darwin: Darwinian simulation study

Description Usage Arguments Value Run length

View source: R/darwin.R

Description

Simulates parameters, runs hydra, then determines if simulated parameter set is viable. Essentially filtering out poor simulations Viable sets are saved as rds files in a predetermined folder

Usage

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darwin(
  seed = NULL,
  nYrs,
  hydraD,
  stockRecruitData,
  simulationRules,
  nSims,
  SRFunctionChoice,
  stochasticity = F,
  inputOptions,
  pathToTPL,
  hydraVersion,
  boolPlot = F
)

Arguments

seed

Integer. Set seed for testing or reproducability. Default = NULL

nYrs

Numeric scalar. Total length of simulation. See Run length section below for details

hydraD

List of current base data (as in hydradata::hydradataList)

stockRecruitData

List. Stock recruitment parameter estimates for differnt functional forms (darwinData)

simulationRules

List. Set of rules used in the simulation of parameters (darwinRules)

nSims

Numeric scalar. Number of parameter sets to simulate

SRFunctionChoice

Numeric Vector. An argument of simulate_parameters

stochasticity

Boolean scalar. TRUE if stochasticity is desired (stock recruitment functions in Hydra)

inputOptions

List. Set of input values to determine run type

pathToTPL

String. Path to location of Hydra executable

hydraVersion

String. Name of the Hydra executable

boolPlot.

Boolean. True if plotting of biomass and catch are required. Default = FALSE

Value

List

nSuccesses

Number of simulated parameter sets that pass the biomass and catch criteria. These successful sets will be saved as rds files in the successfulSims folder, located in the project root

nAttempts

Total Number of simulated parameter sets

Run length

Hydra is currently set up to run for 53 years (1964-2016). This is the historic period in which fishing data is available. To extend the run length to nYrs is adding a period of no fishing of length nYrs-53 years to the start of the model run. It is assumed that all populations have reached an equilibrium. This equilibrium is then used as the starting point for the historic portion of the model run.


andybeet/hydramse documentation built on April 16, 2021, 5:23 a.m.