fitness_func: Calculate mean phenotype and fitness

In salmonMSE: Management Strategy Evaluation for Salmon Species

Calculate mean phenotype and fitness

Description

Quantitative genetics model of mean phenotypic trait and fitness of next brood year.

calc_zbar() is the internal function that calculates mean phenotype.

Usage

fitness_func(
  Egg_NOS,
  Egg_HOS,
  Egg_NOB,
  Egg_HOB,
  zbar_brood,
  fitness_args = list()
)

calc_zbar(
  Egg_NOS,
  Egg_HOS,
  Egg_NOB,
  Egg_HOB,
  zbar_prev,
  fitness_variance,
  theta,
  phenotype_variance,
  heritability
)

Arguments

Egg_NOS	Numeric, egg production by natural-origin spawners
Egg_HOS	Numeric, egg production by hatchery-origin brood
Egg_NOB	Numeric, egg production by natural-origin brood
fitness_args	List, containing fitness_variance, theta, phenotype_variance, heritability, rel_loss, and fitness_floor
zbar_prev	Numeric, mean phenotype of parents
fitness_variance	Numeric, variance (omega-squared) of the fitness function
theta	Numeric length 2, optimum phenotype value for the natural and hatchery environments, respectively.
phenotype_variance	Numeric, variance (sigma-squared) of the phenotypic trait (theta)
heritability	Numeric, heritability (h-squared) of the phenotypic trait

Value

fitness_func returns a list:

• zbar Numeric length 2, mean phenotype of next generation to natural zbar[1] and hatchery zbar[2] environments

• fitness Numeric length 2, fitness of next generation to natural and hatchery environments

• fitness_loss Matrix ⁠[2, 3]⁠ penalty in survival of next generation due to fitness effects

calc_zbar returns numeric length 2, mean phenotype of next generation

salmonMSE documentation built on Aug. 20, 2026, 5:09 p.m.