{"id":16411817,"url":"https://github.com/ijlyttle/covidiowa","last_synced_at":"2026-02-12T03:07:49.948Z","repository":{"id":150080191,"uuid":"342897857","full_name":"ijlyttle/covidIowa","owner":"ijlyttle","description":"County-level COVID-19 Data for Iowa","archived":false,"fork":false,"pushed_at":"2021-10-08T17:29:05.000Z","size":97802,"stargazers_count":0,"open_issues_count":2,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-10-11T15:06:56.004Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"HTML","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/ijlyttle.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2021-02-27T16:04:41.000Z","updated_at":"2021-10-08T17:29:08.000Z","dependencies_parsed_at":"2023-06-05T02:30:43.864Z","dependency_job_id":null,"html_url":"https://github.com/ijlyttle/covidIowa","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/ijlyttle/covidIowa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ijlyttle%2FcovidIowa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ijlyttle%2FcovidIowa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ijlyttle%2FcovidIowa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ijlyttle%2FcovidIowa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ijlyttle","download_url":"https://codeload.github.com/ijlyttle/covidIowa/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ijlyttle%2FcovidIowa/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29355985,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-12T01:03:07.613Z","status":"online","status_checked_at":"2026-02-12T02:00:06.911Z","response_time":55,"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":"2024-10-11T06:46:41.593Z","updated_at":"2026-02-12T03:07:49.932Z","avatar_url":"https://github.com/ijlyttle.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\ndate: \"Compiled at `r format(Sys.time(), '%Y-%m-%d %H:%M:%S', tz = 'UTC')` UTC\"\nparams:\n  publish: \"workflow/data/99-publish\"\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  echo = FALSE,\n  message = FALSE,\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n# covidIowa\n\n```{r}\nlibrary(\"conflicted\")\nlibrary(\"readr\")\nlibrary(\"glue\")\nlibrary(\"dplyr\")\nlibrary(\"scales\")\nlibrary(\"lubridate\")\nlibrary(\"purrr\")\n\nconflict_prefer(\"filter\", \"dplyr\")\n```\n\u003c!-- badges: start --\u003e\n\u003c!-- badges: end --\u003e\n\nThe goal of this repository is to give a county-level summary of COVID-19 cases in Iowa. \nThe data is taken from a series of daily snapshots of the [accessibility page](https://coronavirus.iowa.gov/pages/access) provided by the Iowa Department of Public Health.\n\nIf you want to work with the data yourself, all the code I use is published this repository, check out the [`workflow`](workflow) directory. \nProcessed datasets are also available here:\n\n- [`iowa_county_meta.csv`](https://raw.githubusercontent.com/ijlyttle/covidIowa/master/workflow/data/99-publish/iowa_county_meta.csv): county metadata, things like estimated 2019 population from [ICIP](https://www.icip.iastate.edu/tables/population/counties-estimates) at Iowa State University. \n\n- [`iowa_county_data.csv`](https://raw.githubusercontent.com/ijlyttle/covidIowa/master/workflow/data/99-publish/iowa_county_data.csv): daily numbers by county from IDPH, going back to 2020-05-25.\n\n- [`iowa_county_cases_week.csv`](https://raw.githubusercontent.com/ijlyttle/covidIowa/master/workflow/data/99-publish/iowa_county_data.csv): In addition to county metadata, total positive-tests (and per 100k), one week average of daily positive-tests (and per 100k), and week-over-week change in positive tests (as a ratio).\n\n- [`iowa_cases_week.csv`](https://raw.githubusercontent.com/ijlyttle/covidIowa/master/workflow/data/99-publish/iowa_cases_week.csv): Similar to `iowa_county_cases_week.csv`, but aggregated for the entire state.\n\n## Plots\n\n![](workflow/data/99-publish/iowa_cases.png)\n\n![](workflow/data/99-publish/iowa_change.png)\n```{r}\niowa_county_cases_week_current \u003c- \n  read_csv(\n    fs::path(params$publish, \"iowa_county_cases_week.csv\"), \n    col_types = cols(\n      date = col_date(format = \"\"),\n      fips = col_double(),\n      county = col_character(),\n      population = col_double(),\n      population_group = col_character(),\n      cases_total = col_double(),\n      cases_total_per100k = col_double(),\n      cases_avg_week = col_double(),\n      cases_avg_week_per100k = col_double(),\n      cases_week_growth = col_double()\n    )\n  ) %\u003e%\n  filter(date == max(date))\n```\n\n```{r}\niowa_cases_week \u003c- \n  read_csv(fs::path(params$publish, \"iowa_cases_week.csv\")) %\u003e%\n  mutate(county = \"\")\n```\n\n```{r}\nmake_table \u003c- function(.data, arr, n = 10, by = county) {\n  \n  .data %\u003e%\n  dplyr::arrange({{ arr }}) %\u003e%\n  head(n) %\u003e%\n  dplyr::transmute(\n    {{ by }}, \n    `daily pos. (week avg.)` = round(cases_avg_week, 1),\n    `daily pos. per 100k (week avg.)` = round(cases_avg_week_per100k, 1),\n    `week-over-week change` = scales::label_percent(0.1)(cases_week_growth)\n  ) %\u003e%\n  knitr::kable(align = \"r\")\n}\n```\n\n```{r}\ndate_latest \u003c- unique(iowa_county_cases_week_current$date)\n```\n\n## Tables as of `r date_latest`\n\n```{r}\niowa_since_yesterday \u003c- \n  iowa_cases_week %\u003e%\n  arrange(date) %\u003e%\n  tail(2) %\u003e%\n  transmute(\n    cases_new = cases_total - dplyr::lag(cases_total)\n  ) %\u003e%\n  pluck(\"cases_new\") %\u003e%\n  pluck(2)\n```\n\n\nAs of `r date_latest`, IPDH is reporting `r iowa_since_yesterday` new cases since the previous day. \n\nFor the entire state, over the past week: \n\n```{r}\nmake_table(iowa_cases_week, desc(date), n = 7, by = date)\n```\n\nFor the most-populated counties:\n\n```{r}\nmake_table(iowa_county_cases_week_current, desc(population))\n```\n\nMost positive-cases, per-capita:\n\n```{r}\nmake_table(iowa_county_cases_week_current, desc(cases_avg_week_per100k))\n```\n\nMost growth in positive cases, week-over-week:\n\n```{r}\nmake_table(iowa_county_cases_week_current, desc(cases_week_growth))\n```\n\nBiggest decline in positive cases, week-over-week:\n\n```{r}\nmake_table(iowa_county_cases_week_current, cases_week_growth)\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fijlyttle%2Fcovidiowa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fijlyttle%2Fcovidiowa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fijlyttle%2Fcovidiowa/lists"}