OM-class: Class `'OM'`

Description

An object containing all the parameters needed to control the MSE which can be build from component Stock, Fleet, Obs, and Imp objects.

Arguments

Slots

Name: Name of the operating model

Agency

Name of the agency responsible for the management of the fishery. Character string

Region

Name of the general geographic region of the fishery. Character string

Sponsor

Name of the organization who sponsored the OM. Character string

Latitude

Latitude (decimal degrees). Negative values represent the South of the Equator. Numeric. Single value

Longitude

Longitude (decimal degrees). Negative values represent the West of the Prime Meridian. Numeric. Single value

nsim

The number of simulations

proyears

The number of projected years

interval

The assessment interval - how often would you like to update the management system?

pstar

The percentile of the sample of the management recommendation for each method

maxF

Maximum instantaneous fishing mortality rate that may be simulated for any given age class

reps

Number of samples of the management recommendation for each method. Note that when this is set to 1, the mean value of the data inputs is used.

cpars

A list of custom parameters. Time series are a matrix nsim rows by nyears columns. Single parameters are a vector nsim long

seed

A random seed to ensure users can reproduce results exactly

Source

A reference to a website or article from which parameters were taken to define the operating model

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.

nyears

The number of years for the historical 'spool-up' simulation. Single value. Positive integer

Spat_targ

Distribution of fishing in relation to spatial biomass: fishing distribution is proportional to B^Spat_targ. Uniform distribution lower and upper bounds. Real numbers

EffYears

Years representing join-points (vertices) of time-varying effort. Vector. Non-negative real numbers

EffLower

Lower bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers

EffUpper

Upper bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers

Esd

Additional inter-annual variability in fishing mortality rate. Uniform distribution lower and upper bounds. Non-negative real numbers

qinc

Average percentage change in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers

qcv

Inter-annual variability in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers

L5

Shortest length corresponding to 5 percent vulnerability. Uniform distribution lower and upper bounds. Positive real numbers

LFS

Shortest length that is fully vulnerable to fishing. Uniform distribution lower and upper bounds. Positive real numbers

Vmaxlen

The vulnerability of fish at Stock@Linf. Uniform distribution lower and upper bounds. Fraction

isRel

Selectivity parameters in units of size-of-maturity (or absolute eg cm). Single value. Boolean.

LR5

Shortest length corresponding ot 5 percent retention. Uniform distribution lower and upper bounds. Non-negative real numbers

LFR

Shortest length that is fully retained. Uniform distribution lower and upper bounds. Non-negative real numbers

Rmaxlen

The retention of fish at Stock@Linf. Uniform distribution lower and upper bounds. Non-negative real numbers

DR

Discard rate - the fraction of caught fish that are discarded. Uniform distribution lower and upper bounds. Fraction

SelYears

(Optional) Years representing join-points (vertices) at which historical selectivity pattern changes. Vector. Positive real numbers

AbsSelYears

(Optional) Calendar years corresponding with SelYears (eg 1951, rather than 1), used for plotting only. Vector (of same length as SelYears). Positive real numbers

L5Lower

(Optional) Lower bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers

L5Upper

(Optional) Upper bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers

LFSLower

(Optional) Lower bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers

LFSUpper

(Optional) Upper bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers

VmaxLower

(Optional) Lower bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction

VmaxUpper

(Optional) Upper bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction

CurrentYr

The current calendar year (final year) of the historical simulations (eg 2011). Single value. Positive integer.

MPA

(Optional) Matrix specifying spatial closures for historical years.

Cobs

Log-normal catch observation error expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers

Cbiascv

Log-normal coefficient of variation controlling the sampling of bias in catch observations for each simulation. Uniform distribution lower and upper bounds. Non-negative real numbers

CAA_nsamp

Number of catch-at-age observation per time step. Uniform distribution lower and upper bounds. Positive real numbers

CAA_ESS

Effective sample size (independent age draws) of the multinomial catch-at-age observation error model. Uniform distribution lower and upper bounds. Positive integers

CAL_nsamp

Number of catch-at-length observation per time step. Uniform distribution lower and upper bounds. Positive integers

CAL_ESS

Effective sample size (independent length draws) of the multinomial catch-at-length observation error model. Uniform distribution lower and upper bounds. Positive integers

Iobs

Observation error in the relative abundance indices expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Positive real numbers

Ibiascv

Not Used. Log-normal coefficient of variation controlling error in observations of relative abundance index. Uniform distribution lower and upper bounds. Positive real numbers

Btobs

Log-normal coefficient of variation controlling error in observations of current stock biomass among years. Uniform distribution lower and upper bounds. Positive real numbers

Btbiascv

Uniform-log bounds for sampling persistent bias in current stock biomass. Uniform-log distribution lower and upper bounds. Positive real numbers

beta

A parameter controlling hyperstability/hyperdepletion where values below 1 lead to hyperstability (an index that decreases slower than true abundance) and values above 1 lead to hyperdepletion (an index that decreases more rapidly than true abundance). Uniform distribution lower and upper bounds. Positive real numbers

LenMbiascv

Log-normal coefficient of variation for sampling persistent bias in length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers

Mbiascv

Log-normal coefficient of variation for sampling persistent bias in observed natural mortality rate. Uniform distribution lower and upper bounds. Positive real numbers

Kbiascv

Log-normal coefficient of variation for sampling persistent bias in observed growth parameter K. Uniform distribution lower and upper bounds. Positive real numbers

t0biascv

Log-normal coefficient of variation for sampling persistent bias in observed t0. Uniform distribution lower and upper bounds. Positive real numbers

Linfbiascv

Log-normal coefficient of variation for sampling persistent bias in observed maximum length. Uniform distribution lower and upper bounds. Positive real numbers

LFCbiascv

Log-normal coefficient of variation for sampling persistent bias in observed length at first capture. Uniform distribution lower and upper bounds. Positive real numbers

LFSbiascv

Log-normal coefficient of variation for sampling persistent bias in length-at-full selection. Uniform distribution lower and upper bounds. Positive real numbers

FMSYbiascv

Not used. Log-normal coefficient of variation for sampling persistent bias in FMSY. Uniform distribution lower and upper bounds. Positive real numbers

FMSY_Mbiascv

Log-normal coefficient of variation for sampling persistent bias in FMSY/M. Uniform distribution lower and upper bounds. Positive real numbers

BMSY_B0biascv

Log-normal coefficient of variation for sampling persistent bias in BMSY relative to unfished. Uniform distribution lower and upper bounds. Positive real numbers

Irefbiascv

Log-normal coefficient of variation for sampling persistent bias in relative abundance index at BMSY. Uniform distribution lower and upper bounds. Positive real numbers

Brefbiascv

Log-normal coefficient of variation for sampling persistent bias in BMSY. Uniform distribution lower and upper bounds. Positive real numbers

Crefbiascv

Log-normal coefficient of variation for sampling persistent bias in MSY. Uniform distribution lower and upper bounds. Positive real numbers

Dbiascv

Log-normal coefficient of variation for sampling persistent bias in stock depletion. Uniform distribution lower and upper bounds. Positive real numbers

Dobs

Log-normal coefficient of variation controlling error in observations of stock depletion among years. Uniform distribution lower and upper bounds. Positive real numbers

hbiascv

Log-normal coefficient of variation for sampling persistent bias in steepness. Uniform distribution lower and upper bounds. Positive real numbers

Recbiascv

Log-normal coefficient of variation for sampling persistent bias in recent recruitment strength. Uniform distribution lower and upper bounds. Positive real numbers

TACFrac

Mean fraction of TAC taken. Uniform distribution lower and upper bounds. Positive real number.

TACSD

Log-normal coefficient of variation in the fraction of Total Allowable Catch (TAC) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.

TAEFrac

Mean fraction of TAE taken. Uniform distribution lower and upper bounds. Positive real number.

TAESD

Log-normal coefficient of variation in the fraction of Total Allowable Effort (TAE) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.

SizeLimFrac

The real minimum size that is retained expressed as a fraction of the size of retention. Uniform distribution lower and upper bounds. Positive real number.

SizeLimSD

Log-normal coefficient of variation controlling mismatch between a minimum size limit and the real minimum size retained. Uniform distribution lower and upper bounds. Non-negative real numbers.

Objects from the Class

Objects can be created by calls of the form new('OM', Stock, Fleet, Obs, Imp).

MPA slot

Each row should contain year index (e.g 10 for 10th historical year) followed by fraction of area closed to fishing for each area. i.e. each row represents a change and the number of columns is nareas + 1. The spatial closures are assumed to remain in place for the future projections unless changed by a MP. Default (if left blank) is all areas are open to fishing in historical period.

Details

Almost all of these inputs are a vector of length 2 which describes the upper and lower bounds of a uniform distribution from which to sample the parameter.