outbreaks v1.9.0

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A Collection of Disease Outbreak Data

Empirical or simulated disease outbreak data, provided either as RData or as text files.

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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 .RData files in the data/ 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:

  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)


Contributors (by alphabetic order):

Maintainer: Finlay Campbell (finlaycampbell93@gmail.com)

Functions in outbreaks

Name Description
dengue_yap_2011 Dengue on the Yap Main Islands, Micronesia, 2011
mers_korea_2015 Middle East respiratory syndrome in South Korea, 2015
ebola_kikwit_1995 Ebola in Kikwit, Democratic Republic of the Congo, 1995
covid19_england_nhscalls_2020 Potential COVID19 cases reported through NHS pathways
fluH7N9_china_2013 Influenza A H7N9 in China, 2013
measles_hagelloch_1861 Measles in Hagelloch, Germany, 1861
ebola_sierraleone_2014 Ebola in Sierra Leone, 2014
dengue_fais_2011 Dengue on the island of Fais, Micronesia, 2011
influenza_england_1978_school Influenza in a boarding school in England, 1978
ebola_sim Simulated Ebola 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)
varicella_sim_berlin Simulated Varicella outbreak
smallpox_abakaliki_1967 Smallpox in Abakaliki, Nigeria, 1967
nipah_malaysia Nipah in Malaysia and Sinagapore, 1997-1999
norovirus_derbyshire_2001_school Norovirus in a primary school in Derbyshire, England, 2001
zika_yap_2007 Zika on the Yap Main Islands, Micronesia, 2007
zika_girardot_2015 Zika in Girardot, Colombia, 2015
s_enteritidis_pt59 Salmonella Enteritidis PT59 outbreak
zika_sanandres_2015 Zika in San Andres, Colombia, 2015
rabies_car_2003 Dog Rabies in Central African Republic, 2003-2012
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License GPL (>= 2)
Encoding UTF-8
LazyData true
RoxygenNote 7.1.1
URL https://github.com/reconhub/outbreaks
BugReports https://github.com/reconhub/outbreaks/issues
NeedsCompilation no
Packaged 2020-09-28 09:23:52 UTC; campbellf
Repository CRAN
Date/Publication 2020-09-28 11:20:03 UTC

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