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:
data(package="outbreaks")Table: Data sets in outbreaks
| Item | Title |
|---|---|
| covid19_england_nhscalls_2020 | Potential COVID19 cases reported through NHS pathways |
| 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_sierraleone_2014 | Ebola in Sierra Leone, 2014 |
| 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 |
| nipah_malaysia | Nipah in Malaysia and Sinagapore, 1997-1999 |
| 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 |
| sarscov2_who_2019 | SARS-CoV-2 World Health Organization Situation Reports 2019 Outbreak (COVID-19) |
| smallpox_abakaliki_1967 | Smallpox in Abakaliki, Nigeria, 1967 |
| varicella_sim_berlin | Simulated Varicella outbreak |
| 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):
- Eric Brown
- Finlay Campbell
- Simon Frost
- Thibaut Jombart
- Pierre Nouvellet
- Sang Woo Park
- Juliet R.C. Pulliam
- Jakob Schumacher
- Bertrand Sudre
Maintainer: Finlay Campbell (finlaycampbell93@gmail.com)