outbreaks
A Collection of Disease Outbreak Data
Empirical or simulated disease outbreak data, provided either as RData or as text files.
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
.RDatafiles in thedata/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:
- disease: mandatory
- location: optional
- year: optional
- sim: mandatory if this is a simulated dataset; otherwise data is assume to be an actual outbreak
- other: (any other relevant information)
Contributors (by alphabetic order):
- Finlay Campbell
- Simon Frost
- Thibaut Jombart
- Pierre Nouvellet
- Bertrand Sudre
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!