Welcome to the epiflows package!

epiflows is a package for predicting and visualising spread of infectious diseases based on flows between geographical locations, e.g., countries. epiflows provides functions for calculating spread estimates, handling flow data, and visualization.

Installing the package

To install the current stable, CRAN version of the package, type:

install.packages("epiflows")

To benefit from the latest features and bug fixes, install the development, github version of the package using:

devtools::install_github("reconhub/epiflows")

Note that this requires the package devtools installed.

What does it do?

The main features of the package include:

• epiflows: an S3 class for storing flow data, as well as country metadata
• make_epiflows: a constructor for epiflows
• add_coordinates: add latitude/longitude to the linelist in an epiflows object using ggmap::geocode()
• fn_number_cases_spread: calculate estimates (point estimate and 95% CI) for disease spread from flow data
• get_flow_data: return flow data to and/or from specified location
• get_location_data: return metadata for specified location(s)
• x[i]: subset an epiflows object to location(s) i
• plot: plot flows from an epiflows object on a leaflet world map
• print: print a summary for an epiflows object

Resources

Vignettes

An overview and examples of epiflows are provided in the vignettes:

...

Getting help online

Bug reports and feature requests should be posted on github using the issue system. All other questions should be posted on the RECON forum:
http://www.repidemicsconsortium.org/forum/

Contributions are welcome via pull requests.

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.