Fish Bioenergetics 4.0: An R-Based Modeling Application

Abstract

Bioenergetics modeling is a widely used tool in fisheries management and research. Although popular, currently available software (i.e., Fish Bioenergetics 3.0) has not been updated in over 20 years and is incompatible with newer operating systems (i.e., 64-bit). Moreover, since the release of Fish Bioenergetics 3.0 in 1997, the number of published bioenergetics models has increased appreciably from 56 to 105 models representing 73 species. In this article, we provide an overview of Fish Bioenergetics 4.0 (FB4), a newly developed modeling application that consists of a graphical user interface (Shiny by RStudio) combined with a modeling package used in the R computing environment. While including the same capabilities as previous versions, Fish Bioenergetics 4.0 allows for timely updates and bug fixes and can be continuously improved based on feedback from users. In addition, users can add new or modified parameter sets for additional species and formulate and incorporate modifications such as habitat-dependent functions (e.g., dissolved oxygen, salinity) that are not part of the default package. We hope that advances in the new modeling platform will attract a broad range of users while facilitating continued application of bioenergetics modeling to a wide spectrum of questions in fish biology, ecology, and management.

ACKNOWLEDGMENTS

We acknowledge the contributions of T. B. Johnson (especially for species parameter updates), D. E. Schindler, J. F. Kitchell, K. Hartman, M. Trudel, and D. Beauchamp in providing feedback at various stages of this project. We also thank T. Neeson and M. Colvin for providing useful R scripts that were used in the development of FB4. Last, we recognize the effort displayed by A. K. Carlson, D. J. Dembkowski, L. B. Heironimus, B. J. Smith, D. A. Schuman, J. D. Grote, C. K. Kaiser, M. D. Wagner, S. C. Sindelar, and J. Kientz in updating and verifying the bioenergetics parameters file. The FB4 logo was designed and created by Erinn L. Ipsen at Field Note Studios.

FUNDING

The South Dakota Cooperative Fish and Wildlife Research Unit is jointly sponsored by the U.S. Geological Survey, South Dakota Department of Game, Fish and Parks, South Dakota State University, the Wildlife Management Institute, and the U.S. Fish and Wildlife Service. Any use of trade names is for descriptive purposes only and does not imply endorsement by the U.S. Government.