iphysresearch/eryn

An omni-sampler for Bayesian MCMC

Eryn: a multi-purpose MCMC sampler

Eryn is an advanced MCMC sampler. It has the capability to run with parallel tempering, multiple model types, and unknown counts within each model type using Reversible Jump MCMC techniques. Eryn is heavily based on emcee. The emcee base structure with the Ensemble Sampler, State objects, proposal setup, and storage backends is carried over into Eryn with small changes to account for the increased complexity. In a simple sense, Eryn is an advanced (and slightly more complicated) version of emcee.

If you use Eryn in your publication, please cite the paper arXiv:2303.02164, its zenodo, and emcee. The documentation for Eryn can be found here: mikekatz04.github.io/Eryn. You will find the code on Github: github.com/mikekatz04/Eryn.

Getting Started

Below is a quick set of instructions to get you started with eryn.

pip install eryn

To import eryn:

from eryn.ensemble import EnsembleSampler

See examples notebook for more info. You can also navigate the Documentation pages.

Prerequisites

Eryn has only a few python-based dependencies: tqdm, corner for plotting, numpy, matplotlib.

Installing

If you are not planning to develop the code, you can just install the latest version with the pip installation technique given above. Otherwise, you can just clone the repo and run pip install . inside of the Eryn directory. To run tests on Eryn during development, you can run the following in the main Eryn directory:

python -m unittest discover

Running the Tests

In the main directory of the package run in the terminal:

python -m unittest discover

Contributing

Please read CONTRIBUTING.md for details on our code of conduct, and the process for submitting pull requests to us.

Versioning

We use SemVer for versioning. For the versions available, see the tags on this repository.

Current Version: 1.1.7

Citation

When using this package, please cite at minimum the following sources:

@article{Karnesis:2023ras,
    author = "Karnesis, Nikolaos and Katz, Michael L. and Korsakova, Natalia and Gair, Jonathan R. and Stergioulas, Nikolaos",
    title = "{Eryn : A multi-purpose sampler for Bayesian inference}",
    eprint = "2303.02164",
    archivePrefix = "arXiv",
    primaryClass = "astro-ph.IM",
    month = "3",
    year = "2023"
}

@software{michael_katz_2023_7705496,
  author       = {Michael Katz and
                  Nikolaos Karnesis and
                  Natalia Korsakova},
  title        = {mikekatz04/Eryn: first full release},
  month        = mar,
  year         = 2023,
  publisher    = {Zenodo},
  version      = {v1.0.0},
  doi          = {10.5281/zenodo.7705496},
  url          = {https://doi.org/10.5281/zenodo.7705496}
}

@ARTICLE{2013PASP..125..306F,
       author = {{Foreman-Mackey}, Daniel and {Hogg}, David W. and {Lang}, Dustin and {Goodman}, Jonathan},
        title = "{emcee: The MCMC Hammer}",
      journal = {\pasp},
     keywords = {Astrophysics - Instrumentation and Methods for Astrophysics, Physics - Computational Physics, Statistics - Computation},
         year = 2013,
        month = mar,
       volume = {125},
       number = {925},
        pages = {306},
          doi = {10.1086/670067},
archivePrefix = {arXiv},
       eprint = {1202.3665},
 primaryClass = {astro-ph.IM},
       adsurl = {https://ui.adsabs.harvard.edu/abs/2013PASP..125..306F},
      adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

Depending on which proposals are used, you may be required to cite more sources. Please make sure you do this properly.

Authors

• Michael Katz
• Nikos Karnesis
• Natalia Korsakova
• Jonathan Gair

Contibutors

• Maybe you!

License

This project is licensed under the GNU License - see the LICENSE.md file for details.

Acknowledgments

• We wish to thank S. Babak, M. Le Jeune, S. Marsat, T. Littenberg, and N. Cornish for their useful comments and very fruitful discussions.
• N Stergioulas and N Karnesis acknowledge support from the Gr-PRODEX 2019 funding program (PEA 4000132310).