sars2pack

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Overview

The sars2pack R package provides one-line access to over 40 COVID-related datasets. Datasets are accessed in real time directly from their sources and then transformed to tidy-data form where possible and applicable. The result of each dataset accessor is a ready-to-use R dataset, often a dataframe. Documentation includes dataset descriptions, sources and references, and examples. Online documentation is available in two locations:

• The sars2pack documentation, which includes reference docs and detailed dataset descriptions.
• Extended workflows and use cases, as an online book

Questions addressed by sars2pack

• What are the current and historical total, new cases, and deaths of COVID-19 at the city, county, state, national, and international levels?
• How do changes in infection rates differ across locations?
• What are the non-pharmacological interventions in place at the local and national levels?
• In the United States, what is the geographical distribution of healthcare capacity (ICU beds, total beds, doctors, etc.)?
• What are the published values of key epidemic parameters, as curated from the literature?

Installation

# If you do not have BiocManager installed:
install.packages('BiocManager')

# Then, if sars2pack is not already installed:
BiocManager::install('seandavi/sars2pack')

After the one-time installation, load the packge to get started.

library(sars2pack)

Available datasets

<table class="table table-striped" style="margin-left: auto; margin-right: auto;"> <thead> <tr> <th style="text-align:left;"> name </th> <th style="text-align:left;"> accessor </th> <th style="text-align:left;"> data\_type </th> <th style="text-align:left;"> geographical </th> <th style="text-align:left;"> geospatial </th> <th style="text-align:left;"> region </th> <th style="text-align:left;"> resolution </th> <th style="text-align:left;"> url </th> </tr> </thead> <tbody> <tr> <td style="text-align:left;"> United States county-level geographic details </td> <td style="text-align:left;"> us\_county\_geo\_details </td> <td style="text-align:left;"> c(“demographics”, “geographic”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> admin2 </td> <td style="text-align:left;"> [LINK](https://github.com/josh-byster/fips_lat_long) </td> </tr> <tr> <td style="text-align:left;"> OECD International Unemployment Data </td> <td style="text-align:left;"> oecd\_unemployment\_data </td> <td style="text-align:left;"> c(“economics”, “time series”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> World </td> <td style="text-align:left;"> admin0 </td> <td style="text-align:left;"> [LINK](https://oecd.org) </td> </tr> <tr> <td style="text-align:left;"> healthdata.org COVID-19 Mobility Observations and Projections </td> <td style="text-align:left;"> healthdata\_mobility\_data </td> <td style="text-align:left;"> c(“mobility”, “time series”, “projections”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> International </td> <td style="text-align:left;"> c(“admin0”, “admin1”) </td> <td style="text-align:left;"> [LINK](https://covid19.healthdata.org/projections) </td> </tr> <tr> <td style="text-align:left;"> healthdata.org COVID-19 Testing Observations and Projections </td> <td style="text-align:left;"> healthdata\_testing\_data </td> <td style="text-align:left;"> c(“testing”, “time series”, “projections”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> International </td> <td style="text-align:left;"> c(“admin0”, “admin1”) </td> <td style="text-align:left;"> [LINK](https://covid19.healthdata.org/projections) </td> </tr> <tr> <td style="text-align:left;"> Our World In Data testing and cases reporting </td> <td style="text-align:left;"> owid\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”, “testing”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> World </td> <td style="text-align:left;"> admin0 </td> <td style="text-align:left;"> [LINK](https://ourworldindata.org/coronavirus) </td> </tr> <tr> <td style="text-align:left;"> CovidTracker data </td> <td style="text-align:left;"> covidtracker\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”, “testing”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> admin1 </td> <td style="text-align:left;"> [LINK](https://covidtracking.com/) </td> </tr> <tr> <td style="text-align:left;"> European CDC world tracking </td> <td style="text-align:left;"> ecdc\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> World </td> <td style="text-align:left;"> admin0 </td> <td style="text-align:left;"> [LINK](https://www.ecdc.europa.eu/en/covid-19) </td> </tr> <tr> <td style="text-align:left;"> EU data Github aggregator </td> <td style="text-align:left;"> eu\_data\_cache\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> Europe </td> <td style="text-align:left;"> c(“admin0”, “admin1”) </td> <td style="text-align:left;"> [LINK](https://github.com/covid19-eu-zh/covid19-eu-data) </td> </tr> <tr> <td style="text-align:left;"> USA Facts </td> <td style="text-align:left;"> usa\_facts\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> admin1 </td> <td style="text-align:left;"> [LINK](https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/) </td> </tr> <tr> <td style="text-align:left;"> Johns Hopkins dataset </td> <td style="text-align:left;"> jhu\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> World </td> <td style="text-align:left;"> admin0 </td> <td style="text-align:left;"> [LINK](https://github.com/CSSEGISandData/COVID-19) </td> </tr> <tr> <td style="text-align:left;"> Johns Hopkins US-centric data </td> <td style="text-align:left;"> jhu\_us\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> c(“admin1”, “admin2”) </td> <td style="text-align:left;"> [LINK](https://github.com/CSSEGISandData/COVID-19) </td> </tr> <tr> <td style="text-align:left;"> New York Times county level data </td> <td style="text-align:left;"> nytimes\_county\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> admin2 </td> <td style="text-align:left;"> [LINK](https://raw.githubusercontent.com/nytimes/covid-19-data) </td> </tr> <tr> <td style="text-align:left;"> New York Times state level data </td> <td style="text-align:left;"> nytimes\_state\_data </td> <td style="text-align:left;"> c(“time series”, “cases”, “deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> United States </td> <td style="text-align:left;"> admin1 </td> <td style="text-align:left;"> [LINK](https://raw.githubusercontent.com/nytimes/covid-19-data) </td> </tr> <tr> <td style="text-align:left;"> The Economist: Excess deaths during COVID pandemic </td> <td style="text-align:left;"> economist\_excess\_deaths </td> <td style="text-align:left;"> c(“time series”, “deaths”, “excess deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> International </td> <td style="text-align:left;"> c(“admin0”, “admin1”) </td> <td style="text-align:left;"> [LINK](https://github.com/TheEconomist/covid-19-excess-deaths-tracker) </td> </tr> <tr> <td style="text-align:left;"> The : Excess deaths during COVID pandemic </td> <td style="text-align:left;"> financial\_times\_excess\_deaths </td> <td style="text-align:left;"> c(“time series”, “deaths”, “excess deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-align:left;"> International </td> <td style="text-align:left;"> c(“admin0”, “admin1”) </td> <td style="text-align:left;"> [LINK](https://github.com/Financial-Times/coronavirus-excess-mortality-data) </td> </tr> <tr> <td style="text-align:left;"> US CDC excess deaths dataset </td> <td style="text-align:left;"> cdc\_excess\_deaths </td> <td style="text-align:left;"> c(“time series”, “deaths”, “excess deaths”) </td> <td style="text-align:left;"> TRUE </td> <td style="text-align:left;"> FALSE </td> <td style="text-