Determines if juveniles stay in the delta or out migrate to golden gate during a simulated month. Then the remaining juveniles in the delta rear (growth and survival rates applied) and survival rates are applied to out migrating juveniles

route_and_rear_deltas(
  year,
  month,
  migrants,
  north_delta_fish,
  south_delta_fish,
  north_delta_habitat,
  south_delta_habitat,
  freeport_flows,
  cc_gates_days_closed,
  rearing_survival_delta,
  migratory_survival_delta,
  migratory_survival_bay_delta,
  juveniles_at_chipps,
  growth_rates,
  location_index = c(rep(1, 24), 3, rep(2, 2), rep(4, 4)),
  territory_size,
  stochastic
)

Source

IP-117068

Arguments

year

The current simulation year, 1-20

month

The current simulation month, 1-8

migrants

An n by 4 matrix of juvenile fish by watershed and size class

north_delta_fish

An n by 4 matrix of juvenile fish by watershed and size class

south_delta_fish

An n by 4 matrix of juvenile fish by watershed and size class

north_delta_habitat

A vector of available habitat in square meters

south_delta_habitat

A vector of available habitat in square meters

freeport_flows

Monthly mean flow at freeport in cubic feet per second

cc_gates_days_closed

Number of days the Cross Channel gates are closed during the month

rearing_survival_delta

The rearing survival rate for North and South Delta

migratory_survival_delta

The outmigration survival rate for North and South Delta

migratory_survival_bay_delta

The outmigration survival rate in the Bay Delta

juveniles_at_chipps

The accumulated juveniles at Chipps Island for the current year

growth_rates

The delta growth rate

location_index

Migratory survival probability location index for fish coming from 4 areas (1-4) representing "northern_fish", "cosumnes_mokelumne_fish", "calaveras_fish", or "southern_fish" respectively

territory_size

Array of juvenile fish territory requirements for fill_natal

stochastic

TRUE FALSE value indicating if model is being run stochastically