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Function to simulate expected yield using the Beverton-Holt Yield Per Recruit model for single input parameters

Source: R/yprBH_slot_func.R
yprBH_slot_function.Rd

Function to estimate yield using the Beverton-Holt YPR model. This main function accepts only single values for cf, cm, and minlength. Use the wrapper ypr() function for specifying range of cf, cm, and minlength

Usage

yprBH_slot_func(
  recruitmentTL,
  lowerSL,
  upperSL,
  cfunder,
  cfin,
  cfabove,
  cm,
  loi = NULL,
  lhparms,
  matchRicker = FALSE
)

Arguments

recruitmentTL

A numeric representing the minimum length limit for recruiting to the fishery in mm.

lowerSL

A numeric representing the length of the lower slot limit in mm.

upperSL

A numeric representing the length of the upper slot limit in mm.

cfunder

Single value, conditional fishing mortality under the lower slot limit.

cfin

Single value, conditional fishing mortality within the lower and upper slot limit.

cfabove

Single value, conditional fishing mortality over the upper slot limit.

cm

A numeric representing conditional natural mortality

loi

A numeric vector for lengths of interest. Used to determine number of fish that reach desired lengths.

lhparms

A named vector or list that contains values for each N0, tmax, Linf, K, t0, LWalpha, and LWbeta. See makeLH for definitions of these life history parameters. Also see details.

matchRicker

A logical that indicates whether the yield function should match that in Ricker (). Defaults to TRUE. The only reason to changed to FALSE is to try to match output from FAMS. See the "YPR_FAMSvRICKER" article.

Value

the following calculated and input values in a data.frame

  • yieldTotal is the calculated total yield

  • yieldUnder is the calculated yield under the slot limit

  • yieldIn is the calculated yield within the slot limit

  • yieldAbove is the calculated yield above the slot limit

  • nharvTotal is the calculated total number of harvested fish

  • ndieTotal is the calculated total number of fish that die of natural death

  • nharvestUnder is the number of harvested fish under the slot limit

  • nharvestIn is the number of harvested fish within the slot limit

  • nharvestAbove is the number of harvested fish above the slot limit

  • n0die is the number of fish that die of natural death before entering the fishery at a minimum length

  • ndieUnder is the number of fish that die of natural death between entering the fishery and the lower slot limit

  • ndieIn is the number of fish that die of natural deaths within the slot limit

  • ndieAbove is the number of fish that die of natural deaths above the slot limit

  • nrUnder is the number of fish at time trUnder (time they become harvestable size under the slot limit)

  • nrIn is the number of fish at time trIn (time they reach the lower slot limit size)

  • nrAbove is the number of fish at time trAbove (time they reach the upper slot limit size)

  • trUnder is the time for a fish to recruit to a minimum length limit (i.e., time to enter fishery)

  • trIn is the time for a fish to recruit to a lower length limit of the slot limit

  • trOver is the time for a fish to recruit to a upper length limit of the slot limit

  • avglenUnder is the average length of fish harvested under the slot limit

  • avglenIn is the average length of fish harvested within the slot limit

  • avglenAbove is the average length of fish harvested above the slot limit

  • avgwtUnder is the average weight of fish harvested under the slot limit

  • avgwtIn is the average weight of fish harvested within the slot limit

  • avgwtAbove is the average weight of fish harvested above the slot limit

  • nAtxxx is the number that reach the length of interest supplied. There will be one column for each length of interest.

  • cm A numeric representing conditional natural mortality

  • expUnder is the exploitation rate under the slot limit

  • expIn is the exploitation rate within the slot limit

  • expAbove is the exploitation rate above the slot limit

  • FUnder is the estimated instantaneous rate of fishing mortality under the slot limit

  • FIn is the estimated instantaneous rate of fishing mortality within the slot limit

  • FAbove is the estimated instantaneous rate of fishing mortality above the slot limit

  • MUnder is the estimated instantaneous rate of natural mortality under the slot limit

  • MIn is the estimated instantaneous rate of natural mortality within the slot limit

  • MAbove is the estimated instantaneous rate of natural mortality above the slot limit

  • ZUnder is the estimated instantaneous rate of total mortality under the slot limit

  • ZIn is the estimated instantaneous rate of total mortality within the slot limit

  • ZAbove is the estimated instantaneous rate of total mortality above the slot limit

  • SUnder is the estimated total survival under the slot limit

  • SIn is the estimated total survival within the slot limit

  • SAbove is the estimated total survival above the slot limit

  • cfUnder A numeric representing conditional fishing mortality

  • cfIn A numeric representing conditional fishing mortality

  • cfOver A numeric representing conditional fishing mortality

  • recruitmentTL A numeric representing the minimum length limit for recruiting to the fishery in mm.

  • lowerSL A numeric representing the length of the lower slot limit in mm.

  • upperSL A numeric representing the length of the upper slot limit in mm.

  • N0 A numeric representing the initial number of new recruits entering the fishery OR a vector or list that contains named values for each N0, Linf, K, t0, LWalpha, LWbeta, and tmax

  • Linf A numeric representing the point estimate of the asymptotic mean length (L-infinity) from the von Bertalanffy growth model in mm

  • K A numeric representing the point estimate of the Brody growth coefficient from the von Bertalanffy growth model

  • t0 A numeric representing the point estimate of the x-intercept (i.e., theoretical age at a mean length of 0) from the von Bertalanffy growth model

  • LWalpha A numeric representing the point estimate of alpha from the length-weight regression on the log10 scale.

  • LWbeta A numeric representing the point estimate of beta from the length-weight regression on the log10 scale.

  • tmax An integer representing maximum age in the population in years #'

Details

Details will be filled out later

Author

Jason C. Doll, jason.doll@fmarion.edu

Examples

# Life history parameters to be used below
LH <- makeLH(N0=100,tmax=15,Linf=592,K=0.20,t0=-0.3,LWalpha=-5.528,LWbeta=3.273)

# Estimate yield with fixed parameters
Res_1 <- yprBH_slot_func(recruitmentTL=200,lowerSL=250,upperSL=325,
                       cfunder=0.25,cfin=0.6,cfabove=0.15,cm=0.4,
                       loi=c(200,250,300,325,350),lhparms=LH)
Res_1
#>   yieldTotal yieldUnder  yieldIn yieldAbove nharvTotal ndieTotal nharvestUnder
#> 1   5611.796   903.2554 3813.586   894.9547   19.68287   20.9852      6.154504
#>   nharvestIn nharvestAbove    n0die ndieUnder   ndieIn ndieAbove  nrUnder
#> 1   12.55573     0.9726349 59.32995  10.92831 6.999731  3.057163 40.67005
#>       nrIn  nrAbove  trUnder     trIn  trOver avglenUnder avglenIn avglenAbove
#> 1 23.58723 4.031773 1.761224 2.443479 3.68129    224.3558 280.1859    393.1118
#>   avgwtUnder  avgwtIn avgwtAbove   nAt200   nAt250   nAt300   nAt325   nAt350
#> 1   146.7633 303.7327   920.1343 40.67005 23.58723 7.636027 4.031773 2.895681
#>    cm  expUnder     expIn  expAbove    FUnder       FIn    FAbove    MUnder
#> 1 0.4 0.1981511 0.4879637 0.1182668 0.2876821 0.9162907 0.1625189 0.5108256
#>         MIn    MAbove    ZUnder      ZIn    ZAbove SUnder  SIn SAbove cfUnder
#> 1 0.5108256 0.5108256 0.7985077 1.427116 0.6733446   0.45 0.24   0.51    0.25
#>   cfIn cfOver recruitmentTL lowerSL upperSL  N0 Linf   K   t0 LWalpha LWbeta
#> 1  0.6   0.15           200     250     325 100  592 0.2 -0.3  -5.528  3.273
#>   tmax
#> 1   15