R/rabies_car_2003.R

In reconhub/outbreaks: A Collection of Disease Outbreak Data

#' Dog Rabies in Central African Republic, 2003-2012
#'
#' These data document a dog rabies epidemic from 2003 to 2012 in Bangui,
#' Central African Republic, and its surroundings. Data comprise dates and
#' locations of the cases, as well as viral sequences of the pathogen for most
#' cases.
#'
#' @docType data
#'
#' @format {
#' 
#' A list comprising a \code{data.frame} (\code{$linelist}) and a \code{DNAbin}
#' \code{matrix} (\code{$dna}). \code{$linelist} contains the following
#' variables:
#' 
#' \itemize{
#' 
#' \item \code{$index}: numeric identifier of the case 
#'
#' \item \code{$date}: date of case reporting
#' 
#' \item \code{$latitude}: the latitude of the collection point 
#' 
#' \item \code{$longitude}: the longitude of the collection point
#' 
#' \item \code{$has_dna}: a logical indicating of the case has a matching
#' pathogen sequence in \code{$dna}
#' 
#' }
#'
#' \code{$dna} is a \code{DNAbin} \code{matrix} whose labels are to be matched
#' against \code{$linelist$index}.
#' 
#' }
#'
#' @author Data from Transfer to R and documentation by Thibaut Jombart.
#'
#' @source The data were provided by the Institut Pasteur de Bangui, Bangui,
#'   République Centrafricaine, and the Institut Pasteur, Unit Lyssavirus
#'   Dynamics and Host Adaptation, WHO Collaborating Centre for Reference and
#'   Research on Rabies, Paris, France.
#'
#' @references Cori et al. (submitted) A graph-based evidence synthesis approach
#'   to detecting outbreak clusters: an application to dog rabies.
#' 
#' @examples
#'
#' if (require(incidence) && require(ape)) {
#'   i <- incidence(rabies_car_2003$linelist$date, 28L)
#'   plot(i)
#' 
#'   tre <- nj(dist.dna(rabies_car_2003$dna))
#'   plot(tre, main = "Neighbour-Joining tree")
#'
#' }
"rabies_car_2003"