simfish: 'simfish' simulates codys fishery
In DanOvando/simfish_package: Simulate a Fishery and Data

Description Usage Arguments Value

View source: R/simfish.R

simfish simulates codys fishery

simfish(Nsim = 1, SimYear = 50, depletion = 0, CatchShareN = 1,
  CalcFMSY = 0, SmallNum = 1e-04, InitSmooth = 3, FmortPen = 3,
  RecruitPen = 3, CatchCVn = 0.01, CatchCVs = 0.01, IndexCVn = 0.05,
  IndexCVs = 0.05, LenSampleN = 200, LenSampleS = 200, GrowthSDn = 20,
  GrowthSDs = 20, surv50n = 90, surv95n = 150, surv50s = 90,
  surv95s = 150, MaxAge = 30, NatMn = 0.2, NatMs = 0.2, VonKn = 0.2,
  VonKs = 0.2, LinfN = 300, LinfS = 300, t0n = 0.9, t0s = 0.9,
  mat50n = 6, mat50s = 6, mat95n = 8, mat95s = 8, alphaN = 1.7e-06,
  betaN = 3, alphaS = 1.7e-06, betaS = 3, MaxMovingN = 0,
  MaxMovingS = 0, Move50n = 6, Move50s = 6, Move95n = 10,
  Move95s = 10, steepnessN = 0.7, steepnessS = 0.7, sigmaRn = 0.001,
  sigmaRs = 0.001, RzeroN = 1e+05, RzeroS = 1e+05, sel50n = 190,
  sel50s = 190, sel95n = 225, sel95s = 225, HarvestControl = 3,
  HistoricalF = 0.3, ConstantCatch = 0, ConstantF = 0.1, HCalpha = 0.05,
  HCbeta = 0.5)

`Nsim`	number of simulations
`SimYear`	number of years to run simulation
`depletion`	target depletion
`CatchShareN`	share of the catch in the north parth
`CalcFMSY`	1 or 0 to calculate Fmsy doesn't work now
`SmallNum`	constant to add to zeros
`InitSmooth`	no idea
`FmortPen`	no idea
`RecruitPen`	no idea
`CatchCVn`	CV of the catch in the north
`CatchCVs`	CV of the catch in the south
`IndexCVn`	CV of the survey index in the north
`IndexCVs`	CV of the survey index in the south
`LenSampleN`	number of lengths samples in the north
`LenSampleS`	number of length samples in the south
`GrowthSDn`	growth standard deviation in the north
`GrowthSDs`	growth standard deviation in the south
`surv50n`	lower survey selectivity in the north
`surv95n`	upper survey selectivity in the north
`surv50s`	lower survey selectivity in the south
`surv95s`	upper survey selectivity in the south
`MaxAge`	maximum age of the species
`NatMn`	natural mortality in the north
`NatMs`	natural mortality in the south
`VonKn`	von bert k in the north
`VonKs`	von bert k in the south
`LinfN`	linfinity in the north
`LinfS`	linfinity in the south
`t0n`	t0 in the north
`t0s`	t0 in the south
`mat50n`	lower maturity in the north
`mat50s`	lower maturity in the south
`mat95n`	upper maturity in the north
`mat95s`	upper maturity in the north
`alphaN`	alpha of weight function in the north
`betaN`	beta of weight function in the north
`alphaS`	alpha of weight function in the south
`betaS`	beta of weight function in the south
`MaxMovingN`	maximum moving numbers I think in the north
`MaxMovingS`	maximum moving numbers I think in the south
`Move50n`	lower movement ogive north
`Move50s`	lower movement ogive south
`Move95n`	upper movement ogive north
`Move95s`	upper movement ogive south
`steepnessN`	recruitment steepness in the north
`steepnessS`	recruitment steepness in the south
`sigmaRn`	recruitment deviations in the north
`sigmaRs`	recruitment deviations in the south
`RzeroN`	eq recruitment in the north
`RzeroS`	eq recruitment in the south
`sel50n`	lower fishing selectivity ogive in the north
`sel50s`	lower fishing selectivity ogive in the south
`sel95n`	upper fishing selectivity ogive in the north
`sel95s`	upper fishing selectivity ogive in the south
`HarvestControl`	no idea
`HistoricalF`	historical pattern of fishing mortality
`ConstantCatch`	no idea
`ConstantF`	no idea
`HCalpha`	no idea
`HCbeta`	mo idea