EcoState

Package ecostate fits a state-space mass-balance model EcoState intended for aquatic ecosystems, using mass-balance equations matching those from Ecopath and dynamical equations matching Ecosim. Unlike the Ecopath-with-Ecosim (EwE) package, ecostate fits both biological parameters (e.g., equilibrium biomass and predator-prey vulnerability) and measurement parameters (e.g., catchability coefficients) via fit to time-series data. ecostate also estimates additional process errors representing nonstationarity in growth efficiency, ecotrophic efficient, migration, or other unmodeled processes. These process errors allow biomass patterns to closely match available data, so that resulting consumption (and associated productivity and mortality rates) can accurately be conditioned upon any residual patterns.

Installation

ecostate can be installed from GitHub using:

library(remotes)
install_github( "James-Thorson-NOAA/ecostate" )

Or to access vignettes from your R session, please instead use:

remotes::install_github( "James-Thorson-NOAA/ecostate",
                          build_vignettes = TRUE )
browseVignettes("ecostate")

More details

For more background, please read:

For state-space mass-balance equilibrium and biomass-dynamic modelling

Thorson, J. Kristensen, K., Aydin, K., Gaichas, S., Kimmel, D.G., McHuron, E.A., Nielsen, J.N., Townsend, H., Whitehouse, G.A. (In press) The benefits of hierarchical ecosystem models: demonstration using a new state-space mass-balance model EcoState. Fish and Fisheries. https://doi.org/10.1111/faf.12874

For age-structured dynamics and bottom-up linkages to animal growth:

Thorson, J. T., Aydin, K. H., Cheng, M., Dias, B. S., Kimmel, D. G., & Kristensen, K. (2025). Bottom-up interactions in age-structured stock assessment and state-space mass-balance modelling. https://ecoevorxiv.org/repository/view/8411/

For original development of ecopath for mass-balance equilibria:

Polovina, J. J. (1984). Model of a coral reef ecosystem. Coral Reefs, 3(1), 1–11. https://doi.org/10.1007/BF00306135

For development of ecosim for deterministic biomass and age-structured dynamics:

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., Christensen, V., & Pauly, D. (1997). Structuring dynamic models of exploited ecosystems from trophic mass-balance assessments. Reviews in Fish Biology and Fisheries, 7(2), 139–172. https://doi.org/10.1023/A:1018479526149

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