Note

This tutorial was generated from an IPython notebook that can be downloaded here.

Citing exoplanet & its dependencies

theano version: 1.0.4
pymc3 version: 3.7
exoplanet version: 0.2.1.dev0

The exoplanet package is mostly just glue that connects many other ideas and software. In a situation like this, it can be easy to forget about the important infrastructure upon which our science is built. In order to make sure that you can easily give credit where credit is due, we have tried to make it as painless as possible to work out which citations are expected for a model fit using exoplanet by including a exoplanet.citations.get_citations_for_model() function that introspects the current PyMC3 model and constructs a list of citations for the functions used in that model.

For example, you might compute a quadratically limb darkened light curve using starry (via the exoplanet.light_curve.StarryLightCurve class):

import pymc3 as pm
import exoplanet as xo

with pm.Model() as model:
    u = xo.distributions.QuadLimbDark("u")
    orbit = xo.orbits.KeplerianOrbit(period=10.0)
    light_curve = xo.StarryLightCurve(u)
    transit = light_curve.get_light_curve(r=0.1, orbit=orbit, t=[0.0, 0.1])

    txt, bib = xo.citations.get_citations_for_model()

The exoplanet.citations.get_citations_for_model() function would generate an acknowledgement that cites:

  • PyMC3: for the inference engine and modeling framework,
  • Theano: for the numerical infrastructure,
  • AstroPy: for units and constants,
  • Kipping (2013): for the reparameterization of the limb darkening parameters for a quadratic law, and
  • Luger, et al. (2018): for the light curve calculation.

The first output from exoplanet.citations.get_citations_for_model() gives the acknowledgement text:

print(txt)
This research made use of textsf{exoplanet} citep{exoplanet} and its
dependencies citep{exoplanet:astropy13, exoplanet:astropy18,
exoplanet:exoplanet, exoplanet:kipping13, exoplanet:luger18, exoplanet:pymc3,
exoplanet:theano}.

And the second output is a string with BibTeX entries for each of the citations in the acknowledgement text:

print(bib)
@misc{exoplanet:exoplanet,
  author = {Daniel Foreman-Mackey and Ian Czekala and Eric Agol and
            Rodrigo Luger and Geert Barentsen and Tom Barclay},
   title = {dfm/exoplanet: exoplanet v0.2.0},
   month = aug,
    year = 2019,
     doi = {10.5281/zenodo.3359880},
     url = {https://doi.org/10.5281/zenodo.3359880}
}


@article{exoplanet:pymc3,
    title={Probabilistic programming in Python using PyMC3},
   author={Salvatier, John and Wiecki, Thomas V and Fonnesbeck, Christopher},
  journal={PeerJ Computer Science},
   volume={2},
    pages={e55},
     year={2016},
publisher={PeerJ Inc.}
}


@article{exoplanet:theano,
    title="{Theano: A {Python} framework for fast computation of mathematical
            expressions}",
   author={{Theano Development Team}},
  journal={arXiv e-prints},
   volume={abs/1605.02688},
     year=2016,
    month=may,
      url={http://arxiv.org/abs/1605.02688}
}


@ARTICLE{exoplanet:kipping13,
   author = {{Kipping}, D.~M.},
    title = "{Efficient, uninformative sampling of limb darkening coefficients
              for two-parameter laws}",
  journal = {mnras},
     year = 2013,
    month = nov,
   volume = 435,
    pages = {2152-2160},
      doi = {10.1093/mnras/stt1435},
   adsurl = {http://adsabs.harvard.edu/abs/2013MNRAS.435.2152K},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@article{exoplanet:astropy13,
   author = {{Astropy Collaboration} and {Robitaille}, T.~P. and {Tollerud},
             E.~J. and {Greenfield}, P. and {Droettboom}, M. and {Bray}, E. and
             {Aldcroft}, T. and {Davis}, M. and {Ginsburg}, A. and
             {Price-Whelan}, A.~M. and {Kerzendorf}, W.~E. and {Conley}, A. and
             {Crighton}, N. and {Barbary}, K. and {Muna}, D. and {Ferguson}, H.
             and {Grollier}, F. and {Parikh}, M.~M. and {Nair}, P.~H. and
             {Unther}, H.~M. and {Deil}, C. and {Woillez}, J. and {Conseil}, S.
             and {Kramer}, R. and {Turner}, J.~E.~H. and {Singer}, L. and
             {Fox}, R. and {Weaver}, B.~A. and {Zabalza}, V. and {Edwards},
             Z.~I. and {Azalee Bostroem}, K. and {Burke}, D.~J. and {Casey},
             A.~R. and {Crawford}, S.~M. and {Dencheva}, N. and {Ely}, J. and
             {Jenness}, T. and {Labrie}, K. and {Lim}, P.~L. and
             {Pierfederici}, F. and {Pontzen}, A. and {Ptak}, A. and {Refsdal},
             B. and {Servillat}, M. and {Streicher}, O.},
    title = "{Astropy: A community Python package for astronomy}",
  journal = {aap},
     year = 2013,
    month = oct,
   volume = 558,
    pages = {A33},
      doi = {10.1051/0004-6361/201322068},
   adsurl = {http://adsabs.harvard.edu/abs/2013A%26A...558A..33A},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}

@article{exoplanet:astropy18,
   author = {{Astropy Collaboration} and {Price-Whelan}, A.~M. and
             {Sip{H o}cz}, B.~M. and {G{"u}nther}, H.~M. and {Lim}, P.~L. and
             {Crawford}, S.~M. and {Conseil}, S. and {Shupe}, D.~L. and
             {Craig}, M.~W. and {Dencheva}, N. and {Ginsburg}, A. and
             {VanderPlas}, J.~T. and {Bradley}, L.~D. and
             {P{'e}rez-Su{'a}rez}, D. and {de Val-Borro}, M.
             and {Aldcroft}, T.~L. and {Cruz}, K.~L. and {Robitaille}, T.~P.
             and {Tollerud}, E.~J. and {Ardelean}, C. and {Babej}, T. and
             {Bach}, Y.~P. and {Bachetti}, M. and {Bakanov}, A.~V. and
             {Bamford}, S.~P. and {Barentsen}, G. and {Barmby}, P. and
             {Baumbach}, A. and {Berry}, K.~L.  and {Biscani}, F. and
             {Boquien}, M. and {Bostroem}, K.~A. and {Bouma}, L.~G. and
             {Brammer}, G.~B. and {Bray}, E.~M. and {Breytenbach}, H. and
             {Buddelmeijer}, H. and {Burke}, D.~J. and {Calderone}, G. and
             {Cano Rodr{'{i}}guez}, J.~L. and {Cara}, M. and {Cardoso},
             J.~V.~M. and {Cheedella}, S. and {Copin}, Y. and {Corrales}, L.
             and {Crichton}, D. and {D'Avella}, D. and {Deil}, C. and
             {Depagne}, {'E}. and {Dietrich}, J.~P. and {Donath}, A. and
             {Droettboom}, M. and {Earl}, N. and {Erben}, T. and {Fabbro}, S.
             and {Ferreira}, L.~A. and {Finethy}, T. and {Fox}, R.~T. and
             {Garrison}, L.~H. and {Gibbons}, S.~L.~J. and {Goldstein}, D.~A.
             and {Gommers}, R. and {Greco}, J.~P. and {Greenfield}, P. and
             {Groener}, A.~M. and {Grollier}, F. and {Hagen}, A. and {Hirst},
             P. and {Homeier}, D. and {Horton}, A.~J. and {Hosseinzadeh}, G.
             and {Hu}, L. and {Hunkeler}, J.~S. and {Ivezi{'c}}, {v Z}. and
             {Jain}, A. and {Jenness}, T. and {Kanarek}, G. and {Kendrew}, S.
             and {Kern}, N.~S. and {Kerzendorf}, W.~E. and {Khvalko}, A. and
             {King}, J. and {Kirkby}, D. and {Kulkarni}, A.~M. and {Kumar}, A.
             and {Lee}, A.  and {Lenz}, D.  and {Littlefair}, S.~P. and {Ma},
             Z. and {Macleod}, D.~M. and {Mastropietro}, M. and {McCully}, C.
             and {Montagnac}, S. and {Morris}, B.~M. and {Mueller}, M. and
             {Mumford}, S.~J. and {Muna}, D. and {Murphy}, N.~A. and {Nelson},
             S. and {Nguyen}, G.~H. and {Ninan}, J.~P. and {N{"o}the}, M. and
             {Ogaz}, S. and {Oh}, S. and {Parejko}, J.~K.  and {Parley}, N. and
             {Pascual}, S. and {Patil}, R. and {Patil}, A.~A.  and {Plunkett},
             A.~L. and {Prochaska}, J.~X. and {Rastogi}, T. and {Reddy Janga},
             V. and {Sabater}, J.  and {Sakurikar}, P. and {Seifert}, M. and
             {Sherbert}, L.~E. and {Sherwood-Taylor}, H. and {Shih}, A.~Y. and
             {Sick}, J. and {Silbiger}, M.~T. and {Singanamalla}, S. and
             {Singer}, L.~P. and {Sladen}, P.~H. and {Sooley}, K.~A. and
             {Sornarajah}, S. and {Streicher}, O. and {Teuben}, P. and
             {Thomas}, S.~W. and {Tremblay}, G.~R. and {Turner}, J.~E.~H. and
             {Terr{'o}n}, V.  and {van Kerkwijk}, M.~H. and {de la Vega}, A.
             and {Watkins}, L.~L. and {Weaver}, B.~A. and {Whitmore}, J.~B. and
             {Woillez}, J.  and {Zabalza}, V. and {Astropy Contributors}},
    title = "{The Astropy Project: Building an Open-science Project and Status
              of the v2.0 Core Package}",
  journal = {aj},
     year = 2018,
    month = sep,
   volume = 156,
    pages = {123},
      doi = {10.3847/1538-3881/aabc4f},
   adsurl = {http://adsabs.harvard.edu/abs/2018AJ....156..123A},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}


@article{exoplanet:luger18,
   author = {{Luger}, R. and {Agol}, E. and {Foreman-Mackey}, D. and {Fleming},
             D.~P. and {Lustig-Yaeger}, J. and {Deitrick}, R.},
    title = "{starry: Analytic Occultation Light Curves}",
  journal = {aj},
     year = 2019,
    month = feb,
   volume = 157,
    pages = {64},
      doi = {10.3847/1538-3881/aae8e5},
   adsurl = {http://adsabs.harvard.edu/abs/2019AJ....157...64L},
  adsnote = {Provided by the SAO/NASA Astrophysics Data System}
}