runMSE: runMSE

In laurieKell/biodyn: Biomass Dynamic Model

Description

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

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

Usage

runMSE(om, eql, mp, srDev, uDev, ftar = 0.75, fmin = 0.01, blim = 0.8,
  btrig = 0.4, what = "msy", mult = TRUE,
  range = c(range(om)["maxyear"], c(range(om)["maxyear"]) + 30, interval = 3))

mseBiodyn(om, eql, srDev, control, priors, start = range(om)["maxyear"],
  end = start + 30, interval = 3, uDev = 0.2, u = oem, ftar = 0.7,
  btrig = 0.6, fmin = 0.01, blim = 0.01, what = "msy", mult = TRUE,
  bndF = NULL, maxF = 1, phaseQ = 1,
  cmdOps = paste("-maxfn 500 -iprint 0 -est"), omega = 1, refB = 1,
  trendQ = 1 + FLQuant(cumprod(rep(0, end - dims(trendQ)$minyear + 1)),
  dimnames = list(year = dims(trendQ)$minyear:end)))

Arguments

om	an FLStock object
eql	an FLBRP object that holds the biological parameters for use in the projections
mp	an biodyn object that holds the options for the biomass dynamic assessment model
srDev	a FLQuant with recruitment deviates
uDev	an FLQuant or FLQuants with CPUE residuals
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
range	a vector the starting and end years for the projections, and the interval for running the MP
om	an FLStock object
eql	an FLBRP object that holds the biological parameters for use in the projections
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
srDev	a FLQuant with recruitment deviates
uDev	an FLQuant or FLQuants with CPUE residuals
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

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

See Also

biodyn

biodyn

Examples

## Not run: 
sim()
   
## End(Not run)
## Not run: 
sim()
   
## End(Not run)

laurieKell/biodyn documentation built on May 20, 2019, 7:58 p.m.