A bootstrap sampling routine to estimate life history parameters from fishery catches simulated by simulate_population_harvest(). This function will take n_boots samples (without replacement) from the harvested individuals following either a fixed otolith sampling (FOS) or proportional otolith sampling (POS) strategy. The function then parameterizes the von Bertalanffy growth function and estimates the population coefficient of variation of length at age for each bootstrap sample.

LH_sample <- function(sim_output, n_boots, samp_size, sample_type, supp_large = FALSE, supp_large_n_per_bin = 3, supp_small = FALSE, supp_small_n_per_bin = 3, supp_min_length = 2, constrained = FALSE, t0 = 0, SD_L_const = TRUE, save_bootstraps = FALSE, Amax = NULL, age_max = NULL, Lbin_width = 2)

Arguments

sim_output

output from simulate_population_harvest()

n_boots

number of bootstraps for von Bertalanffy growth function

sample_type

The sampling strategy to be used, either proportional otolith sampling (‘POS’) or fixed otolith sampling (‘FOS’)

supp_large

TRUE / FALSE specifying whether supplemental samples will be collected from large length bins

supp_large_n_per_bin

The number of samples per length bin to be collected from large bins (ignored if supp_large = FALSE)

supp_small

TRUE / FALSE specifying whether supplemental samples will be collected from small length bins

supp_small_n_per_bin

The number of samples per length bin to be collected from small bins (ignored if supp_small = FALSE)

supp_min_length

The minimum length fish that could be collected from the wild fish population

constrained

TRUE / FALSE specifying whether theoretical time at length zero (t0) should be estimated

t0

If constrained = TRUE, the fixed value for t0 (typically 0)

SD_L_const

TRUE / FALSE describing assumptions of population variance in length at age. If TRUE, then standard deviation (√𝜎𝜎2) of length at age is assumed a linear function of age. If FALSE, then the coefficient of variation of length at age is assumed a linear function of age.

save_bootstraps

TRUE / FALSE specifying whether all bootstrap samples will be included in the function output

Amax

Maximum longevity (years). If not specified, this value is taken from sim_output.

age_max

An arbitrary age selected to represent “old” fish (years). If not specified, this value is taken from sim_output.

Lbin_width

The width of each length bin (cm).