recoverySim: Recovery simulator

In TESA-workshops/TESAsamSim: Closed-loop salmon simulator for 2021 TESA workshop

Description

Closed-loop simulation tool to assess management procedures and inform Pacific salmon rebuilding strategies. Originally based on C. Holt's south coast chum model (CSAS 2018). Simulation runs primed with observed SR data (recDat input). The model includes data generation, variation in age structure, survey design, and variable exploitation rules. OM uses Ricker formulation R=S(exp(a-bS)). Additional details in changesToChumModel.md in reports directory.

Usage

recoverySim(
  simPar,
  cuPar,
  catchDat = NULL,
  srDat = NULL,
  variableCU = FALSE,
  makeSubDirs = TRUE,
  ricPars,
  larkPars = NULL,
  tamFRP = NULL,
  cuCustomCorrMat = NULL,
  erCorrMat = NULL,
  dirName,
  nTrials = 100,
  uniqueProd = TRUE,
  random = FALSE
)

Arguments

simPar	Simulation parameters.
cuPar	CU (Conservation Unit) parameters.
catchDat	Historical catch data.
srDat	Historical stock-recruitment data.
variableCU	A logical to determine if CU name should be included in output labels.
makeSubDirs	Should sub-directories by made for outputs?
ricPars	Ricker stock-recruitment parameters.
larkPars	Larkin stock-recruitment parameters.
tamFRP	Fisheries Reference Points for the Total Allowable Mortality rule used for Fraser River Sockeye Salmon.
cuCustomCorrMat	Custom correlation matrix for recruitment residuals.
erCorrMat	Correlation matrix for exploitaion rates.
dirName	Name of directory for outputs.
nTrials	Number of Monte Carlo trials.
uniqueProd	Should all CUs have unique productivities?
random	Should all trials start with a random seed?

TESA-workshops/TESAsamSim documentation built on Feb. 6, 2021, 12:25 a.m.