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 |
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:
.RData
files in the data/
folder (recommended)inst/
folderWe 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:
Maintainer: Finlay Campbell ([email protected])
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 / countryrabies_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 casesOne new dataset added:
Several new datasets added:
First release of the outbreaks package on CRAN!