Package 'LHsampling'

LH_plot

Description

A function that produces plots from the output of LH_sample().

Usage

LH_plot <- function(sample_output, output_type = 'none')

Arguments

sample_output	Output from LH_sample()
output_type	How plots are written and saved: ‘none’ displays in R graphics device only, ’pdf’ produces a single .pdf with all plots, and ‘png' produces a separate .png for each plot.

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LH_sample

Description

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.

Usage

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).

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Simulated population and harvest for Prisitpomoides auricilla

Description

Simulated population for Prisitpomoides auricilla under low fishing mortality (half of natural mortality) using life history parameters from O'Malley et al. 2019 (S1_Auric_lowF).

• $population (dataframe: $age, $length): the simulated population

• $harvest (dataframe: $age, $length): the simulated harvest

• $Avg_age (dataframe: $Ages, $L_age, $M_age, and $Selex): characteristics of the simulated population at age

• $parameters named list of 19 elements including all input parameters used in the simulation and the simulated population coefficient of variation of length at age_max and age_0

Usage

data(S1)

Format

list

References

Schemmel E., Bohaboy E., Kinney M., O'Malley J. (2022) An assessment of sampling strategies for estimating fish growth from fishery-dependent samples.ICES 79(5):1497-1514

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Simulate Population Harvest

Description

This is a IBM to generate a population and catch from the population

Usage

simulate_population_harvest(
  Linf,
  Linf_sd,
  M,
  Lorenzen,
  F,
  mincat,
  catsd,
  maxcat,
  maxcatsd,
  L0,
  L0_sd,
  k,
  k_sd,
  Amax,
  age_max,
  N
)

Arguments

Linf	Von Bertalanffy theoretical asymptotic length (cm)
Linf_sd	Population standard deviation of asymptotic length (cm)
M	Instantaneous natural mortality rate (yr-1)
Lorenzen	TRUE / FALSE specifying whether natural mortality is a function of individual length following Lorenzen (Lorenzen, 2000; Lorenzen, 2005)
F	Apical (fully selected) instantaneous fishing mortality rate (yr-1)
mincat	Minimum length at 50% fishery selectivity (cm)
catsd	Slope of the ascending region of selectivity at length (cm), see details
maxcat	Maximum length at 50% fishery selectivity (cm)
maxcatsd	Slope of the descending region of selectivity at length (cm), see details
L0	Von Bertalanffy length at age 0 (cm)
L0_sd	Population standard deviation of length at age 0 (cm)
k	Von Bertalanffy growth coefficient
k_sd	Population standard deviation of Von Bertalanffy growth coefficient
Amax	Maximum longevity (years)
age_max	An arbitrary age selected to represent “old” fish (years)
N	The number of age 0 fish in each simulated cohort, typical value =100,000

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