GLMPrior is a package designed to define flexible generalized linear model (GLM) prior distributions for any parameter in a BEAST2 phylodynamic analysis. Due to some interface limitations in BEAST2, it currently only works with packages that accept parameters of class Function. For example, BDMM-Prime package for (structured) birth-dath-sampling analyses with constant rates or rates changing over time.
Below you will find information on building GLMPrior from source, citation and license. For general information on the package, installation and set-up instructions, visit project web page:
The below information is largely copied from BDMM-Prime repo.
To build GLMPrior from source you'll need the following to be installed:
- OpenJDK version 17 or greater
- A recent version of OpenJFX
- the Apache Ant build system
Once these are installed and in your execution path, issue the following command from the root directory of this repository:
JAVA_FX_HOME=/path/to/openjfx/ antThe package archive will be left in the dist/ subdirectory.
Note that unless you already have a local copy of the latest
BEAST 2 source
in the directory ../beast2 and the latest
BeastFX source
in the directory ../beastfx relative to the GLMPrior root, the build
script will attempt to download them automatically. Also, other BEAST2
packages that GLMPrior depends on will be downloaded. Thus, most builds
will require a network connection.
Please cite the following papers if using GLMPrior:
- Bouckaert, et al. "BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis", PLoS computational biology, 15(4), e1006650 (2019), doi:10.1371/journal.pcbi.1006650.
TODO GLM
Please cite the following papers if using GLMPrior together with BDMM-Prime:
- Vaughan and Stadler, "Bayesian phylodynamic inference of multi-type population trajectories using genomic data", MBE, 42(6):msaf130 (2025), doi:10.1093/molbev/msaf130
- Scire et al., "Robust Phylodynamic Analysis of Genetic Sequencing Data from Structured Populations", Viruses, 14(8):1648 (2022), doi:10.3390/v14081648.
- Kühnert, et al., "Phylodynamics with Migration: A ComputationalFramework to Quantify Population Structure from Genomic Data", MBE, 33(8):2102-2116 (2016), doi:10.1093/molbev/msw064.
GLMPrior is free software. It is distributed under the terms of version 3 of the GNU General Public License. A copy of this license should be found in the file COPYING located in the root directory of this repository. If this file is absent for some reason, it can also be retrieved from https://www.gnu.org/licenses.