create_biodata: Create biological data

In Bai-Li-NOAA/IFA4EBFM: Interdisciplinary Forecasting Approach for Ecosystem-Based Fisheries Management

Create biological data

Description

This function creates a data list that contains remaining biological data for a stock assessment

Usage

create_biodata(
  nsex = 1,
  narea = 1,
  ages,
  years,
  length_bin,
  mid_length_bin,
  nbin,
  bin_width,
  length_CV,
  annual_weight_path,
  monthly_weight_path,
  species,
  species_labels,
  skip_nrows,
  lw_a = 0.01,
  lw_b = 3,
  k,
  t0 = -0.1,
  winf,
  maturity_at_age,
  natural_mortality_at_age
)

Arguments

nsex	Number of sexes of the species.
narea	Number of areas.
ages	A vector of ages.
years	A vector of years for extracting EwE data.
length_bin	A vector of length bins.
mid_length_bin	A vector of middle point of the length bins.
nbin	Total number of bins.
bin_width	Width of bins.
length_CV	CV about length.
annual_weight_path	A character string shows path to Ecosim annual weight-at-age output file is located.
monthly_weight_path	A character string shows path to Ecosim monthly weight-at-age output file is located.
species	The species to create fishery for. A vector of column names from the catch_annual.csv.
species_labels	Customized names for species columns.
skip_nrows	integer; the number of lines of the data file to skip before reading data.
lw_a	Length-weight coefficients a. W=a*L^b. Default EwE value is 0.01.
lw_b	Length-weight coefficients b. W=a*L^b. Default EwE value is 3.
k	Growth rate parameter of the von Bertalanffy model.
t0	Theoretical age at size 0. Default EwE value is -0.1.
winf	Asymptotic average weight. EwE weight-at-age calculated as Wa = (1-exp(k*age))^3.
maturity_at_age	A vector of maturity-at-age value or time-varying maturity-at-age matrix with rows present years and columns represent ages.
natural_mortality_at_age	A vector of natural mortality-at-age value or time-varying natural mortality-at-age matrix with rows present years and columns represent ages.

Details

The function takes EwE input or output data to create weight-at-age matrix, maturity-at-age matrix,

Value

A data list that includes biological data for set up a stock assessment.

See Also

Other create_data functions: create_fishery()

Bai-Li-NOAA/IFA4EBFM documentation built on May 1, 2024, 9:24 p.m.