R/data.R

In Hackout2/repijson: Tools for Handling EpiJSON (Epidemiology Data) Files

#'
#' Toy line list dataset
#'
#' This dataset replicates the structure of disease outbreak line lists, where the unit of observation is a case. It contains a mixture of patient meta-data (e.g. gender, name) and time-stamped records (e.g. hospital admission).
#'
#' @format A data.frame with 5 rows and 16 columns containing the following variables:
#' \itemize{
#'  \item id ID of the patient
#'  \item name name of the patient
#'  \item dob date of birth of the patient (format: yyyy-mm-dd)
#'  \item gender gender of the patient
#'  \item date.of.onset date of symptom onsets
#'  \item date.of.admission date of hospital admission
#'  \item date.of.discharge date of hospital discharge
#'  \item hospital hospital of admission
#'  \item fever has fever been observed? (yes/no)
#'  \item sleepy has the patient been sleepy? (yes/no)
#'  \item contact1.id ID of contact 1
#'  \item contact1.date date of contact 1
#'  \item contact2.id ID of contact 2
#'  \item contact2.date date of contact 2
#'  \item contact3.id ID of contact 3
#'  \item contact3.date date of contact 3
#' }
#'
#' @author Thibaut Jombart \email{thibautjombart@@gmail.com}
#'
#' @examples
#' data(toyll)
#' toyll
#' 
#' toyll$date.of.onset <- as.POSIXct(toyll$date.of.onset)
#' toyll$date.of.admission <- as.POSIXct(toyll$date.of.admission)
#' toyll$date.of.discharge <- as.POSIXct(toyll$date.of.discharge)
#' toyll$contact1.date <- as.POSIXct(toyll$contact1.date)
#' toyll$contact2.date <- as.POSIXct(toyll$contact2.date)
#' toyll$contact3.date <- as.POSIXct(toyll$contact3.date)
#' 
#' ind.fields <- c(names(toyll)[1:5], "hospital", "fever", "sleepy")
#' x <- as.ejObject(toyll,
#'                  recordAttributes=ind.fields,
#'                  eventDefinitions=list(
#'                  define_ejEvent(name="admission", date="date.of.admission"),
#'                  define_ejEvent(name="discharge", date="date.of.discharge"),
#'                  define_ejEvent(name="contact1", date="contact1.date", attributes="contact1.id"),
#'                  define_ejEvent(name="contact2", date="contact2.date", attributes="contact2.id"),
#'                  define_ejEvent(name="contact3", date="contact3.date", attributes="contact3.id")
#'                  ))
#'
#' x
#'
#'
"toyll"