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salmonMSE (version 0.1.0)

make_Harvest_MMP: Internal salmonMSE functions for converting operating model inputs and outputs

Description

  • SOM2MOM() converts a salmon operating model (SOM) to a multi-stock operating model (MSEtool::MOM)

  • make_Stock() creates the MSEtool::Stock object (openMSE) corresponding to salmon life stage

  • make_Fleet() creates the MSEtool::Fleet object (openMSE) corresponding to the fishery that interacts with the various salmon life stages

  • multiHist2SHist() converts the openMSE historical reconstruction into a salmon Hist object (SHist)

  • MMSE2SMSE() converts the openMSE projection output, along with additional state variables recorded in salmonMSE_env, into a salmon MSE object (SMSE)

  • make_Harvest_MMP() creates a multi-stock management procedure for the harvest component of the operating model by specifying exploitation rates through updating the formal arguments for Harvest_MMP()

salmonMSE() is the wrapper function that coordinates the simulation and the output.

Usage

make_Harvest_MMP(SOM, check = TRUE)
MMSE2SMSE(MMSE, SOM, Harvest_MMP, N, stateN, Ford, H, stateH)
SOM2MOM(SOM, check = TRUE)
make_Stock(
  SOM,
  s = 1,
  g = 1,
  r = 1,
  NOS = TRUE,
  stage = c("immature", "return", "escapement")
)
make_Fleet(SOM, s, NOS = TRUE, stage = c("immature", "return", "escapement"))
multiHist2SHist(multiHist, SOM, check = TRUE)

Value

make_Harvest_MMP: Function of class "MMP" by updating the formal arguments for Harvest_MMP()

MMSE2SMSE: SMSE object

SOM2MOM: MSEtool::MOM object

make_Stock: List containing a MSEtool::Stock object and accompanying custom parameters list

make_Stock: List containing a MSEtool::Fleet object and accompanying custom parameters list

multiHist2SHist: SHist object

Arguments

SOM

An object of class SOM

check

Logical, whether to check the SOM object using check_SOM()

MMSE

Object of class MSEtool::MMSE returned from MSEtool

Harvest_MMP

Optional harvest function created by make_Harvest_MMP()

N

Data frame of natural origin abundance at age saved in the salmonMSE_env environment during the simulation

stateN

Data frame of natural origin state variables saved in the salmonMSE_env environment during the simulation

Ford

Data frame of phenotypic trait values saved in the salmonMSE_env environment during the simulation

H

Data frame of hatchery origin abundance at age saved in the salmonMSE_env environment during the simulation

stateH

Data frame of hatchery origin state variables saved in the salmonMSE_env environment during the simulation

s

Integer, the population integer for which to create the Stock or Fleet object

g

Integer, the life history group for which to create the Stock object. Not relevant if NOS = FALSE

r

Integer, the hatchery release group for which to create the Stock object. Not relevant if NOS = TRUE

NOS

Logical, whether the Stock or Fleet object corresponds to natural origin or hatchery origin fish

stage

Character indicating the corresponding salmon life stage of the Stock or Fleet object

multiHist

Class multiHist object returned from MSEtool