getCumulativeBySubadmin: Retrieve cumulative prevalence of a lineage

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

Retrieve cumulative prevalence of a lineage

Description

Retrieve cumulative prevalence of a PANGO lineage by the immediate administrative level of a location

Usage

getCumulativeBySubadmin(
  pangolin_lineage,
  location = NULL,
  mutations = NULL,
  ndays = NULL
)

Arguments

pangolin_lineage	PANGO lineage name
location	(optional) a location name (if not specified, cumulative prevalence at the country level globally returned)
mutations	(optional) a 'vector' of mutation(s)
ndays	(optional) an 'integer' specifying number of days from current date to calculative cumuative counts (if not specified, no limit on window)

Value

dataframe

Examples

# Worldwide prevalence of B.1.1.7 by country
head(getCumulativeBySubadmin(pangolin_lineage="B.1.1.7"))

# County-level prevalence of B.1.1.7
head(getCumulativeBySubadmin(pangolin_lineage="B.1.1.7", location="California"))

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