IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0145180.html
   My bibliography  Save this article

SPOTting Model Parameters Using a Ready-Made Python Package

Author

Listed:
  • Tobias Houska
  • Philipp Kraft
  • Alejandro Chamorro-Chavez
  • Lutz Breuer

Abstract

The choice for specific parameter estimation methods is often more dependent on its availability than its performance. We developed SPOTPY (Statistical Parameter Optimization Tool), an open source python package containing a comprehensive set of methods typically used to calibrate, analyze and optimize parameters for a wide range of ecological models. SPOTPY currently contains eight widely used algorithms, 11 objective functions, and can sample from eight parameter distributions. SPOTPY has a model-independent structure and can be run in parallel from the workstation to large computation clusters using the Message Passing Interface (MPI). We tested SPOTPY in five different case studies to parameterize the Rosenbrock, Griewank and Ackley functions, a one-dimensional physically based soil moisture routine, where we searched for parameters of the van Genuchten-Mualem function and a calibration of a biogeochemistry model with different objective functions. The case studies reveal that the implemented SPOTPY methods can be used for any model with just a minimal amount of code for maximal power of parameter optimization. They further show the benefit of having one package at hand that includes number of well performing parameter search methods, since not every case study can be solved sufficiently with every algorithm or every objective function.

Suggested Citation

  • Tobias Houska & Philipp Kraft & Alejandro Chamorro-Chavez & Lutz Breuer, 2015. "SPOTting Model Parameters Using a Ready-Made Python Package," PLOS ONE, Public Library of Science, vol. 10(12), pages 1-22, December.
    • Handle: RePEc:plo:pone00:0145180
    DOI: 10.1371/journal.pone.0145180
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145180
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0145180&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0145180?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Patil, Anand & Huard, David & Fonnesbeck, Christopher J., 2010. "PyMC: Bayesian Stochastic Modelling in Python," Journal of Statistical Software, Foundation for Open Access Statistics, vol. 35(i04).
    2. Jeffrey M. Perkel, 2015. "Programming: Pick up Python," Nature, Nature, vol. 518(7537), pages 125-126, February.
    3. Ortiz, Carina & Karltun, Erik & Stendahl, Johan & Gärdenäs, Annemieke I. & Ågren, Göran I., 2011. "Modelling soil carbon development in Swedish coniferous forest soils—An uncertainty analysis of parameters and model estimates using the GLUE method," Ecological Modelling, Elsevier, vol. 222(17), pages 3020-3032.
    4. Gong, Zhejun, 2006. "Estimation of mixed Weibull distribution parameters using the SCEM-UA algorithm: Application and comparison with MLE in automotive reliability analysis," Reliability Engineering and System Safety, Elsevier, vol. 91(8), pages 915-922.
    5. Allan P. O. Williams, 2006. "Impact of Strategies," Palgrave Macmillan Books, in: The Rise of Cass Business School, chapter 13, pages 167-181, Palgrave Macmillan.
    Full references (including those not matched with items on IDEAS)

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. Haga, Chihiro & Hotta, Wataru & Inoue, Takahiro & Matsui, Takanori & Aiba, Masahiro & Owari, Toshiaki & Suzuki, Satoshi N. & Shibata, Hideaki & Morimoto, Junko, 2022. "Modeling Tree Recovery in Wind-Disturbed Forests with Dense Understory Species under Climate Change," Ecological Modelling, Elsevier, vol. 472(C).
    2. A. Chamorro & P. Kraft & G. Pauer & J.-F. Exbrayat & L. Breuer, 2017. "Effect of (quasi-)optimum model parameter sets and model characteristics on future discharge projection of two basins from Europe and Asia," Climatic Change, Springer, vol. 142(3), pages 559-573, June.
    3. Myrgiotis, Vasileios & Blei, Emanuel & Clement, Rob & Jones, Stephanie K. & Keane, Ben & Lee, Mark A. & Levy, Peter E. & Rees, Robert M. & Skiba, Ute M. & Smallman, Thomas Luke & Toet, Sylvia & Willia, 2020. "A model-data fusion approach to analyse carbon dynamics in managed grasslands," Agricultural Systems, Elsevier, vol. 184(C).

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sandberg, Susanne & Sui, Sui & Baum, Matthias, 2019. "Effects of prior market experiences and firm-specific resources on developed economy SMEs' export exit from emerging markets: Complementary or compensatory?," Journal of Business Research, Elsevier, vol. 98(C), pages 489-502.
    2. Zhang, Feng & Jiang, Guohua & Cantwell, John A., 2015. "Subsidiary exploration and the innovative performance of large multinational corporations," International Business Review, Elsevier, vol. 24(2), pages 224-234.
    3. Bruzzone, Octavio A. & Logarzo, Guillermo A. & Aguirre, María B. & Virla, Eduardo G., 2018. "Intra-host interspecific larval parasitoid competition solved using modelling and bayesian statistics," Ecological Modelling, Elsevier, vol. 385(C), pages 114-123.
    4. Liu, Xiaoqi & Lee, Seungjae & Bilionis, Ilias & Karava, Panagiota & Joe, Jaewan & Sadeghi, Seyed Amir, 2021. "A user-interactive system for smart thermal environment control in office buildings," Applied Energy, Elsevier, vol. 298(C).
    5. Onyema E. Ofoegbu, 2014. "The Role of Knowledge Management on Knowledge Management Perfomance: A Case Study of Some Nigerian Banks," Journal of Management and Strategy, Journal of Management and Strategy, Sciedu Press, vol. 5(2), pages 53-62, May.
    6. Andrew Gelman & Daniel Lee & Jiqiang Guo, 2015. "Stan," Journal of Educational and Behavioral Statistics, , vol. 40(5), pages 530-543, October.
    7. Bhardwaj, Chandan & Axsen, Jonn & Kern, Florian & McCollum, David, 2020. "Why have multiple climate policies for light-duty vehicles? Policy mix rationales, interactions and research gaps," Transportation Research Part A: Policy and Practice, Elsevier, vol. 135(C), pages 309-326.
    8. Marius Lux & Wolfgang Karl Hardle & Stefan Lessmann, 2020. "Data driven value-at-risk forecasting using a SVR-GARCH-KDE hybrid," Papers 2009.06910, arXiv.org.
    9. Hrabrin BACHEV, 2010. "Framework For Analisis Of Agrarian Contracts," Management Research and Practice, Research Centre in Public Administration and Public Services, Bucharest, Romania, vol. 2(1), pages 39-66, March.
    10. Hyeseon Choi & Nash Jett DG. Reyes & Minsu Jeon & Lee-Hyung Kim, 2021. "Constructed Wetlands in South Korea: Current Status and Performance Assessment," Sustainability, MDPI, vol. 13(18), pages 1-19, September.
    11. Christine Schleupner & P. Michael Link, 2007. "Potential impacts on important bird habitats in Eiderstedt (Schleswig-Holstein) caused by agricultural land use changes," Working Papers FNU-138, Research unit Sustainability and Global Change, Hamburg University, revised Jun 2007.
    12. Monirosadat Hosseini & Seyyed Morteza Hashemi Toroujeni, 2017. "From Conventional to Technology-Assisted Alternative Assessment for Effective and Efficient Measurement: A Review of the Recent Trends in Comparability Studies," English Literature and Language Review, Academic Research Publishing Group, vol. 3(5), pages 35-45, 05-2017.
    13. Minkkinen, Matti, 2019. "The anatomy of plausible futures in policy processes: Comparing the cases of data protection and comprehensive security," Technological Forecasting and Social Change, Elsevier, vol. 143(C), pages 172-180.
    14. Mihaela Păceşilă & Sofia Elena Colesca, 2020. "Insights on Social Responsibility of NGOS," Systemic Practice and Action Research, Springer, vol. 33(3), pages 311-339, June.
    15. Ortiz, Carina A. & Liski, Jari & Gärdenäs, Annemieke I. & Lehtonen, Aleksi & Lundblad, Mattias & Stendahl, Johan & Ågren, Göran I. & Karltun, Erik, 2013. "Soil organic carbon stock changes in Swedish forest soils—A comparison of uncertainties and their sources through a national inventory and two simulation models," Ecological Modelling, Elsevier, vol. 251(C), pages 221-231.
    16. Begoña Garcia Mariñoso & Izabela Jelovac & Pau Olivella, 2011. "External referencing and pharmaceutical price negotiation," Health Economics, John Wiley & Sons, Ltd., vol. 20(6), pages 737-756, June.
    17. Jorge Mota & António Moreira & Alexandra Alves, 2021. "Impact of Export Promotion Programs on Export Performance," Economies, MDPI, vol. 9(3), pages 1-16, September.
    18. Cheatham, Leah P. & Randolph, Karen A. & Boltz, Laura D., 2020. "Youth with disabilities transitioning from foster care: Examining prevalence and predicting positive outcomes," Children and Youth Services Review, Elsevier, vol. 110(C).
    19. Mumtaz Reina Mendonca, 2016. "Relating Big Five Factor Model to the Acceptance and Use of On-line Shopping," International Journal of Marketing Studies, Canadian Center of Science and Education, vol. 8(3), pages 89-98, June.
    20. Agranov Agranov & Ahrash Dianat & Larry Samuelson & Leeat Yariv, 2021. "Paying to Match: Decentralized Markets with Information Frictions," Working Papers 273, Princeton University, Department of Economics, Center for Economic Policy Studies..

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0145180. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.