outbreaks: a compilation of disease outbreak data
This package compiles a series of disease outbreak data, to be shared during Hackout 3. 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 |
---|---|
ebola.kikwit.1995 | |
ebola.sim.clean | |
ebola.sim | |
fluH7N9.china.2013 | |
influenza.england.1978.school | |
measles.hagelloch.1861 | |
mers.korea.2015 | |
sars.canada.2003 | |
smallpox.abakaliki.1967 |
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 thedata/
folder (recommended) - as a text file in the
inst/
folder - as a function loading/assembling/simulating a dataset
Naming Conventions
We use the lower cases and dots 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:
- disease: mandatory
- location: optional
- year: optional
- sim: mandatory if this is a simulated dataset; otherwise data is assume to be an actual outbreak
- other: (any other relevant information)
Contributors (by alphabetic order):
- Finlay Campbell
- Simon Frost
- Thibaut Jombart
- Pierre Nouvellet
- Bertrand Sudre
Maintainer: Finlay Campbell (f.campbell15@imperial.ac.uk)