{"id":28703012,"url":"https://github.com/epiforecasts/covid19.sgene.utla.rt","last_synced_at":"2025-07-01T22:06:58.245Z","repository":{"id":45874292,"uuid":"326724061","full_name":"epiforecasts/covid19.sgene.utla.rt","owner":"epiforecasts","description":"Local area reproduction numbers and S-gene target failure.","archived":false,"fork":false,"pushed_at":"2021-12-11T00:34:18.000Z","size":67333,"stargazers_count":7,"open_issues_count":1,"forks_count":3,"subscribers_count":6,"default_branch":"main","last_synced_at":"2025-06-14T13:06:26.472Z","etag":null,"topics":["covid-19","open-science","reproduction-number"],"latest_commit_sha":null,"homepage":"https://github.com/epiforecasts/covid19.sgene.utla.rt/blob/main/report.pdf","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","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":"2021-01-04T15:20:15.000Z","updated_at":"2024-05-30T10:33:29.000Z","dependencies_parsed_at":"2022-09-05T05:21:25.532Z","dependency_job_id":null,"html_url":"https://github.com/epiforecasts/covid19.sgene.utla.rt","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/epiforecasts/covid19.sgene.utla.rt","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.sgene.utla.rt","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.sgene.utla.rt/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.sgene.utla.rt/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.sgene.utla.rt/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiforecasts","download_url":"https://codeload.github.com/epiforecasts/covid19.sgene.utla.rt/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.sgene.utla.rt/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263042356,"owners_count":23404459,"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":["covid-19","open-science","reproduction-number"],"created_at":"2025-06-14T13:06:15.796Z","updated_at":"2025-07-01T22:06:58.210Z","avatar_url":"https://github.com/epiforecasts.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Estimating the increase in reproduction number associated with the Delta variant using local area dynamics in England\n\n**This repository is under active development. See the [releases](https://github.com/epiforecasts/covid19.sgene.utla.rt/releases) for stable analyses.**\n\nThis repository contains the data and code for analyses exploring the association between upper-tier local area (UTLA) reproduction number estimates in England and the proportion of COVID-19 tests negative/positive for the S-gene as a proxy for the Alpha/Delta variants. A preprint describing the work in more detail can be found on [medRxiv](https://www.medrxiv.org/content/10.1101/2021.11.30.21267056v1.full).\n\n## Reproducibility\n\n### Data\n\nAll data used in the analysis can be found in the `data` folder in `rds` format. Available data include: \n\n- `utla_rt_with_covariates.rds`: UTLA level weekly reproduction number estimates combined with estimates of the proportion of tests that were S-gene negative, normalised Google mobility data, and tier status by local authority over time.\n- `rt_weekly.rds`: Summarised weekly UTLA reproduction number estimates using both a short and a long generation time.\n- `utla_cases.rds`: UTLA level COVID-19 test positive cases.\n- `sgene_by_utla.rds`: Weekly test positivity data for the S-gene by UTLA.\n- `mobility.rds`: Normalised Google mobility data stratified by context. \n- `tiers.rds`: UTLA level tier level over time.\n\n### Dependencies\n\nThe dependencies for this analysis can be installed using (in the working directory of the analysis):\n\n```r\ninstall.packages(\"devtools\")\ndevtools::install_deps()\n```\n\n### Code\n\nRt estimates from the [EpiForecasts](http://epiforecasts.io/covid) web site can be updated using (here and following in the working directory of the analysis):\n\n```r\nsource(here::here(\"R/extract_rt.r\"))\n```\n\nAll publicly available covariates can be re-extracted using:\n\n```r\nsource(here::here(\"R/extract_public_data.r\"))\n```\n\nAll data sources can then be combined into the analysis dataset using:\n\n```r\nsource(here::here(\"R/combine_data.r\"))\n```\n\nThe statistical models considered can be refit using,\n\n```r\nsource(here::here(\"R/fit_models.r\"))\n```\n\nand compared with\n\n```r\nsource(here::here(\"R/compare_models.r\"))\n```\n\nThe report can be regenerated (once the models have been refit and compared) using:\n\n```r\nrmarkdown::render(\"report.Rmd\")\n```\n\nAlternatively all steps can be reproduced using the following bash script: \n\n```bash \nbash bin/update_analysis.sh\n```\n\n### Archived results\n\nInstead of rerunning the code from scratch archived results can be retrieved from the [OSF](https://osf.io/h6e8n/) which also contains an archive of the code used for the analysis. Note that this will overwrite any files saved in the `output` folder.\n\n```r\nsource(here::here(\"R/download_output.r\"))\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.sgene.utla.rt","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiforecasts%2Fcovid19.sgene.utla.rt","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.sgene.utla.rt/lists"}