Man pages for outbreak-info/R-outbreak-info
outbreak.info R Client
| authenticateUser | Authenticate API |
| epidemiologyDataDictionary | Documentation of Epidemiology API fields |
| genomicsDataDictionary | Documentation of genomics (SARS-CoV-2 variant prevalence) API... |
| getAdmn0 | Retrieve COVID-19 data for all countries |
| getAdmn1ByCountry | Retrieve COVID-19 data for states/provinces in a country or... |
| getAdmn2ByCountry | Retrieve COVID-19 data for all counties in the US. |
| getAdmn2ByState | Retrieve COVID-19 data for counties in a state(s) |
| getAllLineagesByLocation | Retrieve prevalence of lineages by location |
| getByAdmnLevel | Retrieve COVID-19 data for all locations at an administrative... |
| getCollectionDateByLocation | Retrieve most recent collection date |
| getCountryByRegion | Retrieve COVID-19 data for countries in a World Bank... |
| getCumulativeBySubadmin | Retrieve cumulative prevalence of a lineage |
| getCuratedLineages | Lookup curated lineages from outbreak.info |
| getEpiData | Retrieve epidemiological data from outbreak.info |
| getGenomicData | Retrieve data from api.outbreak.info/genomics |
| getGenomicsResponse | Get response from genomics endpoint |
| getGlobalPrevalence | Retrieve global daily prevalence of a lineage |
| getISO3 | Get ISO3 codes |
| getLag | Retrieve lag between collection and submission |
| getLocationData | Retrieve COVID-19 data for given locations |
| getLocationIdGenomic | Get location id codes from genomic API |
| getMetroByCountry | Retrieve COVID-19 data for all metropolitan areas in the US. |
| 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 |
| getResourcesData | Get COVID-19 resource metadata |
| getResourcesResponse | Access outbreak.info Research Library API |
| getSeqCounts | Retrieve sequence count data |
| getSubmissionDateByLocation | Retrieve most recent submission date |
| 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... |
| plotEpiData | Plot COVID-19 data of interest |
| plotMutationHeatmap | Title Compare mutation prevalences between lineages |
| plotPrevalenceDotPlot | Plots a dot plot of prevalences of a variant in a specific... |
| plotPrevalenceOverTime | Plot daily prevalence of a lineage by location |
| searchLocations | Get exact location names |
