Function reference • outbreakinfo

SARS-CoV-2 Variant Prevalence Functions to track SARS-CoV-2 variant prevalence worldwide, by country, by state/province, or by U.S. county. All sequence data is provided by GISAID. Note that these functions require free registration with GISAID, and you’ll need to call `authenticateUser()` at the start of each session.
`genomicsDataDictionary()`	Documentation of genomics (SARS-CoV-2 variant prevalence) API fields
`authenticateUser()`	Authenticate API
`getAllLineagesByLocation()`	Retrieve prevalence of lineages by location
`getCollectionDateByLocation()`	Retrieve most recent collection date
`getGenomicData()`	Retrieve data from api.outbreak.info/genomics
`getGlobalPrevalence()`	Retrieve global daily prevalence of a lineage
`getLocationIdGenomic()`	Get location id codes from genomic API
`getLag()`	Retrieve lag between collection and submission
`getMutationAcrossLineage()`	Retrieve prevalence of mutation across lineages by location
`getMutationDetails()`	Retrieve mutation details
`getMutationsByLineage()`	Retrieve mutations by lineage
`getPrevalence()`	Retrieve daily prevalence of a lineage by location
`getCumulativeBySubadmin()`	Retrieve cumulative prevalence of a lineage
`getSeqCounts()`	Retrieve sequence count data
`getSubmissionDateByLocation()`	Retrieve most recent submission date
`getCuratedLineages()`	Lookup curated lineages from outbreak.info
`lookupSublineages()`	Lookup sublineages for a given Pango lineage or WHO name
`plotAllLineagesByLocation()`	Plot prevalence of lineages by location
`plotChoropleth()`	Basic plotting function to create a choropleth (map with areas shaded by prevalence)
`plotMutationHeatmap()`	Title Compare mutation prevalences between lineages
`plotPrevalenceDotPlot()`	Plots a dot plot of prevalences of a variant in a specific location
`plotPrevalenceOverTime()`	Plot daily prevalence of a lineage by location
Research Library Functions to track metadata of COVID-19 publications, clinical trials, datasets, protocols, and more. Note that unlike the variant prevalence functions, these functions do not require a GISAID account or a call to `authenticateUser()`to use them.
`getResourcesData()`	Get COVID-19 resource metadata
`getResourcesResponse()`	Access outbreak.info Research Library API
Cases & Deaths Functions to track COVID-19 cases and deaths worldwide, by country, by state/province, or by U.S. county. All epidemiological data is provided by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University and the New York Times. Note that unlike the variant prevalence functions, these functions do not require a GISAID account or a call to `authenticateUser()` to use them.
`getAdmn0()`	Retrieve COVID-19 data for all countries
`getAdmn1ByCountry()`	Retrieve COVID-19 data for states/provinces in a country or countries
`getAdmn2ByCountry()`	Retrieve COVID-19 data for all counties in the US.
`getAdmn2ByState()`	Retrieve COVID-19 data for counties in a state(s)
`epidemiologyDataDictionary()`	Documentation of Epidemiology API fields
`getByAdmnLevel()`	Retrieve COVID-19 data for all locations at an administrative level.
`getCountryByRegion()`	Retrieve COVID-19 data for countries in a World Bank region(s)
`getEpiData()`	Retrieve epidemiological data from outbreak.info
`getISO3()`	Get ISO3 codes
`getLocationData()`	Retrieve COVID-19 data for given locations
`getMetroByCountry()`	Retrieve COVID-19 data for all metropolitan areas in the US.
`plotEpiData()`	Plot COVID-19 data of interest
`searchLocations()`	Get exact location names

Reference

SARS-CoV-2 Variant Prevalence

Research Library

Cases & Deaths