outbreaks: a compilation of disease outbreak data

This package compiles a series of publicly available disease outbreak data. Data can be provided as R objects (loaded automatically when loading the package), text files distributed alongside the package, or functions generating a dataset.

The following R datasets are currently available:


Table: Data sets in outbreaks

covid19_england_nhscalls_2020Potential COVID19 cases reported through NHS pathways
dengue_fais_2011Dengue on the island of Fais, Micronesia, 2011
dengue_yap_2011Dengue on the Yap Main Islands, Micronesia, 2011
ebola_kikwit_1995Ebola in Kikwit, Democratic Republic of the Congo, 1995
ebola_sierraleone_2014Ebola in Sierra Leone, 2014
ebola_simSimulated Ebola outbreak
ebola_sim_cleanSimulated Ebola outbreak
fluH7N9_china_2013Influenza A H7N9 in China, 2013
influenza_england_1978_schoolInfluenza in a boarding school in England, 1978
measles_hagelloch_1861Measles in Hagelloch, Germany, 1861
mers_korea_2015Middle East respiratory syndrome in South Korea, 2015
nipah_malaysiaNipah in Malaysia and Sinagapore, 1997-1999
norovirus_derbyshire_2001_schoolNorovirus in a primary school in Derbyshire, England, 2001
rabies_car_2003Dog Rabies in Central African Republic, 2003-2012
s_enteritidis_pt59Salmonella Enteritidis PT59 outbreak
sars_canada_2003Severe Acute Respiratory Syndrome in Canada, 2003
sarscov2_who_2019SARS-CoV-2 World Health Organization Situation Reports 2019 Outbreak (COVID-19)
smallpox_abakaliki_1967Smallpox in Abakaliki, Nigeria, 1967
varicella_sim_berlinSimulated Varicella outbreak
zika_girardot_2015Zika in Girardot, Colombia, 2015
zika_sanandres_2015Zika in San Andres, Colombia, 2015
zika_yap_2007Zika on the Yap Main Islands, Micronesia, 2007

Installing the package

To install the current stable, CRAN version of the package, type:


To benefit from the latest features and bug fixes, install the development, github version of the package using:


Note that this requires the package devtools installed.

Add your own data!

How to add data?

We will try to create a better repository and data submission system at a later stage. The purpose of the current package is only to share examplar datasets during the hackathon. Acceptable forms are:

  • as a .RData files in the data/ folder (recommended)
  • as a text file in the inst/ folder
  • as a function loading/assembling/simulating a dataset

Naming Conventions

We use the lower case throughout, and snake_case (using underscores) to separate words for the files and dataset names, so that for a RData object, a new dataset woud look like: `my_new_data_RData'. Try using informative names, typically using the disease first. Whenever available, order fields as:

  1. disease: mandatory
  2. location: optional
  3. year: optional
  4. sim: mandatory if this is a simulated dataset; otherwise data is assume to be an actual outbreak
  5. other: (any other relevant information)

Contributors (by alphabetic order):

Maintainer: Finlay Campbell (finlaycampbell93@gmail.com)

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GPL (>= 2)


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Last Published

September 28th, 2020

Functions in outbreaks (1.9.0)