README.md
In 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")

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.

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)