get_msy: get_msy

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

get_msy

Description

Calculations of stock dependent quantities over a range of fishing mortalities (F). This is code from the Beaufort Assessment Model converted from ADMB to R.

Usage

get_msy(
  rdat,
  maxF = NULL,
  nFopt = NULL,
  nFres = 100,
  SPR_props = c(0.3, 0.4, 0.5),
  nages = NULL,
  sel_wgted_L = NULL,
  sel_wgted_D = NULL,
  M = NULL,
  reprod = NULL,
  spawn_time_frac = NULL,
  R0 = NULL,
  steep = NULL,
  BiasCor = NULL,
  SR_switch = NULL,
  wgt_mt = NULL,
  wgt_klb = NULL,
  wgt_klb_L = NULL,
  wgt_klb_D = NULL,
  make_plot = FALSE,
  plot_digits = 3
)

Arguments

rdat	BAM output rdat file object
maxF	Maximum fishing mortality rate. numeric vector
nFopt	length of F vector for grid search optimization
nFres	length of F vector for filtering grid search results to limit output size
SPR_props	proportions of SPR to compute reference points at. numeric vector
nages	Number of ages in population model. numeric vector
sel_wgted_L	effort-weighted, recent selectivities toward landings. numeric vector of length nages
sel_wgted_D	effort-weighted, recent selectivities toward discards. numeric vector of length nages
M	Natural mortality rate. numeric vector of length nages
reprod	Reproductive potential at-age vector. numeric vector of length nages
spawn_time_frac	time of year of peak spawning, as a fraction of the year. numeric
R0	Beverton-Holt R0 parameter (virgin recruitment). Numbers of fish at first age (often age-0 or age-1). numeric vector
steep	Beverton-Holt steepness parameter. numeric vector
BiasCor	bias correction. numeric vector
SR_switch	1 for Beverton-Holt, 2 for Ricker, 3 for none (average recruitment). integer
wgt_mt	Weight-at-age in metric tons for fish in the population. numeric vector of length nages
wgt_klb	Weight-at-age in thousand pounds for fish in the population. numeric vector of length nages
wgt_klb_L	Weight-at-age in thousand pounds for fish in the landings. numeric vector of length nages
wgt_klb_D	Weight-at-age in thousand pounds for fish in the discards. numeric vector of length nages
make_plot	Indicate whether or not to plot results. logical
plot_digits	number of significant digits to show in plot. numeric

Author(s)

Erik Williams, Kyle Shertzer, and Nikolai Klibansky

Examples

## Not run: 
rdat <- rdat_VermilionSnapper
res <- get_msy(rdat,make_plot=TRUE)

## End(Not run)

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