Overview | 1. Species parameters | 2. Environmental data | 3. Diet composition | 4. Building the Bioenergetic object | Setup visualisation | 5. Estimating consumption — binary search | Growth trajectory | Energy budget | Full dashboard | 6. Consumption with a fixed feeding level | 7. Bootstrap uncertainty estimation | 8. Result analysis | 9. Ecological interpretation | References
Package: fb4package 2.1.1
fb4package: 'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend
An implementation of the 'Fish Bioenergetics 4.0' framework described in Deslauriers et al. (2017) <doi:10.1080/03632415.2017.1377558>. Provides automated parameter optimization, multi-prey diet modeling, and comprehensive energy budget simulations for fisheries research and aquaculture applications. An optional 'TMB' (Template Model Builder) backend delivers 10-50x speedup in maximum likelihood estimation while maintaining full backward compatibility. Includes species-specific parameter databases and tools for modeling fish growth, consumption, and metabolism under varying environmental conditions.
Authors:
fb4package_2.1.1.tar.gz
fb4package_2.1.1.zip(r-4.7)fb4package_2.1.1.zip(r-4.6)fb4package_2.1.1.zip(r-4.5)
fb4package_2.1.1.tgz(r-4.6-x86_64)fb4package_2.1.1.tgz(r-4.6-arm64)fb4package_2.1.1.tgz(r-4.5-x86_64)fb4package_2.1.1.tgz(r-4.5-arm64)
fb4package_2.1.1.tar.gz(r-4.7-arm64)fb4package_2.1.1.tar.gz(r-4.7-x86_64)fb4package_2.1.1.tar.gz(r-4.6-arm64)fb4package_2.1.1.tar.gz(r-4.6-x86_64)
fb4package_2.1.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fb4package/json (API)
| # Install 'fb4package' in R: |
| install.packages('fb4package', repos = c('https://hansttito.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/hansttito/fb4package/issues
Pkgdown/docs site:https://hansttito.github.io
Datasets:
- fish4_parameters - Fish Bioenergetics 4.0 Official Parameters Database
- fish4_parameters_metadata - Fish Bioenergetics 4.0 Parameters Database Metadata
Last updated from:dacae48416. Checks:11 WARNING, 2 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-arm64 | WARNING | 235 | ||
| linux-devel-x86_64 | WARNING | 238 | ||
| source / vignettes | OK | 316 | ||
| linux-release-arm64 | WARNING | 232 | ||
| linux-release-x86_64 | WARNING | 227 | ||
| macos-release-arm64 | WARNING | 168 | ||
| macos-release-x86_64 | WARNING | 340 | ||
| macos-oldrel-arm64 | WARNING | 190 | ||
| macos-oldrel-x86_64 | WARNING | 310 | ||
| windows-devel | WARNING | 189 | ||
| windows-release | WARNING | 201 | ||
| windows-oldrel | WARNING | 184 | ||
| wasm-release | OK | 158 |
Exports:accumulate_validationsanalyze_composition_by_sizeanalyze_composition_changesanalyze_energy_budgetanalyze_feeding_performanceanalyze_growth_patternsanalyze_growth_temperature_sensitivityanalyze_population_variationassess_diet_qualityBioenergeticcalculate_body_compositioncalculate_confidence_intervalscalculate_consumptioncalculate_contaminant_accumulationcalculate_egestioncalculate_excretioncalculate_final_weight_fb4calculate_mortality_reproductioncalculate_np_ratioscalculate_nutrient_balancecalculate_nutrient_efficienciescalculate_predator_energy_densitycalculate_respirationcalculate_stoichiometric_balancecheck_numeric_valueclampcompare_individualscompare_scenarioscompare_with_redfieldcomprehensive_nutritional_analysiscreate_empty_compositioncreate_result_summaryget_consumption_uncertaintyget_efficiency_uncertaintyget_energy_budget_uncertaintyget_individual_resultsget_parameter_valueget_population_resultsinterpolate_time_seriesis.Bioenergeticis.fb4_resultplot_distributions.fb4_resultplot_growth_temperature_sensitivityplot_sensitivity.fb4_resultplot_uncertainty.fb4_resultpredict_consumption_bootstrappredict_consumption_deltaprepare_simulation_dataprocess_bioenergetic_dataprocess_composition_paramsprocess_consumption_paramsprocess_contaminant_paramsprocess_egestion_paramsprocess_excretion_paramsprocess_mortality_paramsprocess_nutrient_paramsprocess_predator_paramsprocess_respiration_paramsprocess_simulation_settingsprocess_species_parametersrun_fb4run_fb4_simulationsafe_expsafe_sqrtset_dietset_environmentset_parameter_valueset_simulation_settingsupdate_body_compositionvalidate_basic_paramsvalidate_bioenergetic_for_simulationvalidate_body_compositionvalidate_complete_simulation_datavalidate_contaminant_paramsvalidate_data_consistencyvalidate_diet_consistencyvalidate_equation_paramsvalidate_fb4_inputsvalidate_fb4_systemvalidate_fitting_settingsvalidate_fractionvalidate_individual_datavalidate_nutrient_concentrationsvalidate_positivevalidate_predator_energy_paramsvalidate_species_equationsvalidate_temperaturevalidate_temporal_datavalidate_time_series_datavalidation_result
Case Study: Chinook Salmon Bioenergetics
Last update: 2026-06-10
Started: 2026-03-29
Introduction to fb4package
Overview | 1. Species parameters | 2. Environmental and diet data | 3. Building a Bioenergetic object | 4. Running simulations | 4a. Direct simulation — fixed feeding level | 4b. Binary search — fit to a target final weight | 4c. MLE — uncertainty on p from observed weights | 4d. Bootstrap — non-parametric uncertainty | 5. Comparing strategies | 6. Analysing results | 7. Visualising results | 8. Temperature × p sensitivity | 9. Experimental features | Contaminant bioaccumulation | Nutrient regeneration | Mortality rates | References
Last update: 2026-06-10
Started: 2025-07-19
Statistical estimation strategies
Overview | Shared setup | Strategy 1 — Binary search | Strategy 2 — Optimisation (optim) | Strategy 3 — Maximum Likelihood Estimation | Strategy 4 — Bootstrap | Strategy 5 — Hierarchical model (mark-recapture) | Biological context | Simulating a mark-recapture data set | Running the hierarchical model | Assumptions and limitations | Comparing strategies | Strategies 1–4: single-population estimates | Strategy 5: population-level distribution | References
Last update: 2026-06-10
Started: 2026-03-29
Temperature Sensitivity and Climate Change Scenarios
Overview | 1. Base model — juvenile Chinook salmon | 2. Manual sensitivity analysis across temperature offsets | 3. Built-in sensitivity plot | 4. Climate change scenarios — projected growth | 5. Thermal performance window | 6. Management implications | References
Last update: 2026-06-10
Started: 2026-03-29
Validation against FB4-Shiny
Overview | 1. Shared setup | Species parameters — Chinook salmon | Scalar extraction helper | Derived temperature coefficients | Simulation inputs | 2. FB4-Shiny reference implementation | 3. fb4package object | 4. Comparison helper | 5. Five simulation modes | Method 1 — Fixed p-value (direct) | Method 2 — Final weight target (binary search) | Method 3 — Total consumption target (binary search) | Method 4 — Fixed ration as % body weight (direct) | Method 5 — Fixed ration in g/day (direct) | 6. Results summary | Weight trajectory — Methods 1 and 2 | Daily weight residuals | Note on Energy_density | 7. Nutrient sub-model validation | 8. Contaminant sub-model validation | 9. Conclusion | References
Last update: 2026-06-07
Started: 2026-06-07
Exploring the Species Parameter Database
Overview | 1. Loading and inspecting the database | 2. Database structure | 3. Searching the database | By scientific name (partial match) | By common name | 4. Listing available life stages | 5. Comparing consumption parameters across species | Temperature optima distribution | 6. Predator energy density equations | 7. Building a model directly from the database | 8. Adding a custom species | References
Last update: 2026-03-29
Started: 2026-03-29
