Lookup sublineages for a given Pango lineage or WHO name

Source: R/lookupSublineages.R

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)

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")
#> [1] "B.1.427"   "B.1.429"   "B.1.429.1"
lookupSublineages("epsilon", returnQueryString = TRUE)
#> [1] "B.1.427 OR B.1.429 OR B.1.429.1"
# Pango lineage
lookupSublineages("B.1.1.7")
#> [1] "B.1.1.7" "Q.1"     "Q.2"     "Q.3"     "Q.4"     "Q.5"     "Q.6"    
#> [8] "Q.7"     "Q.8"    
#' # Not a recognized lineage
lookupSublineages("VOC-21APR-02")
#> Warning: Lineage VOC-21APR-02 not recognized as a Pango lineage
#> Error in invokeRestart("muffleWarning"): no 'restart' 'muffleWarning' found