The hardware and bandwidth for this mirror is donated by dogado GmbH, the Webhosting and Full Service-Cloud Provider. Check out our Wordpress Tutorial.
If you wish to report a bug, or if you are interested in having us mirror your free-software or open-source project, please feel free to contact us at mirror[@]dogado.de.
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 |
|---|---|
| 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 |
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.
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
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)
Maintainer: Finlay Campbell (finlaycampbell93@gmail.com)
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
Health stats visible at Monitor.