create_biodata: Create biological data

View source: R/create_biodata.R

create_biodataR Documentation

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 June 23, 2022, noon