runMSE: mseBiodyn
In laurieKell/mpb: Management Procedures

mseBiodyn

R Documentation

mseBiodyn

Description

Runs a full MSE using an FLStock object as the Operating Model and biodyn as the Mangement Procedure

Usage

mseBiodyn(
  om,
  eql,
  srDev,
  uDev,
  mp,
  start = range(om)["maxyear"],
  end = start + 30,
  interval = 3,
  oem = oem,
  hcrPar = function(mp, ftar = 0.7, btrig = 0.6, fmin = 0 - 1, blim = 0.001) {    
    hcrParam(ftar = ftar * fmsy(mp), btrig = btrig * bmsy(mp), fmin = fmin * fmsy(mp),
    blim = blim * bmsy(mp)) },
  bndF = NULL,
  bndTac = NULL,
  maxF = 1,
  omega = 1,
  refB = 1,
  qTrend = 0
)

Arguments

`om`	an `FLStock` object
`srDev`	a `FLQuant` with recruitment deviates
`uDev`	an `FLQuant` or `FLQuants` with CPUE residuals
`mp`	an `biodyn` object that holds the options for the biomass dynamic assessment model
`range`	a `vector` the starting and end years for the projections, and the interval for running the MP
`ftar`	a `numeric` with target F in HCR
`fmin`	a `numeric` with minimum F in HCR
`blim`	a `numeric` with biomass limit for HCR
`btrig`	a `numeric` with biomass trigger (i.e. when to reduce F) in HCR
`what`	a `character` that specifies what is to be used for the reference point in the HCR, recycled as required
`mult`	a `logical` that specifies whether quantity in HCR options is a multiplier or probability, recycled as required

Value

a list of data.frames with performance measures from OM and summaries from MP, if con!=NULL will also write to a MYSQL database

Examples

## Not run: 
library(mpb)
library(FLash)
library(FLBRP)

load(om)
load(eql)

om=mpb::fwdWindow(om,eql,end=2030)
om=propagate(om,100)

srDev=FLQuant(0,dimnames=list(year=2000:2030))
srDev=rlnorm(100,srDev,0.3)

om=mpb::fwd(om,catch=catch(om)[,ac(2000:2011)],sr=eql,sr.residuals=srDev)

library(popbio)

mp=mpb::FLBRP2biodyn(  eql,"biodyn")
mp=mpb::FLStock2biodyn(om, "biodyn")

## End(Not run)

laurieKell/mpb documentation built on Sept. 9, 2023, 9:47 p.m.