Introducing ecostate | State-space mass balance modelling | Age- and size-structured dynamics | Theoretical background | Equilibrium calculation | Projecting nonequilibrium dynamics over time | References
Package: ecostate 0.3.0
ecostate: State-Space Mass-Balance Model for Marine Ecosystems
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.
Authors:
ecostate_0.3.0.tar.gz
ecostate_0.3.0.zip(r-4.7)ecostate_0.3.0.zip(r-4.6)ecostate_0.3.0.zip(r-4.5)
ecostate_0.3.0.tgz(r-4.6-any)ecostate_0.3.0.tgz(r-4.5-any)
ecostate_0.3.0.tar.gz(r-4.7-any)ecostate_0.3.0.tar.gz(r-4.6-any)
ecostate_0.3.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ecostate/json (API)
| # Install 'ecostate' in R: |
| install.packages('ecostate', repos = c('https://james-thorson-noaa.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/james-thorson-noaa/ecostate/issues
Pkgdown/docs site:https://james-thorson-noaa.github.io
Datasets:
- eastern_bering_sea - Eastern Bering Sea ecosystem data
- gulf_of_alaska - Eastern Gulf of Alaska data
- whitehouse_2021 - Full rpath inputs for eastern Bering Sea
Last updated from:77c4c3a889. Checks:8 OK, 1 ERROR. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 171 | ||
| source / vignettes | ERROR | 219 | ||
| linux-release-x86_64 | OK | 169 | ||
| macos-release-arm64 | OK | 136 | ||
| macos-oldrel-arm64 | OK | 125 | ||
| windows-devel | OK | 129 | ||
| windows-release | OK | 128 | ||
| windows-oldrel | OK | 118 | ||
| wasm-release | OK | 122 |
Exports:abm3pc_sysadd_equilibriumcompute_nllcompute_tracerdBdtddirmultecostateecostate_controlode23plot_foodwebprint_ecoparsrk4sysstanza_settings
Dependencies:backportscheckmateclicodacpp11farverggnetworkggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixnetworkpillarpkgconfigR6RColorBrewerRcppRcppEigenrlangRTMBS7scalessnastatnet.commontibbleTMButf8vctrsviridisLitewithr
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
ecostate model description
Last update: 2025-08-07
Started: 2025-08-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Adams-Bashford-Moulton for system of equations | abm3pc_sys |
| Compute equilibrium values | add_equilibrium |
| Compute negative log-likelihood for EcoState model | compute_nll |
| Calculate tracers, e.g., trophic level | compute_tracer |
| Dynamics from EcoSim | dBdt |
| Dirichlet-multinomial | ddirmult |
| eastern Bering Sea ecosystem data | eastern_bering_sea |
| fit EcoState model | ecostate |
| Detailed control for ecostate structure | ecostate_control |
| Penrose-Moore pseudoinverse | ginv |
| eastern Gulf of Alaska data | gulf_of_alaska |
| Marginal log-likelihood | logLik.ecostate |
| Non-stiff (and stiff) ODE solvers | ode23 |
| Plot foodweb | plot_foodweb |
| Print EcoSim parameters | print_ecopars |
| Print fitted ecostate object | print.ecostate |
| Classical Runge-Kutta for system of equations | rk4sys |
| Detailed control for stanza structure | stanza_settings |
| Full rpath inputs for eastern Bering Sea | whitehouse_2021 |
