A Collection of Disease Outbreak Data

Empirical or simulated disease outbreak data, provided either as RData or as text files.


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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:

data(package="outbreaks")
Item Title
dengue_fais_2011 Dengue on the island of Fais, Micronesia, 2011
dengue_yap_2011 Dengue on the Yap Main Islands, Micronesia, 2011
ebola_kikwit_1995 Ebola in Kikwit, Democratic Republic of the Congo, 1995
ebola_sim Simulated Ebola outbreak
ebola_sim_clean Simulated Ebola outbreak
fluH7N9_china_2013 Influenza A H7N9 in China, 2013
influenza_england_1978_school Influenza in a boarding school in England, 1978
measles_hagelloch_1861 Measles in Hagelloch, Germany, 1861
mers_korea_2015 Middle East respiratory syndrome in South Korea, 2015
norovirus_derbyshire_2001_school Norovirus in a primary school in Derbyshire, England, 2001
rabies_car_2003 Dog Rabies in Central African Republic, 2003-2012
s_enteritidis_pt59 Salmonella Enteritidis PT59 outbreak
sars_canada_2003 Severe Acute Respiratory Syndrome in Canada, 2003
smallpox_abakaliki_1967 Smallpox in Abakaliki, Nigeria, 1967
zika_girardot_2015 Zika in Girardot, Colombia, 2015
zika_sanandres_2015 Zika in San Andres, Colombia, 2015
zika_yap_2007 Zika on the Yap Main Islands, Micronesia, 2007

Installing the package

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

install.packages("outbreaks")

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

devtools::install_github("reconhub/outbreaks")

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 ([email protected])

News

outbreaks 1.5.0 (2018-12-15)

NEW FEATURES

One new dataset added:

  • nipah_malaysia: human cases of Nipah virus in Malaysia and Singapore, 1997-1999; data are weekly case counts, stratified by state / country

outbreaks 1.4.0

NEW FEATURES

  • rabies_car_2003: dog rabies in Central African Republic, 2003-2012; data comprise dates and locations of the cases, as well as viral sequences of the pathogen for most cases

outbreaks 1.3.0 (2017-05-13)

NEW FEATURES

One new dataset added:

  • s_enteritidis_pt59: Distribution network and genetic clusters of a food-borne outbreak of Salmonella Enteritidis PT59 (98 cases)


outbreaks 1.2.0 (2017-02-04)

NEW FEATURES

Several new datasets added:

  • dengue_fais_2011: Incidence of 157 clinical cases of Dengue fever on the island of Fais, Micronesia
  • dengue_yap_2011: Incidence of 978 clinical cases of Dengue fever on the Yap Main Islands, Micronesia
  • zika_girardot_2015: Incidence of 1936 clinical cases of Zika virus disease in Girardot, Colombia
  • zika_sanandres_2015: Incidence of 928 clinical cases of Zika virus disease in San Andres, Colombia
  • zika_yap_2007: Incidence of 108 clinical cases of Zika virus disease on the Yap Main Islands, Micronesia

MINOR IMPROVEMENTS

  • Bertrand Sudre ([email protected]) added as the contributor of the mers_korea_2015 dataset
  • Now using snake_case throughout


outbreaks 1.1.0 (2016-11-24)

NEW FEATURES

  • mers.korea.2015 has been added to the collection of outbreak datasets; this describes 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


outbreaks 1.0.0 (2016-10-31)

First release of the outbreaks package on CRAN!

Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("outbreaks")

1.5.0 by Finlay Campbell, 9 months ago


https://github.com/reconhub/outbreaks


Report a bug at https://github.com/reconhub/outbreaks/issues


Browse source code at https://github.com/cran/outbreaks


Authors: Thibaut Jombart [aut] , Simon Frost [aut] , Pierre Nouvellet [aut] , Finlay Campbell [aut, cre] , Bertrand Sudre [aut] , Sang Woo Park [ctb] , Juliet R.C. Pulliam [ctb]


Documentation:   PDF Manual  


GPL (>= 2) license


Suggests testthat, covr, ape, incidence


Suggested by epicontacts, epiflows, epitrix, incidence, projections.


See at CRAN