R/getAllLineagesByLocation.R

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

#' @title Retrieve prevalence of lineages by location
#'
#' @description Retrieve prevalence of all lineages above a specified frequency over time by location
#'
#'@param location a location name
#'@param other_threshold minimum prevalence threshold below which lineages are accumulated under "Other" (default=0.05)
#'@param 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)
#'@param ndays the number of days before the current date to be used as a window to accumulate lineages under "Other" (default=180)
#'@param 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
#'@param cumulative `Boolean` (T/F), T returns cumulative prevalence of lineages (default=F)
#'
#'@return dataframe
#'
#'@examples
#'india = getAllLineagesByLocation(location = "India", other_threshold=0.03, ndays=60)
#'india[india$date == "2021-06-25",]
#'
#' @export

getAllLineagesByLocation <- function(location, other_threshold=0.05, nday_threshold=10, ndays=180, other_exclude=NULL, cumulative=F){
  df <- getGenomicData(query_url="prevalence-by-location-all-lineages", location = location, other_threshold = other_threshold, nday_threshold = nday_threshold, ndays = ndays, other_exclude = other_exclude, cumulative = cumulative)
  return(df)
}