This is EpiFusionUtilities, an R package with useful tools for using the EpiFusion joint phylodynamic and epidemiological inference software. The EpiFusionUtilities package can be used to employ the EpiFusion Analysis Framework, a start to finish workflow from data preparation to result parsing, analysis and plotting. This repository contains the package source code, and information on usage. The science behind the EpiFusion software can be found in this publication.
To get started with EpiFusionUtilities you can install it using devtools and the install_github command. In R, that looks like this:
devtools::install_github("https://github.com/ciarajudge/EpiFusionUtilities")
We recommend first consulting the full function reference on the package website, before following the tutorials on the EpiFusion wiki where there is lots of useful instructions on how to use EpiFusionUtilities to interact with the EpiFusion software.
This package is actively maintained and last saw significant updates in January 2025. We encourage any user to point out problems or suggest ideas for improvement by raising an issue, and we will address these (particularly bugs) as quickly as possible. Pull requests are also welcome, but please allow grace in the time we take to review. For an insight into our planned improvements, check the project or issues tab.
We are sharing EpiFusionUtilities as a free software under the GNU General Public License (v3).
Thank you to all the individuals and organisations that have had a role in EpiFusionUtilities' creation and maintenance. These include the London School of Hygiene and Tropical Medicine, and the Royal Veterinary College. Key contributors include Ciara Judge, Oliver Brady, and Sarah Hill.