F_calc: F_calc

In nikolaifish/bamExtras: Functions and Data in Support of Stock Assessments with the Beaufort Assessment Model (BAM)

F_calc

Description

Calculations of stock dependent quantities over a range of fishing mortalities (F). This code calculates spawning potential ratio (SPR), and then maximum sustainable yield (MSY) using equilibrium methods incorporating a stock-recruit relationship. Many of the calculations, particularly the MSY calculations, are based on code written by Kyle Shertzer in a very similar function.

Usage

F_calc(
  ac,
  h = NULL,
  R0 = NULL,
  sigma = 0,
  M,
  Fmax = 1,
  F_n = 101,
  sel,
  PS,
  W,
  ep,
  Px = 0.4,
  plots = FALSE,
  plus_group = TRUE,
  plot_digits = 3
)

Arguments

ac	age classes. numeric vector
h	Beverton-Holt steepness parameter
R0	Beverton-Holt R0 parameter. Numbers of fish at age-a (often age-0 or age-1).
sigma	lognormal bias correction – exp(sigma^2/2)
M	Natural mortality rate
Fmax	Maximum fishing mortality rate
F_n	Number of fishing mortality rates to try
sel	Selectivity at age
PS	Proportion of fish to include in stock calculation, at age (e.g. mature females at age)
W	weight at age
ep	egg production proxy at age (e.g. weight, fecundity)
Px	reference proportion of unfished spawning potential ratio (e.g. Px=.40)
plot_digits	number of significant digits to show in plot

Author(s)

Kyle Shertzer and Nikolai Klibansky

Examples

rdat <- rdat_VermilionSnapper
pr <- rdat$parms
as <- rdat$a.series
F_calc(ac=as$age, h=pr$BH.steep, R0=pr$R0, M=as$M, sel=rdat$sel.age$sel.v.wgted.tot,
       PS=as$mat.female, W=as$weight, ep=as$wgt.klb,
       plots=TRUE)

# When there is no SRR, the function will still compute SPR without computing MSY-based equibrium values
rdat <- rdat_RedSnapper
pr <- rdat$parms
as <- rdat$a.series
F_calc(ac=as$age, M=as$M, sel=rdat$sel.age$sel.v.wgted.tot,
       PS=as$mat.female, W=as$weight, ep=as$wgt.klb,
       plots=TRUE)

nikolaifish/bamExtras documentation built on July 21, 2023, 8:26 a.m.