getAllLineagesByLocation: Retrieve prevalence of lineages by location

In outbreak-info/R-outbreak-info: outbreak.info R Client

Retrieve prevalence of lineages by location

Description

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

Usage

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)
india[india$date == "2021-06-25",]

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