State-Space Mass-Balance Model for Marine Ecosystems
Adams-Bashford-Moulton for system of equations
Compute equilibrium values
Compute negative log-likelihood for EcoState model
Calculate tracers, e.g., trophic level
Dynamics from EcoSim
Dirichlet-multinomial
Detailed control for ecostate structure
fit EcoState model
Penrose-Moore pseudoinverse
Marginal log-likelihood
Non-stiff (and stiff) ODE solvers
Plot foodweb
Print EcoSim parameters
Print fitted ecostate object
Classical Runge-Kutta for system of equations
Detailed control for stanza structure
Fits a state-space mass-balance model for marine ecosystems, which implements dynamics derived from 'Ecopath with Ecosim' ('EwE') <https://ecopath.org/> while fitting to time-series of fishery catch, biomass indices, age-composition samples, and weight-at-age data. 'Ecostate' fits biological parameters (e.g., equilibrium mass) and measurement parameters (e.g., catchability coefficients) jointly with residual variation in process errors, and can include Bayesian priors for parameters.
Useful links