README.md
In reconhub/outbreaks: A Collection of Disease Outbreak Data

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")

| Item | :------------------ | covid19_england_nhscalls_2020 | dengue_fais_2011 | dengue_yap_2011 | ebola_kikwit_1995 | ebola_sierraleone_2014 | ebola_sim | ebola_sim_clean | fluH7N9_china_2013 | influenza_england_1978_school | measles_hagelloch_1861 | mers_korea_2015 | nipah_malaysia | norovirus_derbyshire_2001_school | rabies_car_2003 | s_enteritidis_pt59 | sars_canada_2003 | sarscov2_who_2019 | smallpox_abakaliki_1967 | varicella_sim_berlin | zika_girardot_2015 | zika_sanandres_2015 | zika_yap_2007 | Title | ---------------- | :------------------------------------------------------------------------------ | | Potential COVID19 cases reported through NHS pathways | | Dengue on the island of Fais, Micronesia, 2011 | | Dengue on the Yap Main Islands, Micronesia, 2011 | | Ebola in Kikwit, Democratic Republic of the Congo, 1995 | | Ebola in Sierra Leone, 2014 | | Simulated Ebola outbreak | | Simulated Ebola outbreak | | Influenza A H7N9 in China, 2013 | | Influenza in a boarding school in England, 1978 | | Measles in Hagelloch, Germany, 1861 | | Middle East respiratory syndrome in South Korea, 2015 | | Nipah in Malaysia and Sinagapore, 1997-1999 | | Norovirus in a primary school in Derbyshire, England, 2001 | | Dog Rabies in Central African Republic, 2003-2012 | | Salmonella Enteritidis PT59 outbreak | | Severe Acute Respiratory Syndrome in Canada, 2003 | | SARS-CoV-2 World Health Organization Situation Reports 2019 Outbreak (COVID-19) | | Smallpox in Abakaliki, Nigeria, 1967 | | Simulated Varicella outbreak | | Zika in Girardot, Colombia, 2015 | | Zika in San Andres, Colombia, 2015 | | Zika on the Yap Main Islands, Micronesia, 2007 |

Data sets in outbreaks

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("reconverse/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)