c7a5b8d02f04b92db6a877052561c941 *DESCRIPTION
5171a210679a4bcfbc5ddae127cea375 *LICENSE
26955978a929242d3cf970dfec4fd9df *NAMESPACE
0c61a372ed0b0c071cb7b935dc908d15 *NEWS.md
edb9cff8cf6241d2b24fadb2a81f051a *R/01-consumption.R
b0a5ca8e1aad5db67338c7c72af80b4e *R/02-respiration.R
f9229610d332940a2b5aeaf97f003938 *R/03-egestion-excretion.R
a3b5e46806eadf48935b8f1d8f02e08a *R/04-predator-energy-density.R
950e40837f134b456eb0d1af231c9c7c *R/05-body-composition.R
a2d4135f48cffe3d9e6f828ba51fb014 *R/06-contaminant-accumulation.R
f2b29bf3693650bb17241700cfccc2fa *R/07-nutrient-regeneration.R
521ecc4661fd281efd7e070dd72a3e6e *R/08-mortality-reproduction.R
bca5e086bb1fca01d3327d099d17bae8 *R/09-parameter-processing.R
777ef76312ff1cbf8a57b6d7b5415026 *R/10-data-processing.R
dd833bd68b1a2a09a279e4df4b5a29d5 *R/11.0-core-validators.R
cce6f4865dbd0337776b76ca96c9e082 *R/11.1-basic-validators.R
f99ecc2235fb6a66d00c38d9dbdc2ed9 *R/11.2-parameter-validators.R
36e8805e9b3df0375e714f134217861c *R/11.3-data-validators.R
e9e50b3444c3a78df6afd0b1af57ba01 *R/11.4-main-validators.R
1da23aa7339be95f239c5a3f6ecf5bff *R/12-simulation-engine.R
d090d4c31ff6863af09f3da05ef088ef *R/13.0-bioenergetic-classes.R
13d7a1400afd7dfc50210bfa0f62c6e1 *R/13.1-bioenergetic-methods.R
c656e2877b51f498bab6cf8a73aba106 *R/14.0-run-fb4-orchestrator.R
8feb9ec96d4ca31b8c947f0aed389116 *R/14.0-tmb-shared.R
cd8be35766b5512841b6ffce5aed0ddb *R/14.0.1-strategy-commons.R
5b0f4974247c8cb34d5488c307528169 *R/14.1-strategy-interface.R
50c710165f927435cbd99c2eb0f890d5 *R/14.2.1-strategy-direct.R
bbd5dff9f439b9d7207f6f41cd556597 *R/14.2.2-strategy-binary-search.R
3b5bb257d90fb1a9b0e6d699729eea05 *R/14.2.3-strategy-optim.R
2ad51fd83fc9d956de928dcaa721a59c *R/14.2.4-strategy-bootstrap.R
4b2954b5a77487def7c6ba1971e5ec24 *R/14.2.5-strategy-mle.R
cc710b4980f94e557e3473d96f325128 *R/14.2.6-strategy-hierarchical.R
1980f1721e84db4af47faf2e7a07229d *R/14.3-result-builders.R
54398150a376421be13277860e530773 *R/15.0-analysis-core.R
c675a23344772ef58da9f1eebf334116 *R/15.1-analysis-extraction.R
95ee00d7c32143a9e1a46dd972b702d5 *R/15.2-analysis-nutritional.R
ecf041c05afaea6a665bc50a8b807efe *R/15.3-analysis-sensitivity.R
a020ed7ceb7f411d67717a58e9ec77ab *R/15.4-analysis-uncertainty.R
1952b150eac9bf3ba99a0993a0419940 *R/16-plot-fb4.R
c379c6948a39e0844b8fccdb1970fb98 *R/16.1-plot-core.R
ba0450a5186e29607ce17e9096c32fe1 *R/16.2-plot-daily.R
e78c2b904fbe6d99bba307c38412a586 *R/16.3-plot-analysis.R
1fa6b4f7ff768b9909b628b1ed63e734 *R/16.4-plot-bioenergetic.R
69e4652a6fdd6395abe42fdc9fcec765 *R/data.R
d2dbc64f62ecbeab34387ee9b81e710e *R/fb4package-package.R
25695907feaa83c6f11b12839d2c20d4 *R/utils.R
7c817800f0e557c1cd72837548bd2738 *README.md
9d40159f50a5fc9949cbfe95a2884126 *build/partial.rdb
e6ff20067eef4abeb0dd2ac9e85696af *build/vignette.rds
3ade4ba6db007012edea5ce570e6fe91 *data/fish4_parameters.RData
0095b83a4696a010bc75260c1e79f55e *inst/CITATION
db9e526d006f67bcfe3c131100ef94eb *inst/WORDLIST
96ac7adbd7790d6d12d9e398bfc45452 *inst/doc/fb4-case-study-chinook.R
e0389533a8216b9cb79c2a42ff69e624 *inst/doc/fb4-case-study-chinook.Rmd
5d93155ab7c82520fa3e92671e510cb2 *inst/doc/fb4-case-study-chinook.html
79fa1b44450c7678f9ec4222f526c860 *inst/doc/fb4-introduction.R
cf7ab0fbed1a2203c7dbd3488c0de405 *inst/doc/fb4-introduction.Rmd
31b3889d88895ec19a8be15f964cd91c *inst/doc/fb4-introduction.html
6383aa49cb7f4fea1564b3ea6605f79b *inst/doc/fb4-species-database.R
6484822a7f0a9bb1ea19878bc3071686 *inst/doc/fb4-species-database.Rmd
88cc50832d76b7b8f8dc9982561c7319 *inst/doc/fb4-species-database.html
d96b628f030038c100a89553d7ce32c7 *inst/doc/fb4-statistical-estimation.R
d3b0c9b6e4ee03de5e459761199205b8 *inst/doc/fb4-statistical-estimation.Rmd
601f74e8f912b6a88e0d68b38051c9e5 *inst/doc/fb4-statistical-estimation.html
dd5fae77d436aabf7a9c85fb7f147078 *inst/doc/fb4-temperature-climate.R
1602e44f0f79a2efeaefc3f687bcb3ea *inst/doc/fb4-temperature-climate.Rmd
9c7f8419379b1ffb1a397bd40d42e649 *inst/doc/fb4-temperature-climate.html
97cab331e12c32d05653d305b75b858f *inst/examples/chinook_demo.R
e8fefc76b83f26fbebeb2d8077d693ef *man/Bioenergetic.Rd
ba4d72c40a742c8d4eb760db38aa39eb *man/EQUATION_REQUIREMENTS.Rd
eafa8997b200fb4e8f94ed3dad1ca8a0 *man/FB4-TMB-Shared.Rd
1beae914f306163b7a5c38a3b2837de3 *man/FB4Strategy.Rd
a8b10d444cf3d76bc250648bbdec321c *man/accumulate_validations.Rd
7dd684627615ca79f0cddf7500364dcb *man/add_confidence_bands.Rd
1ee06f01fa5aa37f6e7a95a94c5510f3 *man/add_plot_annotations.Rd
9c003ef58f9ed66faa2b2a0f9a12b33f *man/add_strategy_metadata.Rd
5d92f97fcc7172ea90b82ad7244e3d7d *man/analysis-core.Rd
4370e0fa4ff3c748077a15460a400310 *man/analysis-extraction.Rd
e833c0919128383749f193b58a5c4dff *man/analysis-nutritional.Rd
c3242ff836caeec74a43413fbafba83e *man/analysis-sensitivity.Rd
e8a6b49e0d4737943a25ae218d1d3da8 *man/analyze_composition_by_size.Rd
371ec11123e5b603393436df0e97566b *man/analyze_composition_changes.Rd
43a8f5d632534bb65b3602daf7a8dc5e *man/analyze_energy_budget.Rd
a5c47a564567332a642ad9bfe9983888 *man/analyze_feeding_performance.Rd
092826cb1aaaf4b53ae75a5d42656269 *man/analyze_growth_patterns.Rd
2e434790bddc0709942abd501fe178a9 *man/analyze_growth_temperature_sensitivity.Rd
29e7d819305566ef9e46e8f6e9750cab *man/analyze_population_variation.Rd
9f0dff69092cd8f7986ecfcbe6e18b94 *man/assess_diet_quality.Rd
5549d7af72d9affab6109e68d716bf10 *man/assign_energy_components.Rd
36c1945a5341255997a4b3cf31251b24 *man/basic-validators.Rd
daa3feab2098b71f37e01001d668043f *man/binary_search_p_value.Rd
259d56ca6a86327f89f26d1319844ee2 *man/bioenergetic-classes.Rd
7502d33a2e29ee8c0b239ec37a65b346 *man/bioenergetic-methods.Rd
8ad575f77ed7181b8efd4d2bba26085d *man/body-composition.Rd
84f34efeb26452309dc77ba1b8affa53 *man/bootstrap_p_values.Rd
85bd697f508114220e8b28bb75d1cb88 *man/bootstrap_single_iteration.Rd
64deec5dea64901603799656cd4c4fbc *man/build_composition_df.Rd
847d91c2de0ddecccd21ca12bec9c8f4 *man/build_fb4_result_unified.Rd
ca0eb573321e28b8e098e33f03890604 *man/build_individual_uncertainty.Rd
98ce034e2026b0cbcbb78d14a3c14135 *man/build_population_uncertainty.Rd
d24c4c101e05207d958e8b5adb065f88 *man/build_tmb_uncertainty.Rd
e024651ac28b6dcc894697ff55360eb3 *man/calculate_activity_factor_respiration.Rd
f371e27378050028753de498cb4c5cb3 *man/calculate_body_composition.Rd
266475abf590855693545075b8c06cb1 *man/calculate_combined_survival.Rd
54d2715019b6b0026ecf3e888db37cb4 *man/calculate_component_from_water.Rd
0486523dd4e105cda1a0106bc42409ad *man/calculate_confidence_intervals.Rd
a115e167a78ebc86e91087d982481700 *man/calculate_consumption.Rd
79173be61ba024dae931dce093131de7 *man/calculate_consumption_params_eq2.Rd
1411e2aa96d9046ad21fbbd74e87ca3d *man/calculate_consumption_params_eq3.Rd
a5b199f8bc89ffa976e0a00e34bce36b *man/calculate_contaminant_accumulation.Rd
d0946da5c6b9da961d7d411d69051974 *man/calculate_daily_consumption.Rd
98d058c4aafc4668f2a2900a3519bc88 *man/calculate_daily_metabolism.Rd
4277227eedb1db1c175fc50729024a55 *man/calculate_daily_spawn_energy.Rd
18181b8b6f05a5078a2dfbbf52dedbbf *man/calculate_daily_weight_change.Rd
268ea965bd4594fd8fffd94c224dd980 *man/calculate_dissolved_fraction.Rd
0957c6e0421ce076952ddfe9c5457d30 *man/calculate_egestion.Rd
d39ef9cadf4fcf94f20eb4bd1f49158b *man/calculate_energy_density.Rd
66f771bbbe02084f3254a3bc1b9df255 *man/calculate_excretion.Rd
e1f34ee53f3d2016b103e02f4e081b72 *man/calculate_fat_by_subtraction.Rd
b203163100ce3e200af7bfdc433155a9 *man/calculate_final_weight_fb4.Rd
e626202593c1b7a7ce68ed4a33bd07c3 *man/calculate_fish_water_partition.Rd
0c1ac8cd0a0075912655f793d0b7a158 *man/calculate_gill_efficiency.Rd
ce397940162eafb9b437ebd9d1ef72ae *man/calculate_growth_metrics.Rd
122dcf42875e3b5184bb1bf5ced08343 *man/calculate_mortality_reproduction.Rd
7c0b196f89df1af871bd3ebf132c76d9 *man/calculate_np_ratios.Rd
61c58b33273fe70e853df9e89d5f8fb7 *man/calculate_nutrient_allocation.Rd
50c0e37a43b0a43006d428127ee13263 *man/calculate_nutrient_balance.Rd
8e190acde3f9ac8767088dd401b31267 *man/calculate_nutrient_efficiencies.Rd
81d69f435a7aa7c54a1e0c85a66ecde8 *man/calculate_predator_energy_density.Rd
13ffc196a6bd7466cd0a02a8218aa8ee *man/calculate_progress_interval.Rd
189c2c6b92900d019077252e6c783128 *man/calculate_reproductive_loss.Rd
8db3a4bded84d4f7f223577af61c288e *man/calculate_respiration.Rd
85e5b6667a116519e205a709d1bf62c1 *man/calculate_respiration_params_eq2.Rd
8054af4554e49edca7e63cfb5c2b7dca *man/calculate_sda.Rd
5283988e1e7c58a22dfe787efada0d40 *man/calculate_spawn_energy.Rd
264a8a48edd3aeb5f5f5f0b670e06e15 *man/calculate_stoichiometric_balance.Rd
dad4be625ab4cd7543996656cf6d9391 *man/calculate_temperature_dependent_mortality.Rd
44592efb7941de9abb81811847c9be70 *man/calculate_temperature_factor_consumption.Rd
2f22df63072a69f265b603817f5d61de *man/calculate_temperature_factor_respiration.Rd
ea499541d5934fefad3a34144cecb38a *man/calculate_weight_dependent_mortality.Rd
67bafe3dda3ae7a4dd29dff8b618e70a *man/check_bioenergetic_readiness.Rd
ce5a0568e781e8d934a7f19c7a0a8540 *man/check_numeric_value.Rd
0fa483321aa1a835f213824879a22da6 *man/check_target_achievement.Rd
e576240a88368c4cc666168fc7d2e701 *man/check_tmb_compilation.Rd
3006c56760fa5899e49b698dc97dd7bb *man/check_weight_outliers.Rd
f21233cbc2357483d197515a933ad4fb *man/clamp.Rd
cfceb3ae691fc2395f6bc7a1091159f9 *man/close_save_device.Rd
1a599adf88cf61c5df567fffc19f3e6a *man/compare_individuals.Rd
173c34d92ac22ef9ea29254078e8373b *man/compare_scenarios.Rd
f53df199d82ec73dbaebd057fd874c43 *man/compare_with_redfield.Rd
7c4d4d3c52fa0b7aa38d0b2e7db3396c *man/comprehensive_nutritional_analysis.Rd
3f2e22b8d95a66d05b43e160dc15ef2c *man/compute_likelihood_profile.Rd
6d15b371586881b5ad17a5632eddbf48 *man/consumption-functions.Rd
779d5a2bfd3a9f9bb5915d90cf1697f0 *man/consumption_temp_eq1.Rd
73977a0f1ff604b6a6619c20fca096aa *man/consumption_temp_eq2.Rd
76b5fb1d3827b44cc35548d5462d3a42 *man/consumption_temp_eq3.Rd
6c2b896a160ff3e920c98a4b353e18bf *man/consumption_temp_eq4.Rd
ba135292edf32f3cbae7b70e272cec87 *man/contaminant-accumulation.Rd
1e88a1de0e56841211b4b4b7b5214ca2 *man/contaminant_model_1.Rd
e52e9ef59afac20f93c0425c655f645d *man/contaminant_model_2.Rd
816992a658e63293eac3eb837485c23b *man/contaminant_model_3.Rd
8e21d15683fab5e159ff303654eb594e *man/convert_daily_results_to_dataframe.Rd
4856f8590c6ee044699c21f6fea1fd08 *man/convert_respiration_to_energy.Rd
cc98d97611b6863ea33c3398da26d3a5 *man/convert_to_individual_data.Rd
68ec80736e7734366f65796f853e067b *man/core-validators.Rd
bf3a302807e19e6483b4ca74558e80b7 *man/create_binary_search_strategy.Rd
5c7e493794a6a3d5ac9388157b738aab *man/create_bootstrap_strategy.Rd
8f6d7ef3a760b073af1306a8971542c3 *man/create_direct_strategy.Rd
be01b016db736272838e5f04490bbb7a *man/create_empty_composition.Rd
bde9fbbad3e5a502de5471eb0cb37b3e *man/create_error_result.Rd
35de58f278f9dda198fb519078ce5973 *man/create_execution_plan.Rd
3f92a6bbf080d989760e05691da3b93a *man/create_execution_summary.Rd
0957a01c3932afcf53ee8fbaffcce49c *man/create_fb4_strategy.Rd
798e627dbe8daed48dfe440c950a4216 *man/create_hierarchical_strategy.Rd
77cc4b40d53e4cbbdd217e43e3ced9c6 *man/create_individual_rankings.Rd
d9affa9b7a258c1017045b0090d53cd7 *man/create_individual_summary.Rd
7136d7e48c02fbc2b26cb8f6d24d15ef *man/create_method_specific_data.Rd
fef7e8bde05621956c81494722fabb91 *man/create_mle_strategy.Rd
97f2097a4b01d4ab2e9820013a49d9a6 *man/create_optim_strategy.Rd
040d617907d2ac0a6e9f22da936f9c70 *man/create_result_summary.Rd
6d4b5bc6163831c05b639ad1eb40d4ca *man/create_unified_fit_info.Rd
e65a4266d03bce533d74bf4b0e3fe26b *man/create_unified_summary.Rd
58d1e685ba6a05a7f8419843a3b35fe9 *man/data-processing.Rd
cf1f874c51fa394276dab1342934f99f *man/data-validators.Rd
1517790a162d64172087ef1701c35c98 *man/detect_method.Rd
bfde6a0e3e23b953fc52dc2cf2dba2c5 *man/detect_result_type.Rd
5bd95bc22b2348b5f64f23ad8b580b66 *man/egestion-excretion.Rd
9613f667a69d056e228f3d792425f592 *man/egestion_model_1.Rd
bb24ed9a80233c8c85156472981b3977 *man/egestion_model_2.Rd
6942ca3a63516d98c4cce15cf332c819 *man/egestion_model_3.Rd
5984d0374b303109d6e5b586cfcee24d *man/egestion_model_4.Rd
5b4108301fbb66981c12e86e2455a3db *man/excretion_model_1.Rd
534ef7f8bb85db59c7e063ec65bd78ea *man/excretion_model_2.Rd
c99ea50b11a399710eac6cc556525824 *man/excretion_model_3.Rd
f781be11bdec41a4125056bea2dce10f *man/excretion_model_4.Rd
b663dafe20b8a077d632af268fbc3877 *man/execute_daily_simulation.Rd
ad05a4e3ce578ba4fb52e7e25e10c4f3 *man/execute_hierarchical_tmb.Rd
983176d5fb27e3f6df4d14543e82924c *man/execute_mle_tmb.Rd
02c7e1ad064d803e3c1297def82e604c *man/execute_simulation_with_method.Rd
f6d9403812f4ace1a32d27b8d1ac8c1e *man/extract_adreport_values.Rd
4f50760621af4a3745b1dead31247cb4 *man/extract_basic_parameters.Rd
85ef24db66e66611c954f72c29942b24 *man/extract_data_sources.Rd
3b5c7ba9147e012ae77c082e2e866c23 *man/extract_hierarchical_parameters.Rd
08d5a4c0ff3b04b19b9ce8fd5a1e20fd *man/extract_species_name.Rd
a99596de1e257111a204b1a846e4137d *man/extract_strategy_parameters.Rd
3c4d5714b127eaefbaa4d3c6b587b4e4 *man/extract_tmb_results.Rd
6d53ac46d399958532621d5a84630ddf *man/fb4-analysis-plots.Rd
b7b34a568d864c7b71d199019a1d9849 *man/fb4-bioenergetic-plots.Rd
29cc9f5b593f799c5a73e248a6752437 *man/fb4-daily-plots.Rd
c86978b7e22058b45faceee6423c7a81 *man/fb4-plot-core.Rd
7dcb5ef61793c499405be7d91dc072ba *man/fb4-plots.Rd
6d85b63a0d7489823ea0401b1ad1afc4 *man/fb4package-package.Rd
89ed1240df0f89546629a57f223f32a1 *man/figures/consumption_analysis.png
55d1125e0553008f27cd50e07195c76e *man/figures/energy_budget.png
e3482ef8203ddce042edcab6de328a4e *man/figures/growth_analysis.png
8700e70ee47015e366d3e31adac07ca7 *man/figures/simulation_dashboard.png
5e0e5786b087819c28630d26211a856c *man/figures/temperature_analysis.png
6b50f07093ce47d43a145746a9985103 *man/fish4_parameters.Rd
379bb0b24355d182a9e67a9024c5b362 *man/fish4_parameters_metadata.Rd
85f012dc356b1d1f65a7574989a16890 *man/fit_fb4_binary_search.Rd
86f7974b15d1426e4486db6d765152d7 *man/fit_fb4_bootstrap.Rd
1301e98c7a983caabe3fd64f6cddfbfd *man/fit_fb4_mle.Rd
5aad14a494a77ab25d1521bcf28d2764 *man/fit_fb4_optim.Rd
7352b6b40963caa3993a27b2fdaba3a8 *man/format_statistics_text.Rd
bb9a043a7813db32c7259adeec14b4c4 *man/generate_reproduction_pattern.Rd
6c699cc2fc4ac30a353e3fa87c3e032b *man/get_available_plot_types.Rd
cfdfe0576b64594cca0de9964422d016 *man/get_color_scheme.Rd
7347d8455ecdb7d65d0486bbfbd47a13 *man/get_consumption_uncertainty.Rd
a0c3799dce56065b0c4cd9054d0cb7eb *man/get_efficiency_uncertainty.Rd
39286b726f3000dea4ee5e7cd6d2ff47 *man/get_energy_budget_uncertainty.Rd
1bcaa54a6f2d61776838e87a5c19d54d *man/get_individual_results.Rd
1707b0f95e5db624f3728bc8aaab1b84 *man/get_parameter_value.Rd
fbf5f5ad03506fb741059c2525dd67f8 *man/get_population_results.Rd
3a36a9884d0c1a759fa84ee4dc13c81e *man/has_uncertainty.Rd
3b29c529cc9325c9550d8e7884c631a2 *man/identify_best_scenarios.Rd
d26628469de9cfa8a1c732433e8d3cec *man/interpolate_time_series.Rd
250d1b321c5a99f17f1816ace4c2e824 *man/is.Bioenergetic.Rd
d9463aa621c4818d7a08b1249fcfb4fb *man/is.fb4_result.Rd
03f6382cb82dacc3d98d93fe12142321 *man/log_execution_plan.Rd
2a581ec84c1c31a710511637618a060a *man/main-validators.Rd
2c5a6540d97b3a956f91ac5a9c7bce32 *man/mle_estimate_p_value_lognormal.Rd
2f2ceee7cde1d69ab2ed58e121717573 *man/mortality-reproduction.Rd
8a9d48d6cf862ef67b40bd0a99c22e8f *man/neg_log_likelihood_lognormal.Rd
2de7bd1866a68b48ae222f2de3b2fa46 *man/normalize_diet_proportions.Rd
15ebf44301811dc1091cae79cd68aecf *man/nutrient-regeneration.Rd
f528c3d795193db97a9d7a4305b1196d *man/nutrient_efficiency_block.Rd
fe4b1bd6b0d10f2b4c70af43a2bd5070 *man/op-null-default.Rd
d4269afbef0ebb1aa4bdc25d6dce87fa *man/optim_search_p_value.Rd
0ec5908f402c75d0121d22a1b4e7652b *man/parameter-processing.Rd
632689a8df95b3889cab0be37d979d6e *man/parameter-validators.Rd
02949fff75bda88929995c10ebd8a74a *man/perform_scenario_tests.Rd
a702c558073288c8184797a5eda7a2df *man/plot.Bioenergetic.Rd
f46b52f3bc36bd11f823e346e90a8360 *man/plot.fb4_result.Rd
b60f8aff7b49b96084ea510617d45856 *man/plot_bio_dashboard.Rd
93a1c9639f245cc0c9850be724ee86b9 *man/plot_bio_diet.Rd
1f570523ab543b9ff6061c611186c462 *man/plot_bio_energy.Rd
6f3239b3583c3f5caf650723e6f9114d *man/plot_bio_temperature.Rd
e33cd66c7473f90a263d38598936136e *man/plot_bootstrap_distributions.Rd
8834a18a86ba014551607d9d544e6066 *man/plot_bootstrap_uncertainty.Rd
842f43ea1f9438b09a00ef3d65e7980f *man/plot_consumption.Rd
7abd6c14d6d4a3cdd975c66279a6a402 *man/plot_dashboard.Rd
b68449cf21d287d745978136840127a1 *man/plot_distributions.fb4_result.Rd
38742e7800eda8b66a586f64d700e893 *man/plot_energy.Rd
3abb84d5a581acc6a5c5756338d25261 *man/plot_estimate_panel.Rd
59931d0e54a4b0a08842297060992a7b *man/plot_growth.Rd
2202171eae08cd232e5862545e3325c8 *man/plot_growth_temperature_sensitivity.Rd
2a3529d0fc49a322734521e77ae7ddee *man/plot_growth_vs_temperature.Rd
b256926b8dd15b9a1c09b48c0665ed2f *man/plot_hierarchical_distributions.Rd
ce22e45f0cf82f5f75d56c409037f815 *man/plot_hierarchical_uncertainty.Rd
e1021030d139a30c0c417443c054b741 *man/plot_mle_uncertainty.Rd
9ce22230d35e8780ff87abd67fbbadb1 *man/plot_sensitivity.fb4_result.Rd
39fd78f8133a61000d0a3083457000d0 *man/plot_temperature.Rd
17361f9c724df8cf87777856f4c9926f *man/plot_uncertainty.fb4_result.Rd
b04fdc36743a68a3cfbab9e51d56c4e7 *man/predator-energy-density.Rd
3438165da7eecb1266d0636565887b80 *man/predator_energy_eq1.Rd
64ca9ae6dc2e8e8cb8fa0b77eb658590 *man/predator_energy_eq2.Rd
6d2af3da53420470c4eeaf7bf96eb935 *man/predator_energy_eq3.Rd
9ae94e72ed3261d1d10a3393518a6e73 *man/predict_consumption_bootstrap.Rd
6b4703fbbb4121575c42dbb431cc9bcd *man/predict_consumption_delta.Rd
d91f677defc155631b01fe81417567c7 *man/prepare_simulation_data.Rd
55d1aca0f7842e119ea620335a7ff5d3 *man/print.Bioenergetic.Rd
5c7c0ee489e27d023abb898ce4b46373 *man/print.fb4_result.Rd
6d0257567106fdaaac8cd3a6472b69e2 *man/process_bioenergetic_data.Rd
d679e4ea3535b2df310f3b0c18fa5e21 *man/process_composition_params.Rd
38523adb10efa3b1d1adc399f16e1561 *man/process_consumption_params.Rd
8723990ae71752c0cd515e7f5bd2a003 *man/process_contaminant_params.Rd
9b6419c311545583f1e428ae741e5a51 *man/process_egestion_params.Rd
3cace8e900cf37acc0cce5d7c9ab2046 *man/process_excretion_params.Rd
411edc22e32da5a1c1acb7e402a5ea96 *man/process_mortality_params.Rd
32f22ab27116e70fcc5de42fc426b805 *man/process_nutrient_params.Rd
cce79d94d4831f206a382c3e846bfa48 *man/process_predator_energy_data.Rd
8649b6966a88c635a76ba7bcbca2e28c *man/process_predator_params.Rd
2374999af0f69324927b7dbc6d5e59b6 *man/process_reproduction_data.Rd
a0921dcdbbeb1c59e76ed4e2c5eb29e5 *man/process_reproduction_pattern.Rd
1706fdc418ae47d12a5480cf44fb04c1 *man/process_respiration_params.Rd
0a019868c46026a6df4aaf72bed7ee66 *man/process_simulation_settings.Rd
fbcd7e7e08ad8843690fbc099759e6bb *man/process_species_parameters.Rd
4260d9a4c4349cb66493d1b494bbd721 *man/process_temperature.Rd
ecd126637c835b8f79c94ff002b7e783 *man/report_simulation_progress.Rd
d5ed656d89e3502d0ece60759a823569 *man/report_simulation_summary.Rd
08d0667075d0808dd92d77a2bd255217 *man/respiration-functions.Rd
b3f1727a35e3f1d5242f26e74bd010dc *man/respiration_temp_eq1.Rd
74944e96477a8fac49932dd680dfbe08 *man/respiration_temp_eq2.Rd
6d6bce965c5c85cecf76f5c9067342cc *man/result-builders-unified.Rd
e0597dd53bc1819a4e1953bcc27d7877 *man/run-fb4-orchestrator.Rd
543301d1ae0a8f8d0ffb0690f333885d *man/run_fb4.Bioenergetic.Rd
22dc711899ac8fe6ed0d4e7595775913 *man/run_fb4.Rd
01a202c3bfb3adf4312cdfa9c958d9f5 *man/run_fb4_direct_method.Rd
7d22084d11b86597dc4a924cacf100c1 *man/run_fb4_simulation.Rd
5e28420aaec43ac1d301dae9701923ae *man/run_final_simulation.Rd
46a9a16fc02329fe9e07578e1010a42c *man/run_robust_optimization.Rd
06ce069323c1f0bc587e8c15a3503917 *man/run_single_optimization.Rd
b44b811237e447cb25ed3a3e67dd2107 *man/safe_exp.Rd
77a2669db181424674053fc126977a9c *man/safe_extract_param.Rd
b3d8c830d8dbd4b594dab07a255fdb7e *man/safe_sqrt.Rd
4baa9232de377cf5464e1efb782ea6b0 *man/sdr_assign_scalars.Rd
a3bbe860864276d1018564a0e778443a *man/sdr_pull_est.Rd
0cbcc52d1cc7306a65af3d17af76d705 *man/sdr_pull_se.Rd
d52878bec447779e85f1e4cc3bb3ebed *man/sdr_pull_vec.Rd
11d73f73fbb41ad11b038e7f9608c9ef *man/set_diet.Rd
f523405ab82ff6b70c302812b430b6b0 *man/set_environment.Rd
69b17b5df6c9570514bdb81b703d11d3 *man/set_parameter_value.Rd
daba86a09707d57e2432810ed5bc7d47 *man/set_simulation_settings.Rd
6b4094443b6d3ed6153506bd7f6f2790 *man/setup_plot_layout.Rd
2ab331c57921eab200ee952d994ccd29 *man/setup_save_device.Rd
0432a5af273ef8617d4fc8c6bd71ae0c *man/should_mark_as_fitted.Rd
462ccb66755e5486a6f4f8f9a7ed34d0 *man/simulation-engine.Rd
f83264b816101c2069ce8a62388fc516 *man/solve_weight_iterative.Rd
80b9bf08ff5d053448a095397fdef9b3 *man/solve_weight_linear_segments.Rd
942274ba0c344d5a96c3f6254c9aecbc *man/solve_weight_power_function.Rd
159663f4a6541c7b0ac5001c6c232a82 *man/strategy-binary-search.Rd
2b56fa0a24e3259e79156839cfde5e70 *man/strategy-bootstrap.Rd
9ed51644af26d614a2ee6f0951a9109a *man/strategy-commons.Rd
3ce0896b4a4ae3bb30fc083bdb38fcee *man/strategy-direct.Rd
6766e7bb6d1d31a183656233f3ac14fc *man/strategy-hierarchical.Rd
593b3d259e4feb711d94b221b315e278 *man/strategy-interface.Rd
4804065d7b0cd444465f83b7f7a39d2f *man/strategy-mle.Rd
a53ed7a6281e5e2103cd137718a0c3e9 *man/strategy-optim.Rd
49a407e89e20482b98da206738e88ab1 *man/summary.Bioenergetic.Rd
b30a3494a5e71b0390f8cd4a3ec1b62f *man/summary.fb4_result.Rd
e8fa87c56dd9bd62728f35baf0526268 *man/test_metric_differences.Rd
d20798536f73271302b00969716a341e *man/transform_to_tmb_basic.Rd
ae458bdc32886d826812894fc03cf6c8 *man/transform_to_tmb_hierarchical.Rd
05b4f37b47a2f6eaed891bab77b7d521 *man/uncertainty-prediction.Rd
c3611371a82784a68fbcb33923d314f9 *man/update_body_composition.Rd
a67dea509bb073a13677df3dc936f153 *man/utils.Rd
56d80d5519cb5790cac31f54f6c36f04 *man/validate_backend_compatibility.Rd
ede880c4ea0bc90a71a4f7bcdddb17d3 *man/validate_basic_params.Rd
7f2caa2f58e66232d0a040eb24fb3ff5 *man/validate_bioenergetic_for_simulation.Rd
ba7b98d2af613d01bebbc2ac1e82c3f5 *man/validate_body_composition.Rd
dffebbfb3da0e02684d6471b9c028655 *man/validate_category_equation.Rd
62f4d51288026f5e54e6972f21a3b278 *man/validate_common_strategy_inputs.Rd
2c9a02b9b9a6e49fae12dd41c7434f2e *man/validate_complete_simulation_data.Rd
89f4eea1123d8bd83bb311853f14ffdc *man/validate_contaminant_params.Rd
108c6b63d394c648262aa7392aa0c533 *man/validate_data_consistency.Rd
8927c6394ee4e6176d9e77a13d5ffeef *man/validate_diet_consistency.Rd
9096b679751742a2559b9116cc449fa5 *man/validate_equation_params.Rd
050d88ece2551981ddad3c1fdc8fb55c *man/validate_fb4_inputs.Rd
fd51cb4297d9be06512fc653b48c65bc *man/validate_fb4_result.Rd
bc45bd4dfc1c9aa699ff358cee34f935 *man/validate_fb4_system.Rd
95663b8efed7583c5552317c712c3676 *man/validate_fit_to_strategy_concordance.Rd
3b946d90a2b6dc351a85f1c5c277f81c *man/validate_fitting_settings.Rd
aced01bd9f0bfe8789db6bf9e58ff737 *man/validate_fraction.Rd
35753c87df67fb86130d1ca374e71695 *man/validate_individual_data.Rd
0d5703c084478d31dbf371f92c6a4ed5 *man/validate_numeric_core.Rd
e23819f8d1a814cabcea1e6e331b5114 *man/validate_nutrient_concentrations.Rd
47c7dfb193d5908d24ec488fdbee4546 *man/validate_parameter_ranges.Rd
892f716a8a5a3ab7fb09cc5e271ac78a *man/validate_plot_data.Rd
346d6c97c10bac80cd90c97a3fb5839f *man/validate_positive.Rd
597fd53352121217a1cfc0ecdf7dce1b *man/validate_predator_energy_params.Rd
8c76ee017612ae308ea6d9bd44fe093b *man/validate_predator_requirements.Rd
b22a9daea9b2a664100ffe83548f07e3 *man/validate_range_core.Rd
25a0df24057b7d086806263c5660c0f1 *man/validate_respiration_requirements.Rd
31b9b23da849496c9d8a39388797e491 *man/validate_species_equations.Rd
dc8b30b3d14cbab4554facdd872eebfe *man/validate_statistical_method_inputs.Rd
654d7bfd069d454996886b8ff6a776aa *man/validate_structure_core.Rd
54ba226750435cd09d48bf350b55fb60 *man/validate_temperature.Rd
777509fafd930ca887cbd1ddc7eb5a84 *man/validate_temporal_data.Rd
6a90f76d6d71a3507932da7666313f4f *man/validate_time_series_data.Rd
75daa7b81d182bd72c03366a0511bcd8 *man/validate_tmb_objective.Rd
25c751330bb6a1bdf25fc716aa2f5765 *man/validation_result.Rd
1398a7d0ec478bb81ed22e28435322d0 *src/Makevars
61eaedfc8af086d29fbcbc6e88e66e97 *src/Makevars.win
743a23c8e7c731473876363294f1ca0d *src/fb4_main.cpp
6ca83e5b77af34a99680b5cb1dc7bd99 *src/includes/fb4_body_composition.hpp
daf3d8404bb9fe7343ec9b5e01650936 *src/includes/fb4_consumption.hpp
27a556502d20316da7f55a21f4bd9860 *src/includes/fb4_contaminant_accumulation.hpp
b135723204f13b5a28d7e8dd0c483e88 *src/includes/fb4_egestion_excretion.hpp
230b47c36516299f39f81aef56a5681e *src/includes/fb4_mortality_reproduction.hpp
67e4024439cc8c664af40af1d4bf90e9 *src/includes/fb4_nutrient_regeneration.hpp
30c850ee852a9401ac370c82291b81d6 *src/includes/fb4_predator_energy.hpp
cfd2d056c433b0373c199653a21690b0 *src/includes/fb4_respiration.hpp
52bf48e17d9899de63ef0df794ed7522 *src/includes/fb4_utils.hpp
c9edbab76f322dd3302a563db2e612cc *src/includes/fb4_validation.hpp
363b7cdf45e332dcc2c2121258ca96e2 *src/init.c
332173f20d20942c02019350ea4dcadc *tests/spelling.R
9a306bc10ea72f80b4b32100019757d2 *tests/testthat.R
5cce9f134be9fc8c6527efe15d22cd81 *tests/testthat/helper-setup.R
a8d26b7e8c338fa34bac56a946b3e766 *tests/testthat/test-01-consumption.R
7d8a5d7eb0cc37f9a3aaf02d22c64571 *tests/testthat/test-02-respiration.R
46a26e59380fbd9044eeef2c8fb7bfd2 *tests/testthat/test-03-egestion-excretion.R
e0965c8d936bc9d57300238975f5ac7b *tests/testthat/test-12-simulation.R
1270782b791ee8b98eae241b9e8a221c *tests/testthat/test-14-strategies.R
9b946937e6eafa4dd5bf939f00ec00e0 *tests/testthat/test-14b-strategies-mle-hierarchical.R
0c363e47a87cef82502fc65be8dffffc *tests/testthat/test-15-analysis.R
e0389533a8216b9cb79c2a42ff69e624 *vignettes/fb4-case-study-chinook.Rmd
cf7ab0fbed1a2203c7dbd3488c0de405 *vignettes/fb4-introduction.Rmd
6484822a7f0a9bb1ea19878bc3071686 *vignettes/fb4-species-database.Rmd
d3b0c9b6e4ee03de5e459761199205b8 *vignettes/fb4-statistical-estimation.Rmd
1602e44f0f79a2efeaefc3f687bcb3ea *vignettes/fb4-temperature-climate.Rmd
