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")

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 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:

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):

• Finlay Campbell
• Simon Frost
• Thibaut Jombart
• Pierre Nouvellet
• Bertrand Sudre

Maintainer: Finlay Campbell (f.campbell15@imperial.ac.uk)