params.Rd
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
r_to_r_kitchen_sink_params
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
rear_decay_rate
: More details at rear_decay_rate
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
stray_rate
: More details at 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
..surv_adult_enroute_int
: Intercept, source: calibration
.adult_stray_intercept
: Empirical model fit using 2008–2011 tagging data provided by East Bay Municipal Utility District
.adult_stray_wild
: Coefficient for wild
variable, source: Estimated with coded wire tag data 2010–2013 (Kormos et al. 2012, Palmer-Zwahlen & Kormos 2013-2015, Palmer-Zwahlen et al. 2018)
.adult_stray_natal_flow
: Coefficient for natal_flow
variable, source: Empirical model fit using 2008–2011 tagging data provided by East Bay Municipal Utility District
.adult_stray_cross_channel_gates_closed
: Coefficient for cross_channel_gates_closed
variable, source: Empirical model fit using 2008–2011 tagging data provided by East Bay Municipal Utility District.
.adult_stray_prop_bay_trans
: Coefficient for prop_bay_trans
variable, source: Estimated with coded wire tag data 2010–2013 (Kormos et al. 2012, Palmer-Zwahlen & Kormos 2013-2015, Palmer-Zwahlen et al. 2018)
.adult_stray_prop_delta_trans
: Coefficient for prop_delta_trans
variable, source: Estimated with coded wire tag data 2010–2013 (Kormos et al. 2012, Palmer-Zwahlen & Kormos 2013-2015, Palmer-Zwahlen et al. 2018)
.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
hatchery_allocation
: More details at hatchery_allocation
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
: Boolean value describing if harvest should be restricted to hatchery fish. 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
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_release
: More details at fall_hatchery_release
hatchery_releases_at_chipps
: More details at hatchery_releases_at_chipps
terminal_hatchery_logic
: Boolean value describing if terminal hatchery exist
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
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
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
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_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
freeport_flows
: More details at freeport_flow
cc_gates_days_closed
: More details at delta_cross_channel_closed
growth_rates
: More details at: growth_rates_inchannel
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
growth_rates
: More details at: growth_rates_inchannel
growth_rates_floodplain
: More details at: growth_rates_floodplain
weeks_flooded
: More details at: weeks_flooded
.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
mass_by_size_class
: More details at mass_by_size_class
diversity_group
: More details at diversity_group