Model Parameters

A list containing all parameters needed for running the spring_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

Habitat Inputs

Spawning Adults

Egg to Fry Survival

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)

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

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

Yearling Growth

  • yearling_territory_size: yearling territory size by size class. Source: Expert opinion from SIT members.