Files in fb4package
'Fish Bioenergetics 4.0' Model Implementation with High-Performance 'TMB' Backend
MD5
NEWS.md
README.md
NAMESPACE
DESCRIPTION
LICENSE
R/15.1-analysis-extraction.R
R/14.2.3-strategy-optim.R
R/16.4-plot-bioenergetic.R
R/13.1-bioenergetic-methods.R
R/11.0-core-validators.R
R/01-consumption.R
R/14.0-tmb-shared.R
R/fb4package-package.R
R/11.2-parameter-validators.R
R/15.4-analysis-uncertainty.R
R/15.3-analysis-sensitivity.R
R/14.1-strategy-interface.R
R/11.3-data-validators.R
R/data.R
R/12-simulation-engine.R
R/14.2.2-strategy-binary-search.R
R/15.2-analysis-nutritional.R
R/14.2.5-strategy-mle.R
R/16.1-plot-core.R
R/04-predator-energy-density.R
R/14.2.4-strategy-bootstrap.R
R/16-plot-fb4.R
R/14.3-result-builders.R
R/14.2.6-strategy-hierarchical.R
R/16.3-plot-analysis.R
R/06-contaminant-accumulation.R
R/14.0-run-fb4-orchestrator.R
R/02-respiration.R
R/10-data-processing.R
R/05-body-composition.R
R/03-egestion-excretion.R
R/08-mortality-reproduction.R
R/09-parameter-processing.R
R/14.0.1-strategy-commons.R
R/15.0-analysis-core.R
R/11.4-main-validators.R
R/16.2-plot-daily.R
R/07-nutrient-regeneration.R
R/14.2.1-strategy-direct.R
R/11.1-basic-validators.R
R/utils.R
R/13.0-bioenergetic-classes.R
src/Makevars.win
src/Makevars
src/fb4_main.cpp
src/init.c
src/includes/fb4_utils.hpp
src/includes/fb4_mortality_reproduction.hpp
src/includes/fb4_egestion_excretion.hpp
src/includes/fb4_nutrient_regeneration.hpp
src/includes/fb4_body_composition.hpp
src/includes/fb4_validation.hpp
src/includes/fb4_predator_energy.hpp
src/includes/fb4_contaminant_accumulation.hpp
src/includes/fb4_respiration.hpp
src/includes/fb4_consumption.hpp
inst/CITATION
inst/WORDLIST
inst/doc/fb4-temperature-climate.Rmd
inst/doc/fb4-case-study-chinook.html
inst/doc/fb4-species-database.R
inst/doc/fb4-species-database.Rmd
inst/doc/fb4-case-study-chinook.Rmd
inst/doc/fb4-statistical-estimation.R
inst/doc/fb4-statistical-estimation.Rmd
inst/doc/fb4-temperature-climate.html
inst/doc/fb4-introduction.R
inst/doc/fb4-case-study-chinook.R
inst/doc/fb4-introduction.html
inst/doc/fb4-temperature-climate.R
inst/doc/fb4-introduction.Rmd
inst/doc/fb4-statistical-estimation.html
inst/doc/fb4-species-database.html
inst/examples/chinook_demo.R
build/vignette.rds
build/partial.rdb
tests/testthat.R
tests/spelling.R
tests/testthat/test-02-respiration.R
tests/testthat/test-01-consumption.R
tests/testthat/test-14b-strategies-mle-hierarchical.R
tests/testthat/test-03-egestion-excretion.R
tests/testthat/test-12-simulation.R
tests/testthat/helper-setup.R
tests/testthat/test-15-analysis.R
tests/testthat/test-14-strategies.R
vignettes/fb4-temperature-climate.Rmd
vignettes/fb4-species-database.Rmd
vignettes/fb4-case-study-chinook.Rmd
vignettes/fb4-statistical-estimation.Rmd
vignettes/fb4-introduction.Rmd
data/fish4_parameters.RData
man/calculate_nutrient_balance.Rd
man/FB4Strategy.Rd
man/create_method_specific_data.Rd
man/egestion-excretion.Rd
man/validate_respiration_requirements.Rd
man/transform_to_tmb_basic.Rd
man/update_body_composition.Rd
man/fb4-plots.Rd
man/basic-validators.Rd
man/create_execution_summary.Rd
man/bioenergetic-methods.Rd
man/validate_structure_core.Rd
man/validate_basic_params.Rd
man/fish4_parameters.Rd
man/data-processing.Rd
man/validate_nutrient_concentrations.Rd
man/validate_parameter_ranges.Rd
man/extract_adreport_values.Rd
man/process_contaminant_params.Rd
man/safe_extract_param.Rd
man/predator_energy_eq1.Rd
man/validation_result.Rd
man/comprehensive_nutritional_analysis.Rd
man/normalize_diet_proportions.Rd
man/build_individual_uncertainty.Rd
man/compare_with_redfield.Rd
man/nutrient-regeneration.Rd
man/run_fb4_simulation.Rd
man/plot_temperature.Rd
man/plot_bio_temperature.Rd
man/calculate_respiration_params_eq2.Rd
man/analyze_population_variation.Rd
man/validate_time_series_data.Rd
man/convert_respiration_to_energy.Rd
man/validate_common_strategy_inputs.Rd
man/calculate_daily_consumption.Rd
man/plot_bio_diet.Rd
man/run_fb4_direct_method.Rd
man/process_species_parameters.Rd
man/create_hierarchical_strategy.Rd
man/build_fb4_result_unified.Rd
man/execute_daily_simulation.Rd
man/print.Bioenergetic.Rd
man/solve_weight_power_function.Rd
man/data-validators.Rd
man/uncertainty-prediction.Rd
man/prepare_simulation_data.Rd
man/process_egestion_params.Rd
man/extract_tmb_results.Rd
man/fit_fb4_optim.Rd
man/calculate_combined_survival.Rd
man/get_population_results.Rd
man/perform_scenario_tests.Rd
man/create_error_result.Rd
man/validate_individual_data.Rd
man/process_bioenergetic_data.Rd
man/set_parameter_value.Rd
man/create_individual_summary.Rd
man/validate_data_consistency.Rd
man/get_available_plot_types.Rd
man/calculate_progress_interval.Rd
man/plot_sensitivity.fb4_result.Rd
man/check_bioenergetic_readiness.Rd
man/plot_mle_uncertainty.Rd
man/extract_basic_parameters.Rd
man/mle_estimate_p_value_lognormal.Rd
man/calculate_mortality_reproduction.Rd
man/op-null-default.Rd
man/calculate_egestion.Rd
man/bioenergetic-classes.Rd
man/detect_method.Rd
man/process_excretion_params.Rd
man/extract_hierarchical_parameters.Rd
man/create_mle_strategy.Rd
man/validate_backend_compatibility.Rd
man/calculate_confidence_intervals.Rd
man/build_tmb_uncertainty.Rd
man/predator_energy_eq3.Rd
man/contaminant_model_3.Rd
man/report_simulation_summary.Rd
man/egestion_model_3.Rd
man/consumption_temp_eq1.Rd
man/format_statistics_text.Rd
man/binary_search_p_value.Rd
man/calculate_spawn_energy.Rd
man/parameter-processing.Rd
man/summary.Bioenergetic.Rd
man/calculate_excretion.Rd
man/detect_result_type.Rd
man/safe_exp.Rd
man/fit_fb4_binary_search.Rd
man/validate_species_equations.Rd
man/process_consumption_params.Rd
man/validate_fb4_inputs.Rd
man/sdr_pull_vec.Rd
man/interpolate_time_series.Rd
man/build_population_uncertainty.Rd
man/get_energy_budget_uncertainty.Rd
man/get_consumption_uncertainty.Rd
man/validate_body_composition.Rd
man/transform_to_tmb_hierarchical.Rd
man/parameter-validators.Rd
man/mortality-reproduction.Rd
man/plot_bootstrap_distributions.Rd
man/fb4-daily-plots.Rd
man/extract_species_name.Rd
man/validate_fitting_settings.Rd
man/assess_diet_quality.Rd
man/respiration_temp_eq2.Rd
man/contaminant-accumulation.Rd
man/fit_fb4_bootstrap.Rd
man/validate_fraction.Rd
man/contaminant_model_2.Rd
man/fb4-bioenergetic-plots.Rd
man/plot_distributions.fb4_result.Rd
man/FB4-TMB-Shared.Rd
man/calculate_nutrient_allocation.Rd
man/calculate_fat_by_subtraction.Rd
man/process_reproduction_pattern.Rd
man/process_nutrient_params.Rd
man/calculate_temperature_factor_consumption.Rd
man/fit_fb4_mle.Rd
man/strategy-binary-search.Rd
man/run_fb4.Bioenergetic.Rd
man/plot_estimate_panel.Rd
man/fb4-analysis-plots.Rd
man/validate_contaminant_params.Rd
man/calculate_activity_factor_respiration.Rd
man/create_unified_fit_info.Rd
man/calculate_energy_density.Rd
man/process_mortality_params.Rd
man/add_strategy_metadata.Rd
man/predator_energy_eq2.Rd
man/get_parameter_value.Rd
man/run_robust_optimization.Rd
man/set_environment.Rd
man/calculate_stoichiometric_balance.Rd
man/core-validators.Rd
man/process_temperature.Rd
man/plot_dashboard.Rd
man/close_save_device.Rd
man/calculate_consumption_params_eq3.Rd
man/strategy-bootstrap.Rd
man/process_predator_energy_data.Rd
man/excretion_model_3.Rd
man/run_fb4.Rd
man/check_tmb_compilation.Rd
man/plot.fb4_result.Rd
man/process_predator_params.Rd
man/compare_scenarios.Rd
man/plot_hierarchical_uncertainty.Rd
man/check_numeric_value.Rd
man/compare_individuals.Rd
man/validate_fb4_system.Rd
man/generate_reproduction_pattern.Rd
man/add_confidence_bands.Rd
man/sdr_pull_est.Rd
man/summary.fb4_result.Rd
man/validate_temporal_data.Rd
man/process_simulation_settings.Rd
man/plot_growth.Rd
man/consumption_temp_eq4.Rd
man/analyze_energy_budget.Rd
man/analyze_feeding_performance.Rd
man/validate_predator_energy_params.Rd
man/validate_statistical_method_inputs.Rd
man/calculate_consumption.Rd
man/extract_strategy_parameters.Rd
man/get_efficiency_uncertainty.Rd
man/excretion_model_1.Rd
man/calculate_weight_dependent_mortality.Rd
man/accumulate_validations.Rd
man/process_respiration_params.Rd
man/validate_fb4_result.Rd
man/strategy-mle.Rd
man/analyze_composition_changes.Rd
man/neg_log_likelihood_lognormal.Rd
man/create_optim_strategy.Rd
man/create_result_summary.Rd
man/predator-energy-density.Rd
man/check_weight_outliers.Rd
man/calculate_daily_metabolism.Rd
man/excretion_model_2.Rd
man/has_uncertainty.Rd
man/plot_bio_energy.Rd
man/calculate_predator_energy_density.Rd
man/process_composition_params.Rd
man/set_simulation_settings.Rd
man/convert_to_individual_data.Rd
man/fb4package-package.Rd
man/execute_simulation_with_method.Rd
man/execute_hierarchical_tmb.Rd
man/nutrient_efficiency_block.Rd
man/consumption_temp_eq2.Rd
man/egestion_model_2.Rd
man/calculate_growth_metrics.Rd
man/plot_bio_dashboard.Rd
man/predict_consumption_bootstrap.Rd
man/plot_growth_vs_temperature.Rd
man/extract_data_sources.Rd
man/calculate_fish_water_partition.Rd
man/plot.Bioenergetic.Rd
man/add_plot_annotations.Rd
man/plot_energy.Rd
man/calculate_temperature_factor_respiration.Rd
man/calculate_daily_spawn_energy.Rd
man/calculate_sda.Rd
man/fish4_parameters_metadata.Rd
man/consumption-functions.Rd
man/calculate_daily_weight_change.Rd
man/validate_range_core.Rd
man/bootstrap_single_iteration.Rd
man/validate_positive.Rd
man/solve_weight_iterative.Rd
man/clamp.Rd
man/create_individual_rankings.Rd
man/execute_mle_tmb.Rd
man/plot_growth_temperature_sensitivity.Rd
man/validate_fit_to_strategy_concordance.Rd
man/create_direct_strategy.Rd
man/validate_category_equation.Rd
man/setup_plot_layout.Rd
man/analysis-extraction.Rd
man/utils.Rd
man/bootstrap_p_values.Rd
man/validate_bioenergetic_for_simulation.Rd
man/calculate_body_composition.Rd
man/validate_equation_params.Rd
man/should_mark_as_fitted.Rd
man/print.fb4_result.Rd
man/setup_save_device.Rd
man/predict_consumption_delta.Rd
man/analyze_growth_temperature_sensitivity.Rd
man/consumption_temp_eq3.Rd
man/plot_consumption.Rd
man/calculate_consumption_params_eq2.Rd
man/calculate_gill_efficiency.Rd
man/plot_bootstrap_uncertainty.Rd
man/EQUATION_REQUIREMENTS.Rd
man/check_target_achievement.Rd
man/validate_diet_consistency.Rd
man/analyze_composition_by_size.Rd
man/strategy-commons.Rd
man/egestion_model_4.Rd
man/process_reproduction_data.Rd
man/is.Bioenergetic.Rd
man/validate_temperature.Rd
man/compute_likelihood_profile.Rd
man/create_empty_composition.Rd
man/strategy-direct.Rd
man/get_color_scheme.Rd
man/analysis-nutritional.Rd
man/simulation-engine.Rd
man/create_bootstrap_strategy.Rd
man/contaminant_model_1.Rd
man/is.fb4_result.Rd
man/create_execution_plan.Rd
man/body-composition.Rd
man/solve_weight_linear_segments.Rd
man/sdr_assign_scalars.Rd
man/calculate_np_ratios.Rd
man/create_fb4_strategy.Rd
man/result-builders-unified.Rd
man/strategy-interface.Rd
man/plot_hierarchical_distributions.Rd
man/analysis-core.Rd
man/test_metric_differences.Rd
man/calculate_temperature_dependent_mortality.Rd
man/calculate_dissolved_fraction.Rd
man/log_execution_plan.Rd
man/analysis-sensitivity.Rd
man/build_composition_df.Rd
man/calculate_final_weight_fb4.Rd
man/validate_plot_data.Rd
man/identify_best_scenarios.Rd
man/Bioenergetic.Rd
man/assign_energy_components.Rd
man/validate_tmb_objective.Rd
man/run-fb4-orchestrator.Rd
man/excretion_model_4.Rd
man/calculate_reproductive_loss.Rd
man/fb4-plot-core.Rd
man/validate_complete_simulation_data.Rd
man/strategy-optim.Rd
man/egestion_model_1.Rd
man/calculate_component_from_water.Rd
man/plot_uncertainty.fb4_result.Rd
man/respiration-functions.Rd
man/convert_daily_results_to_dataframe.Rd
man/run_final_simulation.Rd
man/calculate_contaminant_accumulation.Rd
man/sdr_pull_se.Rd
man/respiration_temp_eq1.Rd
man/main-validators.Rd
man/get_individual_results.Rd
man/create_binary_search_strategy.Rd
man/run_single_optimization.Rd
man/analyze_growth_patterns.Rd
man/strategy-hierarchical.Rd
man/optim_search_p_value.Rd
man/validate_predator_requirements.Rd
man/calculate_respiration.Rd
man/safe_sqrt.Rd
man/report_simulation_progress.Rd
man/calculate_nutrient_efficiencies.Rd
man/validate_numeric_core.Rd
man/set_diet.Rd
man/create_unified_summary.Rd
man/figures/growth_analysis.png
man/figures/consumption_analysis.png
man/figures/temperature_analysis.png
man/figures/simulation_dashboard.png
man/figures/energy_budget.png
