lookupSublineages: Lookup sublineages for a given Pango lineage or WHO name
In outbreak-info/R-outbreak-info: outbreak.info R Client

lookupSublineages

R Documentation

Lookup sublineages for a given Pango lineage or WHO name

Description

Retrieve all sublineages of a given Pango lineage or WHO designation. Based on a phylogeny maintained by the [Pango team](https://github.com/cov-lineages/lineages-website/blob/master/data/lineages.yml) to grab all sublineages associated with a lineage, and a curated list of Variants of Concern, Variants of Interest, Variants Under Monitoring, and de-escalated variants maintained by the [outbreak.info team](https://outbreak.info/situation-reports)

Usage

lookupSublineages(lineage, returnQueryString = FALSE)

Arguments

`lineage`	String with the name of a Pango lineage or WHO name
`returnQueryString`	Boolean to return a query string to be piped into functions like getPrevalence (collapses vector by '"OR"')

Value

list containing the sublineages associated with that lineage or WHO designation

Examples

# WHO-designated lineages
lookupSublineages("epsilon")
lookupSublineages("epsilon", returnQueryString = TRUE)
# Pango lineage
lookupSublineages("B.1.1.7")
#' # Not a recognized lineage
lookupSublineages("VOC-21APR-02")

outbreak-info/R-outbreak-info documentation built on March 2, 2023, 9:58 a.m.