Retrieve prevalence of lineages by location — getAllLineagesByLocation • outbreakinfo

Retrieve prevalence of all lineages above a specified frequency over time by location

getAllLineagesByLocation(
  location,
  other_threshold = 0.05,
  nday_threshold = 10,
  ndays = 180,
  other_exclude = NULL,
  cumulative = F
)

Arguments

location: a location name
other_threshold: minimum prevalence threshold below which lineages are accumulated under "Other" (default=0.05)
nday_threshold: minimum number of days in which the prevalence of a lineage must be below other_threshold to be accumulated under "Other" (default=10)
ndays: the number of days before the current date to be used as a window to accumulate lineages under "Other" (default=180)
other_exclude: (optional) lineage(s) that are NOT to be included under "Other" even if the conditions specified by the three thresholds above are met
cumulative: `Boolean` (T/F), T returns cumulative prevalence of lineages (default=F)

Value

dataframe

Examples

india = getAllLineagesByLocation(location = "India", other_threshold=0.03, ndays=60)
#> Retrieving data... 
india[india$date == "2021-06-25",]
#>            date total_count lineage_count lineage prevalence prevalence_rolling
#> 1131 2021-06-25         300           300   other          1                  1