R/mers_korea_2015.R

In Hackout3/outbreaks: A Collection of Disease Outbreak Data

##'  Middle East respiratory syndrome in South Korea, 2015
##'
##'  These datasets correspond to the initial information collected by the Epidemic Intelligence
##'  group at European Centre for Disease Prevention and Control (ECDC) during the first weeks of the
##'  outbreak of Middle East respiratory syndrome (MERS-CoV) outbreak (South Korea) in 2015.  The
##'  data were used to follow the daily evolution of this outbreak using public information
##'  available.
##'
##'  This dataset is meant for teaching purposes; it  represents neither the final outbreak investigation
##'  results nor a consolidated and complete description of the transmission chain.
##'
##' @docType data
##'
##' @format A list of two dataframes:
##'
##'   \code{$linelist}: A dataframe of MERS-CoV cases and their attributes
##'     \itemize{
##'       \item id: Unique identifier
##'       \item age: Age
##'       \item age_class: Age using 10-year groups
##'       \item sex: Sex
##'       \item place_infect: Probable region of infection
##'       \item reporting_ctry: Country reporting the case
##'       \item loc_hosp: Local hospital name where the case was hospitalized
##'       \item dt_onset: Date of onset of symptoms
##'       \item dt_report: Date of reporting
##'       \item week_report: Week number of date of reporting
##'       \item dt_start_exp: Date of first probable exposure to another MERS Co-V case
##'       \item dt_end_exp: Date of last probable exposure to another MERS Co-V case
##'       \item dt_diag: Date of MERS Co-V diagnosis
##'       \item outcome: Outcome (alive or dead)
##'       \item dt_death: Date of death
##'     }
##'
##'
##'  \code{$contacts}: A dataframe describing the relationship between MERS Co-V cases
##'    \itemize{
##'      \item from: Unique identifier of the probably source patient
##'      \item to: Unique identifier of the secondary case
##'      \item exposure: Probable place of exposure
##'      \item diff_dt_onset: Time in days between two successive cases
##'    }
##'
##'
##' @rdname mers_korea_2015
##'
##' @aliases mers_korea_2015
##'
##' @author Data collected by the European Centre for Disease Prevention and Control (Epidemic
##' Intelligence and Response section, contact: Bertrand Sudre (\email{
##' bertrand.sudre@ecdc.europa.eu}) and Kaja Kaasik Aaslav(\email{Kaja.KaasikAaslav@ecdc.europa.eu}).
##' Transfer to R and documentation by Bertrand Sudre (\email{ bertrand.sudre@ecdc.europa.eu}).
##'
##' @references More information on the intial stage of the outbreak in the following reference:
##' Penttinen PM, Kaasik-Aaslav K, Friaux A, Donachie A, Sudre B, Amato-Gauci AJ, Memish ZA,
##' Coulombier D. Taking stock of the first 133 MERS coronavirus cases globally--Is the epidemic
##' changing?  Euro Surveill. 2013 Sep 26;18(39). pii: 20596. PubMed PMID: 24094061.
##'
##' @examples
##' ## show the line list describing MERS Co-V cases and their attributes
##' head(mers_korea_2015$linelist)
##'
##' ## show the relationships between MERS Co-V cases
##' head(mers_korea_2015$contacts)
##'
"mers_korea_2015"