OM-class: Class `'OM'`

Description

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

Arguments

Slots

Name: Name of the operating model

nsim

The number of simulations

proyears

The number of projected years

nyears

The number of years for the historical simulation

maxage

The maximum age of individuals that is simulated (there is no 'plus group': individuals die off beyone the maximum age so there isn't a huge cost to simulating more older age classes)

R0

The magnitude of unfished recruitment. This is normally fixed to some arbitrary value since it simply scales the simulated numbers)

M

Natural mortality rate (uniform distribution)

M2

Optional vector of M-at-age (must be length maxage)

Msd

Inter-annual variability in natural mortality rate expressed as a coefficient of variation (uniform distribution)

Mgrad

Mean temporal trend in natural mortality rate, expressed as a percentage change in M per year (uniform distribution)

Mexp

Exponent of the Lorenzen function assuming an inverse relationship between M and weight (uniform distribution)

Fdisc

Fraction of discarded fish that die

h

Steepness of the stock recruit relationship (uniform distribution)

SRrel

Type of stock-recruit relationship (1)Beverton-Holt (2) Ricker

Linf

Maximum length (uniform distribution)

K

von B. growth parameter k (uniform distribution)

t0

von B. theoretical age at length zero (uniform distribution)

LenCV

Coefficient of variation of length-at-age (assumed constant for all age classes (uniform distribution)

Ksd

Inter-annual variability in growth parameter k (uniform distribution)

Kgrad

Mean temporal trend in growth parameter k, expressed as a percentage change in k per year (uniform distribution)

Linfsd

Inter-annual variability in maximum length - uniform distribution

Linfgrad

Mean temporal trend in maximum length, expressed as a percentage change in Linf per year (uniform distribution)

recgrad

Mean temporal trend in log-normal recruitment deviations (uniform distribution)

AC

Autocorrelation in recruitment deviations rec(t)=AC*rec(t-1)+(1-AC)*sigma(t) (uniform distribution)

a

Length-weight parameter alpha (uniform distribution)

b

Length-weight parameter beta (uniform distribution)

D

Current level of stock depletion (Bcurrent/Bunfished) (uniform distribution)

Size_area_1

The size of area 1 relative to area 2 (uniform distribution)

Frac_area_1

The fraction of the unfished biomass in stock 1 (uniform distribution)

Prob_staying

The probability of inviduals in area 1 remaining in area 1 over the course of one year

beta

A parameter controlling hyperstability/hyperdepletion. I^beta therefore 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)

Spat_targ

Distribution of fishing in relation to spatial biomass: F is proportional to B^Spat_targ (uniform distribution)

LFS

Shortest length that is fully vulnerable to fishing (uniform distribution)

L5

Shortest length at 5 percent vulnerability (uniform distribution)

Vmaxlen

The vulnerability of the longest (oldest) fish (uniform distribution)

LR5

Shortest length corresponding ot 5 percent retention (uniform distribution)

LFR

Shortest length that is fully retained (uniform distribution)

Rmaxlen

The retention of the longest (oldest) fish (uniform distribution)

DR

Discard rate - fraction of caught fish that are discarded (must be <= 1) (uniform distribution)

SelYears

Vector of verticies that index years where historical selectivity pattern changed. Leave empty to ignore

AbsSelYears

vector of absolute year values that correspond to year indices in SelYears. Used only for plotting

L5Lower

Optional vector of values of length SelYears, specifiying lower limits of L5 (use ChooseSelect function to set these. Overrides L5 above)

L5Upper

Optional vector of values of length SelYears, specifiying upper limits of L5 (use ChooseSelect function to set these. Overrides L5 above)

LFSLower

Optional vector of values of length SelYears, specifiying lower limits of LFS (use ChooseSelect function to set these. Overrides LFS above)

LFSUpper

Optional vector of values of length SelYears, specifiying upper limits of LFS (use ChooseSelect function to set these. Overrides LFS above)

VmaxLower

Optional vector of values of length SelYears, specifiying lower limits of Vmaxlen (use ChooseSelect function to set these. Overrides Vmaxlen above)

VmaxUpper

Optional vector of values of length SelYears, specifiying upper limits of Vmaxlen (use ChooseSelect function to set these. Overrides Vmaxlen above)

isRel

Are the selectivity parameters relative to size-of-maturity? TRUE or FALSE

L50

Length at 50 percent maturity (uniform distribution)

L50_95

Length increment from 50 to 95 percent maturity (uniform distribution)

Esd

Inter-annual variability in fishing mortality rate

EffYears

Vector of verticies, years at which to simulate varying relative effort

EffLower

Lower bound on relative effort corresponding to EffYears (uniform distribution)

EffUpper

Uppper bound on relative effort corresponding to EffYears (uniform distribution)

qinc

Average percentage change in fishing efficiency (uniform distribution)(applicable only to forward projection and input controls)

qcv

Inter-annual variability in fishing efficiency (uniform distribution)(applicable only to forward projection and input controls)

CurrentYr

The current calendar year (final year) of the historical simulations (e.g. 2011)

Cobs

Log-normal catch observation error expressed as a coefficient of variation (uniform distribution)

Cbiascv

A coefficient of variation controlling the sampling of bias in catch observations for each simulation (uniform distribution)

CAA_nsamp

Number of catch-at-age observation per time step (uniform distribution)

CAA_ESS

Effective sample size (independent age draws) of the multinomial catch-at-age observation error model (uniform distribution)

CAL_nsamp

Number of catch-at-length observation per time step (uniform distribution)

CAL_ESS

Effective sample size (independent length draws) of the multinomial catch-at-length observation error model (uniform distribution)

CALcv

Lognormal, variability in the length at age (uniform distribution)

Iobs

Observation error in the relative abundance indices expressed as a coefficient of variation (uniform distribution)

Perr

The extent of inter-annual log-normal recruitment variability (sigma R)(uniform distribution)

Period

Period for cylical recruitment pattern in years (uniform distribution). Leave empty to ignore

Amplitude

Amplitude in deviation from long-term average recruitment during recruitment cycle, both positive and negative (uniform distribution). E.g., a range from 0 to 0.5 means recruitment decreases or increases by up to 50% each cycle. Leave empty to ignore

Mcv

Persistent bias in the prescription of natural mortality rate sampled from a log-normal distribution with coefficient of variation (Mcv)(uniform distribution)

Kcv

Persistent bias in the prescription of growth parameter k sampled from a log-normal distribution with coefficient of variation (Kcv)(uniform distribution)

t0cv

Persistent bias in the prescription of t0 sampled from a log-normal distribution with coefficient of variation (t0cv)(uniform distribution)

Linfcv

Persistent bias in the prescription of maximum length sampled from a log-normal distribution with coefficient of variation (Linfcv)(uniform distribution)

LFCcv

Persistent bias in the prescription of lenght at first capture sampled from a log-normal distribution with coefficient of variation (LFCcv)(uniform distribution)

LFScv

Persistent bias in the prescription of length-at-fully selection sampled from a log-normal distribution with coefficient of variation (LFScv)(uniform distribution)

B0cv

Persistent bias in the prescription of maximum lengthunfished biomass sampled from a log-normal distribution with coefficient of variation (B0cv)(uniform distribution)

FMSYcv

Persistent bias in the prescription of FMSY sampled from a log-normal distribution with coefficient of variation (FMSYcv)(uniform distribution)

FMSY_Mcv

Persistent bias in the prescription of FMSY/M sampled from a log-normal distribution with coefficient of variation (FMSY_cv)(uniform distribution)

BMSY_B0cv

Persistent bias in the prescription of BMsY relative to unfished sampled from a log-normal distribution with coefficient of variation (BMSY_B0cv)(uniform distribution)

rcv

Persistent bias in the prescription of intrinsic rate of increase sampled from a log-normal distribution with coefficient of variation (rcv)(uniform distribution)

LenMcv

Persistent bias in the prescription of length at 50 percent maturity sampled from a log-normal distribution with coefficient of variation (A50cv)(uniform distribution)

Dbiascv

Persistent bias in the prescription of stock depletion sampled from a log-normal distribution with coefficient of variation (Linfcv)(uniform distribution)

Dcv

Imprecision in the prescription of stock depletion among years, expressed as a coefficient of variation (uniform distribution)

Btbias

Persistent bias in the prescription of current stock biomass sampled from a uniform-log distribution with range (Btbias)(uniform distribution)

Btcv

Imprecision in the prescription of current stock biomass among years expressed as a coefficient of variation (uniform distribution)

Fcurbiascv

Persistent bias in the prescription of current fishing mortality rate sampled from a log-normal distribution with coefficient of variation (Fcurcv)(uniform distribution)

Fcurcv

Imprecision in the prescription of current fishing mortality rate among years expressed as a coefficient of variation (uniform distribution)

hcv

Persistent bias in steepness (uniform distribution)

Icv

Observation error in realtive abundance index expressed as a coefficient of variation (uniform distirbution)

maxagecv

Bias in the prescription of maximum age (uniform distribution)

Reccv

Bias in the knowledge of recent recruitment strength (uniform distribution)

Irefcv

Bias in the knowledge of the relative abundance index at BMSY (uniform distribution)

Brefcv

Bias in the knowledge of BMSY (uniform distribution)

Crefcv

Bias in the knowledge of MSY(uniform distribution)

cpars

A list of custom parameters (single parameters are a vector nsim long, time series are a matrix nsim rows by nyears columns)

seed

A random seed to ensure users can reproduce results exactly

Source

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

TACSD

lognormal standard deviation in fraction of TAC taken (uniform distribution)

TACFrac

Mean fraction of TAC taken (uniform distribution) (can be an improper fraction greater than 1)

ESD

lognormal standard deviation in fraction of TAE taken(uniform distribution)

EFrac

Mean fraction of recommended effort taken (uniform distribution)

SizeLimSD

lognormal error in size limit implementation (uniform distribution)

SizeLimFrac

Mean fraction of the size limit (uniform distribution) (can be an improper fraction greater than 1)

Objects from the Class

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