Package Rpath is an R/Rcpp implementation of the Ecopath (mass-balance) and Ecosim (dynamic simulation) methods for the modeling of food webs. The Rpath package includes sensitivity analysis tools, bioenergetics forcing, and the ability to develop adaptive dynamic simulations with annual adjustment/feedback for use in management strategy evaluations and similar analyses.
Installation
To install the package and build all of the vignettes locally
remotes::install_github("noaa-edab/Rpath",build_vignettes=TRUE)`If you experience issues installing the package using remotes or don’t need the vignettes locally then please use this alternative
pak::pak("noaa-edab/Rpath")More details
For more background, please see:
For Rpath description and methods:
Lucey, S. M., Gaichas, S. K., & Aydin, K. Y. (2020). Conducting reproducible ecosystem modeling using the open source mass balance model Rpath. Ecological Modelling 427(2020), 109057. https://doi.org/10.1016/j.ecolmodel.2020.109057.
For use of Rpath for management strategy evaluations:
Lucey, S. M., Aydin, K. Y., Gaichas, S. K., Cadrin, S. X., Fay, G., Fogarty, M. J., & Punt, A. (2021). Evaluating fishery management strategies using an ecosystem model as an operating model. Fisheries Research 234(2021), 105780. https://doi.org/10.1016/j.fishres.2020.105780.
For incorporation of bioenergetics into Rpath simulations:
Heinichen, M., McManus, M. C., Lucey, S. M., Aydin, K. Y., Humphries, A., Innes-Gold, A., & Collie, J. (2022). Incorporating temperature-dependent fish bioenergetics into a Narragansett Bay food web model. Ecological Modelling 466(2022), 109911. https://doi.org/10.1016/j.ecolmodel.2022.109911.
For use of Rpath sensitivity tools:
Whitehouse, G.A., & Aydin, K.Y. (2020). Assessing the sensitivity of three Alaska marine food webs to perturbations: an example of Ecosim simulations using Rpath. Ecological Modelling 429(2020), 109074. https://doi.org/10.1016/j.ecolmodel.2020.109074.
For original development of Ecopath and Ecosim:
Polovina, J. J. (1984). Model of a coral reef ecosystem. Coral Reefs 3(1), 1–11. https://doi.org/10.1007/BF00306135.
Christensen, V., & Walters, C. J. (2004). Ecopath with Ecosim: Methods, capabilities and limitations. Ecological Modelling 172(2), 109–139. https://doi.org/10.1016/j.ecolmodel.2003.09.003.
Walters, C., Pauly, D., Christensen, V., & Kitchell, J. F. (2000). Representing Density Dependent Consequences of Life History Strategies in Aquatic Ecosystems: EcoSim II. Ecosystems 3(1), 70–83. https://doi.org/10.1007/s100210000011.
Disclaimer
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