EpiInf

Documentation Source Code

EpiInf is a BEAST 2 package for performing exact inference of stochastic compartmental epidemiological model parameters using particle filtering to compute the prior probability density of a tree. Joint inference of prevalence trajectories is also performed.

Installation

To install EpiInf, follow these steps:

  1. Install the most recent version of BEAST 2.
  2. Open the BEAUti programme.
  3. Select "Manage Packages" from the "File" menu.
  4. EpiInf should be in the list of packages. Select this and then click Install/Upgrade.
  5. Once the successful installation is reported, close the package manager and RESTART BEAUti.

Documentation

The documentation for EpiInf can be found here. The algorithm implemented by EpiInf is described in the following paper:

  • TG Vaughan, GE Leventhal, DA Rasmussen, AJ Drummond, D Welch, T Stadler, Estimating Epidemic Incidence and Prevalence from Genomic Data, Molecular Biology and Evolution, msz106, DOI: 10.1093/molbev/msz106.
Please cite this paper if your use of EpiInf leads to published research.

License

EpiInf is distributed under version 3 of the GNU General Public License.