Rpath: an open source food web model

Sean M. Lucey

2025-01-31

Source: vignettes/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")

Use the command remotes::install_github("noaa-edab/Rpath",build_vignettes=TRUE) to install 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 13 January 2023).
Christensen, V., and Walters, C. J. 2004. Ecopath with Ecosim: Methods, capabilities, and limitations. Ecologial Modelling, 172: 109–139.
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 16 April 2021).
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. http://www.sciencedirect.com/science/article/pii/S0165783620302976 (Accessed 9 December 2020).
Polovina, J. J. 1984. Model of a coral reef ecosystem I. The ECOPATH model and its application to French Frigate Shoals. Coral Reefs, 3: 1–11.
Walters, C. J., 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.
Walters, C. J., and Martell, S. J. D. 2004. Fisheries Ecology and Management. Princeton University Press, Princeton.
Walters, C. J., 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.
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 13 January 2023).