Harvest_MMP: Harvest component of operating model

Description

A function used by openMSE to specify the fishing effort during the projections. salmonMSE updates the arguments of this function from the salmon operating model.

Usage

Harvest_MMP(
  x = 1,
  DataList,
  reps = 1,
  u_terminal,
  u_preterminal,
  K_PT,
  K_T,
  type_PT = "u",
  type_T = "u",
  MSF_PT = FALSE,
  MSF_T = FALSE,
  m,
  release_mort,
  p_terminal = c(2, 5),
  p_preterminal = c(1, 4),
  pkey = data.frame(p = 1:6, s = 1),
  p_natural = 1:3,
  p_hatchery = 4:6,
  ...
)

Value

A nested list of MSEtool::Rec objects, same dimension as DataList

Arguments

x: Simulation number
DataList: A nested list of MSEtool::Data objects by stock then fleet, generated by MSEtool::multiMSE()
reps: The number of stochastic replicates to be returned by the function
u_terminal: Numeric vector by population (s). Harvest rate of retained catch in the terminal fishery
u_preterminal: Single numeric. Harvest rate of retained catch in the pre-terminal fishery
K_PT: Single numeric. Total retained catch in the pre-terminal fishery
K_T: Numeric vector by population (s). Total retained catch in the terminal fishery
type_PT: Single character, containing either "catch" or "u". Indicates whether to manage by harvest rate or total catch numbers for preterminal fisheries
type_T: Character vector by population (s), containing either "catch" or "u". indicates whether to manage by harvest rate or total catch numbers for terminal fisheries
MSF_PT: Single logical, whether to implement mark-selective fishing for the preterminal fishery
MSF_T: Logical vector by population (s), whether to implement mark-selective fishing for the terminal fishery
m: Numeric vector by population (s). Mark rate of hatchery origin fish, as a proxy for fishery retention. Only used to calculate the fishing effort. Retention in the operating model is specified in the MSEtool::MOM object
release_mort: Matrix [2, s]. Release mortality of discarded fish in the pre-terminal (1st row) and terminal (2nd row) fishery. Only used if MSF_PT = TRUE or MSF_T[s] = TRUE. Only used to calculate the fishing effort. Release mortality in the operating model is specified in the MSEtool::MOM object
p_terminal: Numeric vector. Population index (p) for the recruitment that experiences the terminal fishing mortality
p_preterminal: Numeric vector. Population index (p) for immature fish that experience the pre-terminal fishing mortality
pkey: Data frame that assigns openMSE population by life stage and origin (p) to salmonMSE population (s)
p_natural: Numeric vector. Population index (p) for natural origin fish
p_hatchery: Numeric vector. Population index (p) for hatchery origin fish
...: Not used