toyll: Toy line list dataset

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

Description

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).

Usage

toyll

Format

A data.frame with 5 rows and 16 columns containing the following variables:

• id ID of the patient

• name name of the patient

• dob date of birth of the patient (format: yyyy-mm-dd)

• gender gender of the patient

• date.of.onset date of symptom onsets

• date.of.admission date of hospital admission

• date.of.discharge date of hospital discharge

• hospital hospital of admission

• fever has fever been observed? (yes/no)

• sleepy has the patient been sleepy? (yes/no)

• contact1.id ID of contact 1

• contact1.date date of contact 1

• contact2.id ID of contact 2

• contact2.date date of contact 2

• contact3.id ID of contact 3

• contact3.date date of contact 3

Author(s)

Thibaut Jombart [e-mail]

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

repijson documentation built on May 29, 2017, 2:12 p.m.