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

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