Function reference • fallRunDSM

Life Cycle Model and Model Parameters The fall run life cycle model and it’s parameters
`fall_run_model()`	Fall Run Chinook Model
`params` `params_2019` `params_2022` `r_to_r_baseline_params` `r_to_r_kitchen_sink_params`	Model Parameters
Survival Sub-models Functions that calculate survival
`surv_adult_enroute()`	Adult En Route Survival
`apply_enroute_survival()`	Apply enroute survival to adult salmon
`surv_adult_prespawn()`	Adult Prespawn Survival
`surv_egg_to_fry()`	Egg to Fry Survival
`surv_juv_bypass()`	Juvenile Bypass Survival
`surv_juv_delta()`	Juvenile Delta Survival
`surv_juv_outmigration_delta()`	Juvenile Delta Outmigration Survival
`surv_juv_outmigration_sac()`	Juvenile Mainstem Sacramento Outmigration Survival
`surv_juv_outmigration_san_joaquin()`	Juvenile San Joaquin Outmigration Survival
`surv_juv_rear()`	Juvenile Rearing Survival
`spawn_success()`	Spawning Success
`ocean_entry_success()`	Ocean Entry Success
Growth and Movement Sub-models Functions that calculate growth and movement
`adult_stray()`	Adult Straying
`apply_straying()`	Apply Straying
`compute_adult_stray_rates()`	Adult Straying for Hatchery Origin Fish
`stray_returning_adults()`	Apply Straying to Returning Adults
`harvest_adults()`	Harvest Adults Function
`juvenile_month_dynamic()`	Juvenile Month Dynamics
`pulse_movement()`	Juvenile Pulse Movement
`snow_globe_movement()` `genetic_movement()`	Fry fish movement out of natal tributaries
`temperature_movement()`	Temperature Movement
`time_movement()`	Time Movmenet
`fill_natal()` `fill_regional()` `fill_natal_dens_depend()`	Filling Natal Tributary and Regional Habitat
`fill_regional_dens_depend()`	Fill Regional - Density Dependent Fill Hypothesis
`route()`	Route Natal Streams
`route_and_rear_deltas()`	Route and Rear in the Deltas
`route_bypass()`	Route Bypass
`route_regional()`	Route Regions
`route_to_south_delta()`	Route To South Delta
`growth()`	Growth Transition Probability
`growth_floodplain()`	Floodplain Growth Transition Probability
`rear()`	Rearing Function
`migrate()`	Juvenile Migration
`ocean_transition_month()`	Ocean Transition Month
`bioenergetics_transitions`	Bioenergetics Transistion Matrices
`get_growth_rates()`	Get Growth Rates
Datasets Data used by the lifecycle model
`adult_seeds`	Adult Seeds
`adult_harvest_rate`	Adult Harvest Rate
`cross_channel_stray_rate`	Cross Channel Stray Rate
`growth_rates_inchannel` `growth_rates_floodplain`	Growth Rates
`hatchery_allocation`	Hatchery Allocation
`diversity_group`	Diversity Groups
`mass_by_size_class`	Mass by Size Class
`month_return_proportions`	Month Return Proportions
`natural_adult_removal_rate`	Natural Spawners Removal Rate
`proportion_hatchery`	Proportion Hatchery
`stray_rate`	Stray Rate
`hatchery_release_proportion_bay`	Bay Proportion Hatchery Releases
`hatchery_stray_betareg`	Hatchery Stray Model
`hatchery_to_bay_distance`	Hatchery to Chipps Island (rkm)
`prey_density`	Prey Density Vector defining prey density level ("low", "med", "hi", "max") by watershed
`prey_density_delta`	Prey Density Delta Vector defining prey density level ("low", "med", "hi", "max") for North and South Delta
`straying_destinations`	Straying Destinations
`fall_hatchery_release`	Fall Hatchery Release
`hatchery_releases_at_chipps`	Hatchery Release at Chipps
`fecundity_by_age`	Fecundity Lookup
`r2r_adult_harvest_rate`	Adult Harvest Rate
Wrapper and Helper Functions Convenience functions that call multiple sub-models or are used within submodels.
`get_habitat()`	Get habitat Values
`get_rearing_survival()`	Get Rearing Survival Rates
`get_migratory_survival()`	Get Migratory Survival Rates
`territory_by_size()`	Territory Size Requirement
`gamma_MOM()`	Method of Moments Gamma Parameter Estimation
`days_in_month()`	Days in Month
`pretty_num()`	Pretty Number

Reference

Life Cycle Model and Model Parameters

Survival Sub-models

Growth and Movement Sub-models

Datasets

Wrapper and Helper Functions