IDEAS home Printed from https://ideas.repec.org/a/eee/ecomod/v202y2007i1p38-51.html
   My bibliography  Save this article

Calibration of the NEMURO nutrient–phytoplankton–zooplankton food web model to a coastal ecosystem: Evaluation of an automated calibration approach

Author

Listed:
  • Rose, Kenneth A.
  • Megrey, Bernard A.
  • Werner, Francisco E.
  • Ware, Dan M.

Abstract

A one spatial-box version of the NEMURO oceanic lower trophic food web model was applied to a coastal upwelling environment typified by West Coast Vancouver Island. We used both ad hoc calibration and the automatic calibration program PEST. NEMURO was first calibrated to 1 year of monthly field data using the usual ad hoc approach of trial and error changes to 18 candidate parameters. Four PEST calibrations were then performed. The first three PEST calibrations used model predictions in year 10 from the ad hoc calibration as data in a twin experiment design; the fourth PEST calibration repeated the ad hoc procedure by having PEST calibrate NEMURO to the field data. When provided with ad hoc calibration model predictions as data, PEST accurately recovered the known 18 parameter values, even when small and large phytoplankton were lumped into total phytoplankton. When 57 parameters were allowed to vary PEST-estimated reasonable values for all 57 parameters, but they differed from the ad hoc calibrated values. However, when applied to the field data, PEST-estimated parameter values that differed greatly from the ad hoc values. The PEST calibration fitted some of the field data better than the ad hoc calibration but at the cost of unequal small and large phytoplankton concentrations. Thus, with proper and careful implementation, PEST offers a viable approach for objective calibration of NEMURO to site-specific monitoring data. We recommend that automatic calibration methods, such as PEST, be used for application of the NEMURO model to new locations. When the field data allow for specification of time series for each phytoplankton and zooplankton state variable, PEST will provide an objective, defensible, and repeatable way to calibrate the many parameters of the NEMURO model. If the available data are insufficient for specification of each state variable, then ad hoc calibration will likely be needed to allow for inclusion of qualitative decisions about model fit. Use of PEST in this situation will provide better understanding of the data-model mis-matches and will provide an alternative calibration to the necessary, but subjective, ad hoc calibration. Comparison of the ad hoc and PEST calibrations (even if unsuccessful) will help in the interpretation of the ad hoc calibration. Robust parameter estimation by any method depends on the quality and consistency of the calibration dataset.

Suggested Citation

  • Rose, Kenneth A. & Megrey, Bernard A. & Werner, Francisco E. & Ware, Dan M., 2007. "Calibration of the NEMURO nutrient–phytoplankton–zooplankton food web model to a coastal ecosystem: Evaluation of an automated calibration approach," Ecological Modelling, Elsevier, vol. 202(1), pages 38-51.
    • Handle: RePEc:eee:ecomod:v:202:y:2007:i:1:p:38-51
    DOI: 10.1016/j.ecolmodel.2006.08.016
    as

    Download full text from publisher

    File URL: http://www.sciencedirect.com/science/article/pii/S0304380006004558
    Download Restriction: Full text for ScienceDirect subscribers only
    File URL: https://libkey.io/10.1016/j.ecolmodel.2006.08.016?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
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    References listed on IDEAS

    as
    1. Kishi, Michio J. & Kashiwai, Makoto & Ware, Daniel M. & Megrey, Bernard A. & Eslinger, David L. & Werner, Francisco E. & Noguchi-Aita, Maki & Azumaya, Tomonori & Fujii, Masahiko & Hashimoto, Shinji & , 2007. "NEMURO—a lower trophic level model for the North Pacific marine ecosystem," Ecological Modelling, Elsevier, vol. 202(1), pages 12-25.
    2. Yoshie, Naoki & Yamanaka, Yasuhiro & Rose, Kenneth A. & Eslinger, David L. & Ware, Daniel M. & Kishi, Michio J., 2007. "Parameter sensitivity study of the NEMURO lower trophic level marine ecosystem model," Ecological Modelling, Elsevier, vol. 202(1), pages 26-37.
    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. Megrey, Bernard A. & Rose, Kenneth A. & Ito, Shin-ichi & Hay, Douglas E. & Werner, Francisco E. & Yamanaka, Yasuhiro & Aita, Maki Noguchi, 2007. "North Pacific basin-scale differences in lower and higher trophic level marine ecosystem responses to climate impacts using a nutrient-phytoplankton–zooplankton model coupled to a fish bioenergetics m," Ecological Modelling, Elsevier, vol. 202(1), pages 196-210.
    2. Ross, Karen A. & Bedward, Michael & Ellis, Murray V. & Deane, Andrew & Simpson, Christopher C. & Bradstock, Ross A., 2008. "Modelling the dynamics of white cypress pine Callitris glaucophylla woodlands in inland south-eastern Australia," Ecological Modelling, Elsevier, vol. 211(1), pages 11-24.
    3. Malone, R.W. & Nolan, B.T. & Ma, L. & Kanwar, R.S. & Pederson, C. & Heilman, P., 2014. "Effects of tillage and application rate on atrazine transport to subsurface drainage: Evaluation of RZWQM using a six-year field study," Agricultural Water Management, Elsevier, vol. 132(C), pages 10-22.
    4. Kishi, Michio J. & Kashiwai, Makoto & Ware, Daniel M. & Megrey, Bernard A. & Eslinger, David L. & Werner, Francisco E. & Noguchi-Aita, Maki & Azumaya, Tomonori & Fujii, Masahiko & Hashimoto, Shinji & , 2007. "NEMURO—a lower trophic level model for the North Pacific marine ecosystem," Ecological Modelling, Elsevier, vol. 202(1), pages 12-25.
    5. Werner, Francisco E. & Ito, Shin-Ichi & Megrey, Bernard A. & Kishi, Michio J., 2007. "Synthesis of the NEMURO model studies and future directions of marine ecosystem modeling," Ecological Modelling, Elsevier, vol. 202(1), pages 211-223.
    6. Rose, Kenneth A. & Werner, Francisco E. & Megrey, Bernard A. & Aita, Maki Noguchi & Yamanaka, Yasuhiro & Hay, Douglas E. & Schweigert, Jake F. & Foster, Matthew Birch, 2007. "Simulated herring growth responses in the Northeastern Pacific to historic temperature and zooplankton conditions generated by the 3-dimensional NEMURO nutrient–phytoplankton–zooplankton model," Ecological Modelling, Elsevier, vol. 202(1), pages 184-195.
    7. Rose, Kenneth A. & Sable, Shaye & DeAngelis, Donald L. & Yurek, Simeon & Trexler, Joel C. & Graf, William & Reed, Denise J., 2015. "Proposed best modeling practices for assessing the effects of ecosystem restoration on fish," Ecological Modelling, Elsevier, vol. 300(C), pages 12-29.
    8. Megrey, Bernard A. & Rose, Kenneth A. & Klumb, Robert A. & Hay, Douglas E. & Werner, Francisco E. & Eslinger, David L. & Smith, S. Lan, 2007. "A bioenergetics-based population dynamics model of Pacific herring (Clupea harengus pallasi) coupled to a lower trophic level nutrient–phytoplankton–zooplankton model: Description, calibration, and se," Ecological Modelling, Elsevier, vol. 202(1), pages 144-164.
    9. Bracis, Chloe & Lehuta, Sigrid & Savina-Rolland, Marie & Travers-Trolet, Morgane & Girardin, Raphaël, 2020. "Improving confidence in complex ecosystem models: The sensitivity analysis of an Atlantis ecosystem model," Ecological Modelling, Elsevier, vol. 431(C).
    10. González-Sanchis, Marí a & Del Campo, Antonio D. & Molina, Antonio J. & Fernandes, Tarcí sio J.G., 2015. "Modeling adaptive forest management of a semi-arid Mediterranean Aleppo pine plantation," Ecological Modelling, Elsevier, vol. 308(C), pages 34-44.

    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. Fujii, Masahiko & Yamanaka, Yasuhiro & Nojiri, Yukihiro & Kishi, Michio J. & Chai, Fei, 2007. "Comparison of seasonal characteristics in biogeochemistry among the subarctic North Pacific stations described with a NEMURO-based marine ecosystem model," Ecological Modelling, Elsevier, vol. 202(1), pages 52-67.
    2. Kearney, Kelly A. & Stock, Charles & Aydin, Kerim & Sarmiento, Jorge L., 2012. "Coupling planktonic ecosystem and fisheries food web models for a pelagic ecosystem: Description and validation for the subarctic Pacific," Ecological Modelling, Elsevier, vol. 237, pages 43-62.
    3. Komatsu, Kosei & Matsukawa, Yasuo & Nakata, Kaoru & Ichikawa, Tadafumi & Sasaki, Katsuyuki, 2007. "Effects of advective processes on planktonic distributions in the Kuroshio region using a 3-D lower trophic model and a data assimilative OGCM," Ecological Modelling, Elsevier, vol. 202(1), pages 105-119.
    4. Miho Ishizu & Yasumasa Miyazawa & Tomohiko Tsunoda & Xinyu Guo, 2019. "Development of a Biogeochemical and Carbon Model Related to Ocean Acidification Indices with an Operational Ocean Model Product in the North Western Pacific," Sustainability, MDPI, vol. 11(9), pages 1-28, May.
    5. Megrey, Bernard A. & Rose, Kenneth A. & Klumb, Robert A. & Hay, Douglas E. & Werner, Francisco E. & Eslinger, David L. & Smith, S. Lan, 2007. "A bioenergetics-based population dynamics model of Pacific herring (Clupea harengus pallasi) coupled to a lower trophic level nutrient–phytoplankton–zooplankton model: Description, calibration, and se," Ecological Modelling, Elsevier, vol. 202(1), pages 144-164.
    6. Werner, Francisco E. & Ito, Shin-Ichi & Megrey, Bernard A. & Kishi, Michio J., 2007. "Synthesis of the NEMURO model studies and future directions of marine ecosystem modeling," Ecological Modelling, Elsevier, vol. 202(1), pages 211-223.
    7. Mukai, Daiki & Kishi, Michio J. & Ito, Shin-ichi & Kurita, Yutaka, 2007. "The importance of spawning season on the growth of Pacific saury: A model-based study using NEMURO.FISH," Ecological Modelling, Elsevier, vol. 202(1), pages 165-173.
    8. Terui, Takeshi & Kishi, Michio J., 2008. "Population dynamics model of Copepoda (Neocalanus cristatus) in the northwestern subarctic Pacific," Ecological Modelling, Elsevier, vol. 215(1), pages 77-88.
    9. Brewin, Robert J.W. & Sathyendranath, Shubha & Hirata, Takafumi & Lavender, Samantha J. & Barciela, Rosa M. & Hardman-Mountford, Nick J., 2010. "A three-component model of phytoplankton size class for the Atlantic Ocean," Ecological Modelling, Elsevier, vol. 221(11), pages 1472-1483.
    10. Ruzicka, James J. & Wainwright, Thomas C. & Peterson, William T., 2011. "A simple plankton model for the Oregon upwelling ecosystem: Sensitivity and validation against time-series ocean data," Ecological Modelling, Elsevier, vol. 222(6), pages 1222-1235.
    11. Xing, Lei & Zhang, Chongliang & Chen, Yong & Shin, Yunne-Jai & Verley, Philippe & Yu, Haiqing & Ren, Yiping, 2017. "An individual-based model for simulating the ecosystem dynamics of Jiaozhou Bay, China," Ecological Modelling, Elsevier, vol. 360(C), pages 120-131.
    12. Yoshie, Naoki & Yamanaka, Yasuhiro & Rose, Kenneth A. & Eslinger, David L. & Ware, Daniel M. & Kishi, Michio J., 2007. "Parameter sensitivity study of the NEMURO lower trophic level marine ecosystem model," Ecological Modelling, Elsevier, vol. 202(1), pages 26-37.
    13. Salacinska, K. & El Serafy, G.Y. & Los, F.J. & Blauw, A., 2010. "Sensitivity analysis of the two dimensional application of the Generic Ecological Model (GEM) to algal bloom prediction in the North Sea," Ecological Modelling, Elsevier, vol. 221(2), pages 178-190.
    14. Fiechter, Jerome, 2012. "Assessing marine ecosystem model properties from ensemble calculations," Ecological Modelling, Elsevier, vol. 242(C), pages 164-179.
    15. Masuda, Yoshio & Yamanaka, Yasuhiro & Hirata, Takafumi & Nakano, Hideyuki & Kohyama, Takashi S., 2020. "Inhibition of competitive exclusion due to phytoplankton dispersion: a contribution for solving Hutchinson's paradox," Ecological Modelling, Elsevier, vol. 430(C).
    16. Kishi, Michio J. & Kashiwai, Makoto & Ware, Daniel M. & Megrey, Bernard A. & Eslinger, David L. & Werner, Francisco E. & Noguchi-Aita, Maki & Azumaya, Tomonori & Fujii, Masahiko & Hashimoto, Shinji & , 2007. "NEMURO—a lower trophic level model for the North Pacific marine ecosystem," Ecological Modelling, Elsevier, vol. 202(1), pages 12-25.
    17. Zuenko, Yury I., 2007. "Application of a lower trophic level model to a coastal sea ecosystem," Ecological Modelling, Elsevier, vol. 202(1), pages 132-143.
    18. Batchelder, Harold P. & Kashiwai, Makoto, 2007. "Ecosystem modeling with NEMURO within the PICES Climate Change and Carrying Capacity program," Ecological Modelling, Elsevier, vol. 202(1), pages 7-11.
    19. Morales, Mark M. & Fiechter, Jerome & Field, John C. & Kashef, Neosha S & Hazen, Elliott L. & Carr, Mark H., 2024. "Development and application of a bioenergetics growth model for multiple early life stages of an ecologically important marine fish," Ecological Modelling, Elsevier, vol. 488(C).
    20. Kakehi, Shigeho & Abo, Jun-ichi & Miyamoto, Hiroomi & Fuji, Taiki & Watanabe, Kazuyoshi & Yamashita, Hideyuki & Suyama, Satoshi, 2020. "Forecasting Pacific saury (Cololabis saira) fishing grounds off Japan using a migration model driven by an ocean circulation model," Ecological Modelling, Elsevier, vol. 431(C).

    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:eee:ecomod:v:202:y:2007:i:1:p:38-51. 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: Catherine Liu (email available below). General contact details of provider: http://www.journals.elsevier.com/ecological-modelling .

    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.