route_and_rear_deltas: Route and Rear in the Deltas
In CVPIA-OSC/lateFallRunDSM: Structured Decision Fall Run Model for CVPIA

route_and_rear_deltas

R Documentation

Route and Rear in the Deltas

Description

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

Usage

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
)

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
`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
`freeport_flow`	Monthly mean flow at freeport in cubic feet per second
`cc_gates_closed`	Number of days the Cross Channel gates are closed during the month