Model Parameters

A list containing all parameters needed for running the fall_run_model. Parameters with a single period in front are model or submodel coefficients. Parameters with double periods in front of them are calibrated model parameters.

params

params_2019

params_2022

r_to_r_baseline_params

Habitat Inputs

  • spawning_habitat: More details at fr_spawn

  • inchannel_habitat_fry: More details at fr_fry

  • inchannel_habitat_juvenile: More details at fr_juv

  • floodplain_habitat: More details at fr_fp

  • sutter_habitat: More details at sutter_habitat

  • yolo_habitat: More details at yolo_habitat

  • delta_habitat: More details at delta_habitat

  • spawn_decay_rate: More details at spawn_decay_rate

  • spawn_decay_multiplier: More details at spawn_decay_multiplier

  • rear_decay_rate: More details at rear_decay_rate

Spawning Adults

  • prop_flow_natal: More details at proportion_flow_natal

  • south_delta_routed_watersheds: More details at south_delta_routed_watersheds

  • cc_gates_days_closed: More details at delta_cross_channel_closed

  • cross_channel_stray_rate: More details at cross_channel_stray_rate

  • gates_overtopped: More details at gates_overtopped

  • tisdale_bypass_watershed: More details at tisdale_bypass_watershed

  • yolo_bypass_watershed: More details at yolo_bypass_watershed

  • migratory_temperature_proportion_over_20: More details at migratory_temperature_proportion_over_20

  • flows_oct_nov: More details at flows_oct_nov

  • flows_apr_may: More details at flows_apr_may

  • monthly_mean_pdo: More details at monthly_mean_pdo

  • ..surv_adult_enroute_int: Intercept, source: calibration

  • .adult_en_route_migratory_temp: Coefficient for migratory_temp variable, source: Schreck et al. (1994)

  • .adult_en_route_bypass_overtopped: Coefficient for bypass_overtopped variable, source: Expert opinion Ted Sommer, California Department of Water Resources (tributaries above bypasses only)

  • .adult_en_route_adult_harvest_rate: Adult harvest rate, source: (Palmer-Zwahlen & Kormos 2013-2015, Palmer-Zwahlen et al. 2018)

  • degree_days: More details at degree_days

  • month_return_proportions: More details at month_return_proportions

  • ..surv_adult_prespawn_int: Intercept, source: Calibration Estimate

  • .adult_prespawn_deg_day: Coefficient for deg_day variable, source: Colvin et al. (2018)

  • prob_nest_scoured: More details at prob_nest_scoured

  • spawn_success_sex_ratio: Variable describing the female to male spawning ratio, default 0.5, source: expert opinion from SIT members.

  • spawn_success_redd_size: Variable describing the size of redds including defensible space, default value 9.29 square meters, source: expert opinion from SIT members.

  • spawn_success_fecundity: Variable describing the number of eggs per female, default value 5522, source: Moyle, P. B. 2002. Inland Fishes of California. University of California Press, Berkeley CA

  • fecundity_lookup: More details at fecundity_by_age

  • hatchery_release: More details at fall_hatchery_release

  • natural_adult_removal_rate: More details at natural_adult_removal_rate

  • adult_harvest_rate: More details at r2r_adult_harvest_rate

  • restrict_harvest_to_hatchery_ocean: Boolean value describing if harvest should be restricted to hatchery fish in the ocean. Defaults to FALSE

  • restrict_harvest_to_hatchery_trib: Boolean value describing if harvest should be restricted to hatchery fish in tributaries. Defaults to FALSE

  • ocean_harvest_percentage: Numeric value describing the proportion of ocean fish that are harvested. Defaults to .5 based on Table II-1

  • tributary_harvest_percentage: Numeric value describing the proportion of in-river fish that are harvested. Quantities vary by tributary as described by Table II-1

  • no_cohort_harvest_years: Vector listing cohort of fish with restricted harvest.

  • intelligent_crr_harvest: Boolean value describing if harvest should be restricted to limit quantities based on cohort replacement rate. Defaults to FALSE

  • intelligent_habitat_harvest: Boolean value describing if harvest should be restricted to limit quantities based on habitat. Defaults to FALSE

  • preserve_tribal_harvest: Boolean value describing if tribal in river harvest should be preserved. Defaults to FALSE

Egg to Fry Survival

  • proportion_hatchery: More details at proportion_hatchery

  • prob_nest_scoured: More details at prob_nest_scoured

  • mean_egg_temp_effect: More details at egg_temperature_effect

  • .surv_egg_to_fry_proportion_natural: Coefficient for proportion_natural variable, source: Chilcote et al. 2011

  • .surv_egg_to_fry_scour: Coefficient for scour variable, source: Montgomery et al. 1996

  • ..surv_egg_to_fry_int: Intercept, source: Calibration

Hatchery Releases

Tributary Rearing Survival

  • avg_temp: More details at stream_temperature

  • prob_strand_early: More details at prob_strand_early

  • prob_strand_late: More details at prob_strand_late

  • proportion_diverted: More details at proportion_diverted

  • total_diverted: More details at total_diverted

  • weeks_flooded: More details at weeks_flooded

  • prop_high_predation: More details at prop_high_predation

  • contact_points: More details at contact_points

  • ..surv_juv_rear_int: Intercept, source: calibration (varies by tributary)

  • .surv_juv_rear_contact_points: Coefficient for contact_points variable, source: inherited from previous calibration

  • ..surv_juv_rear_contact_points: Coefficient for contact_points variable, source: calibration

  • .surv_juv_rear_prop_diversions: Coefficient for prop_diversions variable, source: Newman and Brandes 2010

  • ..surv_juv_rear_prop_diversions: Coefficient for prop_diversions variable, source: calibration

  • .surv_juv_rear_total_diversions: Coefficient for total_diversions variable, source: inherited from previous calibration

  • ..surv_juv_rear_total_diversions: Coefficient for total_diversions variable, source: calibration

  • .surv_juv_rear_avg_temp_thresh: Coefficient for avg_temp_thresh variable, source: Runge et al 2008

  • .surv_juv_rear_high_predation: Coefficient for high_predation variable, source: Cavallo et al. 2012

  • .surv_juv_rear_stranded: Coefficient for stranded variable, source: USFWS 2006 and CDWR 2006

  • .surv_juv_rear_medium: Size related intercept for medium sized fish, source: Connor et al. 2004

  • .surv_juv_rear_large: Size related intercept for large sized fish, source: Connor et al. 2004

  • .surv_juv_rear_floodplain: Additional intercept for floodplain rearing benefit, source: Sommer et al. (2001)

  • prey_density: More details at prey_density

  • prey_density_delta: More details at prey_density_delta

Bypass Rearing Survival

  • avg_temp: See Tributary Rearing Survival avg_temp above

  • prop_high_predation: See Tributary Rearing Survival prop_high_predation above

  • ..surv_juv_bypass_int: Intercept, source: calibration

  • .surv_juv_bypass_avg_temp_thresh: Coefficient for avg_temp_thresh variable, source: Marine and Chech 2004

  • .surv_juv_bypass_high_predation: Coefficient for high_predation variable, source: Cavallo et al. 2012

  • .surv_juv_bypass_medium: Size related intercept for medium sized fish, source: Connor et al. 2004

  • .surv_juv_bypass_large: Size related intercept for large sized fish, source: Connor et al. 2004

  • .surv_juv_bypass_floodplain: Additional intercept for floodplain rearing benefit, source: Sommer et al. 2001

Delta Rearing Survival

  • avg_temp_delta: More details at delta_temperature

  • delta_proportion_diverted: More details at delta_proportion_diverted

  • delta_total_diverted: More details at delta_total_diverted

  • delta_contact_points: More details at delta_contact_points

  • delta_prop_high_predation: More details at delta_prop_high_predation

  • ..surv_juv_delta_int: Intercept, source: calibration

  • .surv_juv_delta_contact_points: Coefficient for contact_points variable, source: inherited from previous calibration

  • ..surv_juv_delta_contact_points: Coefficient for contact_points variable, source: calibration

  • .surv_juv_delta_total_diverted: Coefficient for total_diversions variable, source: inherited from previous calibration

  • ..surv_juv_delta_total_diverted: Coefficient for total_diversions variable, source: calibration

  • .surv_juv_delta_avg_temp_thresh: Coefficient for avg_temp_thresh variable, source: Marine and Chech 2004

  • .surv_juv_delta_high_predation: Coefficient for high_predation variable, source: Cavallo et al. 2012

  • .surv_juv_delta_prop_diverted: Coefficient for prop_diversions variable, source: Newman and Brandes 2010

  • .surv_juv_delta_medium: Size related intercept for medium sized fish, source: Connor et al. 2004

  • .surv_juv_delta_large: Size related intercept for large sized fish, source: Connor et al. 2004

Tributary Migratory Survival

  • cc_gates_prop_days_closed: More details at delta_cross_channel_closed

  • upper_sacramento_flows: More details at upper_sacramento_flows

  • freeport_flows: More details at freeport_flow

  • vernalis_flows: More details at vernalis_flow

  • stockton_flows: More details at stockton_flow

  • vernalis_temps: More details at vernalis_temperature

  • prisoners_point_temps: More details at prisoners_point_temperature

  • CVP_exports: More details at cvp_exports

  • SWP_exports: More details at swp_exports

  • ..surv_juv_outmigration_sj_int Intercept, source: calibration

  • .surv_juv_outmigration_san_joquin_medium Size related intercept for medium sized fish, source: Connor et al. 2004

  • .surv_juv_outmigration_san_joaquin_large Size related intercept for large sized fish, source: Connor et al. 2004

  • min_survival_rate Estimated survival rate if temperature threshold is exceeded, source: expert opinion

  • avg_temp: More details at stream_temperature

Delta Migratory Survival

  • delta_inflow: More details at delta_inflow

  • avg_temp_delta: More details at delta_temperature

  • delta_proportion_diverted: More details at delta_proportion_diverted

  • .surv_juv_outmigration_sac_delta_intercept_one Intercept for model one, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_intercept_two Intercept for model two, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_intercept_three Intercept for model three, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_delta_flow Coefficient for delta_flow variable, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_avg_temp Coefficient for avg_temp variable, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_perc_diversions Coefficient for perc_diversions variable, source: this parameter and function have been deprecated and its documentation is for archival purposes.

  • .surv_juv_outmigration_sac_delta_medium Size related intercept for medium sized fish, source: Connor et al. 2004

  • .surv_juv_outmigration_sac_delta_large Size related intercept for large sized fish, source: Connor et al. 2004

Delta Routing and Rearing

Tributary Routing

  • prop_pulse_flows: More details at proportion_pulse_flows

  • proportion_flow_bypass: More details at proportion_flow_bypasses

  • .pulse_movement_intercept: Intercept, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_proportion_pulse: Coefficient for proportion_pulse variable, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_medium: Size related intercept for medium sized fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_large: Size related intercept for large sized fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_vlarge: Size related intercept for very large sized fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_medium_pulse: Additional coefficient for proportion_pulse variable for medium size fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_large_pulse: Additional coefficient for proportion_pulse variable for large size fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • .pulse_movement_very_large_pulse: Additional coefficient for proportion_pulse variable for very large size fish, source: Empirical model fit to CVPIA Chinook salmon screw trap abundance estimates from American River, Stanislaus River, Feather River, Mokelumne River, Sacramento River, Tuolumne River, Clear Creek 2008–2015.

  • territory_size: More details at territory_by_size

Tributary Rearing

Ocean Entry Success

  • .ocean_entry_success_length: Size related intercept representing the fork lengths for each size classes, source: Satterthwaite et al.2014

  • ..ocean_entry_success_int: Intercept, source: Calibration (Varies by tributary)

  • .ocean_entry_success_months: Coefficient for month variable, source: Satterthwaite et al.2014

Generating Model Outputs