salmonMSE (version 0.1.0)

SAR_fitness: Update natural mortality of juveniles

Description

Internal function that updates juvenile natural mortality in the marine environement due to fitness

• SAR_fitness() calculates the new natural mortality value

• makeRel_SAR generates a list for openMSE to use in the simulations

Usage

SAR_fitness(
  x = -1,
  y = 1,
  envir = c("natural", "hatchery"),
  rel_loss = 1,
  s = 1,
  nyears,
  Mbase
)
makeRel_SAR(
  p_smolt = 1,
  s = 1,
  envir = c("natural", "hatchery"),
  rel_loss,
  nyears,
  Mbase
)

Value

• smolt_func() returns a numeric for the ratio of the realized smolt production vs. the hypothetical value if there were no hatchery, en route mortality, or habitat improvement

• makeRel_smolt returns a list that is passed to openMSE as a inter-population relationship

Arguments

x

Integer, simulation number from openMSE

y

Integer, simulation year (including historical years)

envir

Character, whether to obtain the fitness value for the natural or hatchery environment.

rel_loss

Numeric, the loss exponent for the juveniles

s

Integer, the salmonMSE population index. Used to search for the fitness value

nyears

Integer, the number of historical years in the operating model

Mbase

Array [nsim, n_age, proyears] the base natural mortality value in the openMSE operating model.

p_smolt

Integer, the population index for the juvenile population in the openMSE model