{"id":28702869,"url":"https://github.com/epiforecasts/covid19.slovakia.mass.testing","last_synced_at":"2025-07-18T21:32:03.903Z","repository":{"id":54250948,"uuid":"317067690","full_name":"epiforecasts/covid19.slovakia.mass.testing","owner":"epiforecasts","description":" Data and code accompanying the preprint \"The effectiveness of population-wide screening in reducing SARS-CoV-2 infection prevalence in Slovakia\"","archived":false,"fork":false,"pushed_at":"2021-03-01T16:53:47.000Z","size":33568,"stargazers_count":2,"open_issues_count":0,"forks_count":6,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-07-18T03:18:42.736Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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.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":"2020-11-30T00:01:32.000Z","updated_at":"2021-03-01T16:53:50.000Z","dependencies_parsed_at":"2022-08-13T10:01:01.884Z","dependency_job_id":null,"html_url":"https://github.com/epiforecasts/covid19.slovakia.mass.testing","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/epiforecasts/covid19.slovakia.mass.testing","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.slovakia.mass.testing","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.slovakia.mass.testing/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.slovakia.mass.testing/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.slovakia.mass.testing/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/epiforecasts","download_url":"https://codeload.github.com/epiforecasts/covid19.slovakia.mass.testing/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/epiforecasts%2Fcovid19.slovakia.mass.testing/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":265837531,"owners_count":23836557,"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":"2025-06-14T13:05:43.093Z","updated_at":"2025-07-18T21:32:03.838Z","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- \"The effectiveness of population-wide screening in reducing SARS-CoV-2 infection prevalence in Slovakia\"\n```\n\n# The effectiveness of population-wide screening in reducing SARS-CoV-2 infection prevalence in Slovakia\n\nThis repository contains the data and code for our manuscript:\n\nPavelka S, Van-Zandvoort K, Abbott S, Sherratt K, Majdan M, CMMID COVID-19 working group, Jarčuška P, Krajčí M, Flasche S*, Funk S* (*: equal contribution),  _`r Title`_. Available at \u003chttps://cmmid.github.io/topics/covid19/Slovakia.html\u003e.\n\n### How to download or install\n\nYou can download the compendium as a zip from from this URL: \u003chttps://github.com/sbfnk/covid19.slovakia.mass.testing/archive/master.zip\u003e.\n\nOr you can install this compendium as an R package, `covid19.slovakia.mass.testing`, from GitHub with:\n\n```{r gh-installation, eval = FALSE}\n# install.packages(\"devtools\")\nremotes::install_github(\"sbfnk/covid19.slovakia.mass.testing\")\n```\n\n### Included data sets\n\nThe repository contains three data sets:\n\nThe testing data set `ms.tst` can be loaded with\n```{r mstst, eval = FALSE}\ndata(ms.tst)\n```\n\nIncidence of cases confirmed by PCR per county `PCR.inc` can be accessed with\n```{r pcrinc, eval = FALSE}\ndata(PCR.inc)\n```\n\nThe `Rt.county` data set contains the estimated median reproduction number in each county on 22 October 2020. \n\n```{r Rt.county, eval = FALSE}\ndata(Rt.county)\n```\n\nThis data set can be re-created using the The [EpiNow2](https://epiforecasts.io/EpiNow2/) R package by running (noting that it can take a long time to run depending on the hardware available).\n\n```{r reproduce_r, eval = FALSE}\nsource(here::here(\"data-raw\", \"scripts\", \"rt.r\"))\nsource(here::here(\"data-raw\", \"scripts\", \"convert_data.r\"))\n```\n\nThe [EpiNow2](https://epiforecasts.io/EpiNow2/) R package that is used to estimate the reproduction numbers uses generation times and delay distributions saved in `data-raw/data`. They can be re-generated by running.\n\n```{r reproduce_r_distributions, eval = FALSE}\nsource(here::here(\"data-raw\", \"scripts\", \"rt-distributions.r\"))\n```\n\nThe Google mobility data set for Slovakia `mob.slo` visualised in Supplementary Figure S4 can be accessed with\n\n```{r mob.slo, eval = FALSE}\ndata(mob.slo)\n```\n\n### Figures and tables\n\nTo regenerate Table 1, run\n```{r county_table, eval = FALSE}\ncounty_table(\"table1.pdf\")\n```\n\nTo regenerate Fig. 1, run\n```{r pcr_incidence, eval = FALSE}\npcr_incidence()\n```\n\nTo regenerate Fig. 2, run\n```{r risk_ratios, eval = FALSE}\nrr \u003c- risk_ratios()\nrr$figures$a\nrr$figures$b\nrr$figures$c\nrr$tables\n```\n\nTo generate Table S1 and estimate the adjusted prevalence ratio, run\n```{r regression, eval = FALSE}\nr \u003c- regression()\n```\n\nTo regenerate Fig. S4, run\n```{r mobility, eval = FALSE}\nmobility()\n```\n\nTo regenerate Fig. S6, run\n```{r bed_occupancy, eval = FALSE}\nbed_occupancy()\n```\n\nTo regenerate Fig. S7, run\n```{r prevalence, eval = FALSE}\nprevalence()\n```\n\n### Minimum specificity\n\nTo estimate minimum specificity, run\n```{r min_spec}\nestimate_min_specificity()\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.slovakia.mass.testing","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fepiforecasts%2Fcovid19.slovakia.mass.testing","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fepiforecasts%2Fcovid19.slovakia.mass.testing/lists"}