yield_curves: Compute various per-recruit analyses

In inspktrgadget/gadgetSim: Create Gadget replicates for use in simulation studies

Description

These functions compute yield-per-recruit, spawning stock biomass (ssb) per recruit, and an overall yield curve given fishing mortality, natural mortality, ages, the growth function, the length-weight relationship, recruitment, selectivity, and maturity.

Usage

ypr_curve(fish_mort, nat_mort, ages, growth_fun = vb, growth_params = NULL,
  lw_rel = lw, lw_params = NULL, sel_fun = logistic_selectivity,
  sel_params = NULL)

ssb_rec_curve(fish_mort, nat_mort, ages, growth_fun = vb,
  growth_params = NULL, lw_rel = lw, lw_params = NULL,
  mat_fun = logistic_selectivity, mat_params = NULL,
  sel_fun = logistic_selectivity, sel_params = NULL)

yield_curve(fish_mort, nat_mort, ages, growth_fun = vb,
  growth_params = NULL, lw_rel = lw, lw_params = NULL,
  rec_fun = bev_holt, rec_params = NULL, mat_fun = logistic_selectivity,
  mat_params = NULL, sel_fun = logistic_selectivity, sel_params = NULL,
  ...)

Arguments

fish_mort	Numeric. A vector depicting fishing mortality
nat_mort	Numeric. A vector of either length 1 or the same length as ages
ages	Numeric vector representing ages
growth_fun	The name of the growth function to be used
growth_params	List of named elements corresponding to arguments to growth_fun
lw_rel	Function name determining the length-weight relationship
lw_params	List of named elements corresponding to arguments to lw_rel
sel_fun	Function determining the length-based selectivity of the fleet
sel_params	List of named elements corresponding to arguments to sel_fun
sel_fun	Function determining maturity ogive of the stock
sel_params	List of named elements corresponding to arguments to sel_fun

Details

ypr_curve produces a vector of yield-per-recruit at each value in fish_mort, ssb_rec_curve returns a vector with values for spawning-stock-biomass or spawners per recruit, and yield_curve provides a vector with values for yield corresponding to each value in fish_mort

Value

A vector the same length as fish_mort which corresponds to the ypr, ssb per recruit, or overall yield at the respective value of fish_mort

Examples

curve(ypr_curve(fish_mort = x, nat_mort = 0.2, ages = 0:20,
                growth_fun = vb,
                growth_params = list(linf = 125, k = 0.15, t0 = -0.5),
                lw_rel = lw, lw_params = list(alpha = 7e-06, beta = 3.1),
                sel_fun = logistic_selectivity,
                sel_params = list(alpha = 0.25, l50 = 40)),
      from = 0, to = 2, ylab = "YPR")
curve(ssb_rec_curve(fish_mort = x, nat_mort = 0.2, ages = 0:20,
                    growth_fun = "vb",
                    growth_params = list(linf = 125, k = 0.15, t0 = -0.5),
                    lw_rel = "lw",
                    lw_params = list(alpha = 7e-06, beta = 3.1),
                    mat_fun = "logistic_selectivity",
                    mat_params = list(alpha = 0.25, l50 = 30),
                    sel_fun = "logistic_selectivity",
                    sel_params = list(alpha = 0.25, l50 = 40)),
      from = 0, to = 2, ylab = "SSB per recruit")
curve(yield_curve(fish_mort = x, nat_mort = 0.2, ages = 0:20,
                  growth_params = list(linf = 125, k = 0.15, t0 = -0.5),
                  lw_params = list(alpha = 7e-06, beta = 3.1),
                  rec_params = list(mu = 4e8, lambda = 1.067e08),
                  mat_params = list(alpha = 0.25, 30),
                  sel_params = list(alpha = 0.25, 40)), 0, 2, ylab = "Yield")

inspktrgadget/gadgetSim documentation built on May 10, 2019, 9:51 a.m.