Stock-class: Class "Stock"
In zanbi/DLMtool: Data-Limited Methods Toolkit

Description Slots Objects from the Class Author(s) Examples

An operating model component that specifies the parameters of the population dynamics model

Name: The name of the Stock object. Single value. Character string
Common_Name: Common name of the species. Character string
Species: Scientific name of the species. Genus and species name. Character string
maxage: The maximum age of individuals that is simulated (there is no 'plus group'). Single value. Positive integer
R0: The magnitude of unfished recruitment. Single value. Positive real number
M: Natural mortality rate. Uniform distribution lower and upper bounds. Positive real number
M2: (Optional) Natural mortality rate at age. Vector of length 'maxage'. Positive real number
Mexp: Exponent of the Lorenzen function assuming an inverse relationship between M and weight. Uniform distribution lower and upper bounds. Real numbers <= 0.
Msd: Inter-annual variability in natural mortality rate expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Mgrad: No longer used. Previously mean temporal trend in natural mortality rate, expressed as a percentage change in M per year.
h: Steepness of the stock recruit relationship. Uniform distribution lower and upper bounds. Values from 1/5 to 1
SRrel: Type of stock-recruit relationship. Single value, switch (1) Beverton-Holt (2) Ricker. Integer
Perr: Process error, the CV of lognormal recruitment deviations. Uniform distribution lower and upper bounds. Non-negative real numbers
AC: Autocorrelation in recruitment deviations rec(t)=AC*rec(t-1)+(1-AC)*sigma(t). Uniform distribution lower and upper bounds. Non-negative real numbers
Period: (Optional) Period for cyclical recruitment pattern in years. Uniform distribution lower and upper bounds. Non-negative real numbers
Amplitude: (Optional) Amplitude in deviation from long-term average recruitment during recruitment cycle (eg a range from 0 to 1 means recruitment decreases or increases by up to 100% each cycle). Uniform distribution lower and upper bounds. 0 < Amplitude < 1
Linf: Maximum length. Uniform distribution lower and upper bounds. Positive real numbers
K: von Bertalanffy growth parameter k. Uniform distribution lower and upper bounds. Positive real numbers
t0: von Bertalanffy theoretical age at length zero. Uniform distribution lower and upper bounds. Non-positive real numbers
LenCV: Coefficient of variation of length-at-age (assumed constant for all age classes). Uniform distribution lower and upper bounds. Positive real numbers
Ksd: Inter-annual variability in growth parameter k expressed as coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Kgrad: No longer used. Previously mean temporal trend in growth parameter k, expressed as a percentage change in k per year.
Linfsd: Inter-annual variability in maximum length expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Linfgrad: No longer used. Previously mean temporal trend in maximum length, expressed as a percentage change in Linf per year.
L50: Length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
L50_95: Length increment from 50 percent to 95 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
D: Current level of stock depletion SSB(current)/SSB(unfished). Uniform distribution lower and upper bounds. Fraction
a: Length-weight parameter alpha. Single value. Positive real number
b: Length-weight parameter beta. Single value. Positive real number
Size_area_1: The size of area 1 relative to area 2. Uniform distribution lower and upper bounds. Positive real numbers
Frac_area_1: The fraction of the unfished biomass in stock 1. Uniform distribution lower and upper bounds. Positive real numbers
Prob_staying: The probability of inviduals in area 1 remaining in area 1 over the course of one year. Uniform distribution lower and upper bounds. Positive fraction.
Fdisc: Fraction of discarded fish that die. Uniform distribution lower and upper bounds. Non-negative real numbers
Source: A reference to a website or article from which parameters were taken to define the stock object. Single value. Character string.