getPrevalence: Retrieve daily prevalence of a lineage by location

View source: R/getPrevalence.R

getPrevalenceR Documentation

Retrieve daily prevalence of a lineage by location

Description

Retrieves the daily prevalence of a PANGO lineage(s) by location

Usage

getPrevalence(
  pangolin_lineage = NULL,
  location = NULL,
  mutations = NULL,
  cumulative = FALSE,
  logInfo = TRUE
)

Arguments

pangolin_lineage

(optional) PANGO lineage name or vector of PANGO lineage names. Either ‘pangolin_lineage' or 'mutations' needs to be specified. A list of lineages will return a long dataframe with 'lineage' as a variable; if you want to calculate the prevalence of lineage1 or lineage2 together, enter the lineages separated by " OR ". For instance, to calculate the prevalence of Delta, you’ll need to supply '"B.1.617.2 OR AY.1 OR AY.2 OR ..."' **Be sure to include the space around "OR" and it must be capitalized.**

location

(optional) a location name

mutations

(optional) a 'vector' of mutation(s). Either 'pangolin_lineage' or 'mutations' needs to be specified. Mutations should be specified in the format 'gene:mutation', like "S:E484K"

cumulative

(optional) 'Boolean' (T/F), T returns cumulative prevalence since first day of detection

logInfo

(optional) 'Boolean' (T/F), T logs helper messages during API calls.

Value

dataframe

Examples

# lineage: P.1 in Brazil
p1_brazil = getPrevalence(pangolin_lineage = "P.1", location = "Brazil")

# AY.4, AY.34, and B.1.617.2 in Brazil (AY.4, AY.34, and B.1.617.2 separately)
delta_and_brazil = getPrevalence(pangolin_lineage = c("AY.4", "AY.34", "B.1.617.2"), location = "Brazil")
delta_and_brazil[delta_and_brazil$date == "2021-09-01",]

# AY.4 OR B.1.617.2 in Brazil (AY.4, AY.34 and B.1.617.2 combined)
delta_or_brazil = getPrevalence(pangolin_lineage = "AY.4 OR AY.34 OR B.1.617.2", location = "Brazil")
delta_or_brazil[delta_and_brazil$date == "2021-09-01",]

# S:E484K mutation prevalence worldwide
se484k = getPrevalence(mutations = c("S:E484K"))

# B.1.1.7 + S:E484K mutation worldwide
b117_se484k = getPrevalence(pangolin_lineage = "B.1.1.7", mutations = c("S:E484K"))

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