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phymcmc

Wrapper of github.com/dfm/emcee providing convenient functions and scripts

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phymcmc is a wrap of github/dfm/emcee. It provides a model class a parameter class to describe one's model and associated parameters. Having defined a model and a parameter instance, phymcmc functions, scripts and modules can be used to, e.g., fit the model to data to obtain so-called best-fit parameters; or obtain posterior parameter likelihood distributions (PostPLDs) based on the MCMC process implemented in emcee, save the results in a phymcmc-defined hdf5 file format. The phymcmc hdf5 files can be parsed/analysed by phymcmc-provided scripts to, e.g., draw diagnostic plots to evaluate whether the runs have converged, draw histograms of individual parameter's PostPLDs, draw pair-wise PostPLDs to identify correlations using github/dfm/corner.py, or obtain p-values when comparing parameter PostPLDs for 2 different sets of data (2 hdf5 files). It has been used in a number of publications by the phymbie research group. See the examples directory to get started.

Attribution

If you make use of this code, make sure to cite it.

The BibTeX entry is:

@MANUAL{phymcmc,
    AUTHOR = "Catherine A. A. Beauchemin",
    TITLE = "{phymcmc}: {A} convenient wrapper for emcee",
    YEAR = "2022",
    PUBLISHER = "{GitHub}",
    JOURNAL = "{GitHub} repository",
    HOWPUBLISHED = "\url{https://github.com/cbeauc/phymcmc}"
}

License

Copyright 2014-2022 Catherine Beauchemin and contributors.

phymcmc is free software made available under the GNU General Public License Version 3. For details see the LICENSE file.

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Wrapper for github.com/dfm/emcee offering a number of convenient parsing, analysis, and plotting scripts and functions for data/outputs generaged by emcee.

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