Package: ecostate 0.2.0
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 fiting 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_0.2.0.tar.gz
ecostate_0.2.0.zip(r-4.5)ecostate_0.2.0.zip(r-4.4)ecostate_0.2.0.zip(r-4.3)
ecostate_0.2.0.tgz(r-4.4-any)ecostate_0.2.0.tgz(r-4.3-any)
ecostate_0.2.0.tar.gz(r-4.5-noble)ecostate_0.2.0.tar.gz(r-4.4-noble)
ecostate_0.2.0.tgz(r-4.4-emscripten)ecostate_0.2.0.tgz(r-4.3-emscripten)
ecostate.pdf |ecostate.html✨
ecostate/json (API)
NEWS
# 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
- eastern_bering_sea - Eastern Bering Sea ecosystem data
- whitehouse_2021 - Full rpath inputs for eastern Bering Sea
Last updated 2 hours agofrom:0d66ddb431. Checks:OK: 7. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Nov 25 2024 |
R-4.5-win | OK | Nov 25 2024 |
R-4.5-linux | OK | Nov 25 2024 |
R-4.4-win | OK | Nov 25 2024 |
R-4.4-mac | OK | Nov 25 2024 |
R-4.3-win | OK | Nov 25 2024 |
R-4.3-mac | OK | Nov 25 2024 |
Exports:abm3pc_sysadd_equilibriumcompute_nllcompute_tracerdBdtddirmultecostateecostate_controlode23plot_foodwebprint_ecoparsrk4sysstanza_settings
Dependencies:backportscheckmateclicodacolorspacecpp11fansifarverggnetworkggplot2ggrepelgluegtableigraphisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnetworknlmepillarpkgconfigR6RColorBrewerRcppRcppEigenrlangRTMBscalessnastatnet.commontibbleTMButf8vctrsviridisLitewithr
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 |
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 |