_pkgdown.yml

template:
  params:
    ganalytics: G-VK9KSJ8ENE
    bootswatch: flatly
reference:
- title: "SARS-CoV-2 Variant Prevalence"
  desc: >
    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](https://www.gisaid.org/). Note that these functions require free
    **[registration with GISAID](https://www.gisaid.org/registration/register/)**, and
    you'll need to call `authenticateUser()` at the start of each session.
- contents:
  - genomicsDataDictionary
  - authenticateUser
  - getAllLineagesByLocation
  - getCollectionDateByLocation
  - getGenomicData
  - getGlobalPrevalence
  - getLocationIdGenomic
  - getLag
  - starts_with("getMutation")
  - getPrevalence
  - getCumulativeBySubadmin
  - getSeqCounts
  - getSubmissionDateByLocation
  - getCuratedLineages
  - lookupSublineages
  - plotAllLineagesByLocation
  - plotChoropleth
  - plotMutationHeatmap
  - plotPrevalenceDotPlot
  - plotPrevalenceOverTime
- title: "Research Library"
  desc: >
    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.
- contents:
  - getResourcesData
  - getResourcesResponse
- title: "Cases & Deaths"
  desc: >
    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)](https://github.com/CSSEGISandData/COVID-19)
    at Johns Hopkins University
    and the [New York Times](https://github.com/nytimes/covid-19-data).  Note that unlike the variant prevalence functions, these functions **do not require a GISAID account**
    or a call to `authenticateUser()` to use them.
- contents:
  - starts_with("getAdm")
  - epidemiologyDataDictionary
  - getByAdmnLevel
  - getCountryByRegion
  - getEpiData
  - getISO3
  - getLocationData
  - getMetroByCountry
  - plotEpiData
  - searchLocations