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Rpath: an open source food web model

Source: vignettes/Rpath.Rmd
Rpath.Rmd

Rpath is an implementation of the ecosystem model Ecopath with Ecosim (EwE; Polovina (1984); Christensen and Pauly (1992); Walters et al. (1997); Christensen and Walters (2004); Walters and Martell (2004); Walters et al. (2008)).

Articles for model setup, running Rpath and running Rsim describe some of the basic functionality of the package using a fictional ecosystem, R Ecosystem. Any resemblance to an actual ecosystem is purely coincidental.

To see the underlying mathematics please refer to Lucey et al. (2020). For additional features, see Whitehouse and Aydin (2020) for ecosense and Lucey et al. (2021) for management strategy evaluation capability.

Installation

If necessary, first install the remotes() package: install.packages("remotes")

remotes::install_github("noaa-edab/Rpath",build_vignettes=TRUE)` to install Rpath and the vignettes.

If you experience issues installing the package, please use this alternative

pak::pak("noaa-edab/Rpath")

References

Christensen, V., and Pauly, D. 1992. ECOPATH II — a software for balancing steady-state ecosystem models and calculating network characteristics. Ecological Modelling, 61: 169–185. https://www.sciencedirect.com/science/article/pii/0304380092900168 (Accessed 9 April 2025).
Christensen, V., and Walters, C. J. 2004. Ecopath with Ecosim: Methods, capabilities and limitations. Ecological Modelling, 172: 109–139. https://www.sciencedirect.com/science/article/pii/S030438000300365X (Accessed 9 April 2025).
Lucey, S. M., Gaichas, S. K., and Aydin, K. Y. 2020. Conducting reproducible ecosystem modeling using the open source mass balance model Rpath. Ecological Modelling, 427: 109057. https://www.sciencedirect.com/science/article/pii/S0304380020301290 (Accessed 9 April 2025).
Lucey, S. M., Aydin, K. Y., Gaichas, S. K., Cadrin, S. X., Fay, G., Fogarty, M. J., and Punt, A. 2021. Evaluating fishery management strategies using an ecosystem model as an operating model. Fisheries Research, 234: 105780. https://www.sciencedirect.com/science/article/pii/S0165783620302976 (Accessed 9 April 2025).
Polovina, J. J. 1984. Model of a coral reef ecosystem. Coral Reefs, 3: 1–11. https://doi.org/10.1007/BF00306135 (Accessed 9 April 2025).
Walters, C., Christensen, V., and Pauly, D. 1997. Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Reviews in Fish Biology and Fisheries, 7: 139–172. https://doi.org/10.1023/A:1018479526149 (Accessed 9 April 2025).
Walters, C., Martell, S. J. D., Christensen, V., and Mahmoudi, B. 2008. An Ecosim Model for Exploring Gulf of Mexico Ecosystem Management Options: Implications of Including Multistanza Life-History Models for Policy Predictions. Bulletin of Marine Science, 83: 251–271.
Walters, C. J., and Martell, S. J. D. 2004. Fisheries Ecology and Management Princeton University Press. https://press.princeton.edu/books/paperback/9780691115450/fisheries-ecology-and-management (Accessed 9 April 2025).
Whitehouse, G. A., and 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: 109074. https://www.sciencedirect.com/science/article/pii/S0304380020301460 (Accessed 9 April 2025).