n# Copyright notice\n\nContains shapefiles from the Office for National Statistics licensed under the Open Government Licence v.3.0. Contains OS data © Crown copyright and database right 2022.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.lfd.england","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiforecasts%2Fcovid19.lfd.england","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.lfd.england/lists"}