'OM'An object containing all the parameters needed to control the MSE which can be build from component Stock, Fleet, Obs, and Imp objects.
NameName of the operating model
AgencyName of the agency responsible for the management of the fishery. Character string
RegionName of the general geographic region of the fishery. Character string
SponsorName of the organization who sponsored the OM. Character string
LatitudeLatitude (decimal degrees). Negative values represent the South of the Equator. Numeric. Single value
LongitudeLongitude (decimal degrees). Negative values represent the West of the Prime Meridian. Numeric. Single value
nsimThe number of simulations
proyearsThe number of projected years
intervalThe assessment interval - how often would you like to update the management system?
pstarThe percentile of the sample of the management recommendation for each method
maxFMaximum instantaneous fishing mortality rate that may be simulated for any given age class
repsNumber 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.
cparsA list of custom parameters. Time series are a matrix nsim rows by nyears columns. Single parameters are a vector nsim long
seedA random seed to ensure users can reproduce results exactly
SourceA reference to a website or article from which parameters were taken to define the operating model
Common_NameCommon name of the species. Character string
SpeciesScientific name of the species. Genus and species name. Character string
maxageThe maximum age of individuals that is simulated (there is no 'plus group'). Single value. Positive integer
R0The magnitude of unfished recruitment. Single value. Positive real number
MNatural 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
MexpExponent of the Lorenzen function assuming an inverse relationship between M and weight. Uniform distribution lower and upper bounds. Real numbers <= 0.
MsdInter-annual variability in natural mortality rate expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
MgradMean temporal trend in natural mortality rate, expressed as a percentage change in M per year. Uniform distribution lower and upper bounds. Real numbers
hSteepness of the stock recruit relationship. Uniform distribution lower and upper bounds. Values from 1/5 to 1
SRrelType of stock-recruit relationship. Single value, switch (1) Beverton-Holt (2) Ricker. Integer
PerrProcess error, the CV of lognormal recruitment deviations. Uniform distribution lower and upper bounds. Non-negative real numbers
ACAutocorrelation 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
LinfMaximum length. Uniform distribution lower and upper bounds. Positive real numbers
Kvon Bertalanffy growth parameter k. Uniform distribution lower and upper bounds. Positive real numbers
t0von Bertalanffy theoretical age at length zero. Uniform distribution lower and upper bounds. Non-positive real numbers
LenCVCoefficient of variation of length-at-age (assumed constant for all age classes). Uniform distribution lower and upper bounds. Positive real numbers
KsdInter-annual variability in growth parameter k. Uniform distribution lower and upper bounds. Non-negative real numbers
KgradMean temporal trend in growth parameter k, expressed as a percentage change in k per year. Uniform distribution lower and upper bounds. Real numbers
LinfsdInter-annual variability in maximum length. Uniform distribution lower and upper bounds. Non-negative real numbers
LinfgradMean temporal trend in maximum length, expressed as a percentage change in Linf per year. Uniform distribution lower and upper bounds. Real numbers
L50Length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
L50_95Length increment from 50 percent to 95 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
DCurrent level of stock depletion SSB(current)/SSB(unfished). Uniform distribution lower and upper bounds. Fraction
aLength-weight parameter alpha. Single value. Positive real number
bLength-weight parameter beta. Single value. Positive real number
Size_area_1The size of area 1 relative to area 2. Uniform distribution lower and upper bounds. Positive real numbers
Frac_area_1The fraction of the unfished biomass in stock 1. Uniform distribution lower and upper bounds. Positive real numbers
Prob_stayingThe probability of inviduals in area 1 remaining in area 1 over the course of one year. Uniform distribution lower and upper bounds. Positive fraction.
FdiscFraction of discarded fish that die. Uniform distribution lower and upper bounds. Non-negative real numbers
nyearsThe number of years for the historical 'spool-up' simulation. Single value. Positive integer
Spat_targDistribution of fishing in relation to spatial biomass: fishing distribution is proportional to B^Spat_targ. Uniform distribution lower and upper bounds. Real numbers
EffYearsYears representing join-points (vertices) of time-varying effort. Vector. Non-negative real numbers
EffLowerLower bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
EffUpperUpper bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
EsdAdditional inter-annual variability in fishing mortality rate. Uniform distribution lower and upper bounds. Non-negative real numbers
qincAverage percentage change in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
qcvInter-annual variability in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
L5Shortest length corresponding to 5 percent vulnerability. Uniform distribution lower and upper bounds. Positive real numbers
LFSShortest length that is fully vulnerable to fishing. Uniform distribution lower and upper bounds. Positive real numbers
VmaxlenThe vulnerability of fish at Stock@Linf. Uniform distribution lower and upper bounds. Fraction
isRelSelectivity parameters in units of size-of-maturity (or absolute eg cm). Single value. Boolean.
LR5Shortest length corresponding ot 5 percent retention. Uniform distribution lower and upper bounds. Non-negative real numbers
LFRShortest length that is fully retained. Uniform distribution lower and upper bounds. Non-negative real numbers
RmaxlenThe retention of fish at Stock@Linf. Uniform distribution lower and upper bounds. Non-negative real numbers
DRDiscard 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
CurrentYrThe current calendar year (final year) of the historical simulations (eg 2011). Single value. Positive integer. .
MPA(Optional) Matrix specifying spatial closures for historical years. 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.
CobsLog-normal catch observation error expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
CbiascvLog-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_nsampNumber of catch-at-age observation per time step. Uniform distribution lower and upper bounds. Positive real numbers
CAA_ESSEffective sample size (independent age draws) of the multinomial catch-at-age observation error model. Uniform distribution lower and upper bounds. Positive integers
CAL_nsampNumber of catch-at-length observation per time step. Uniform distribution lower and upper bounds. Positive integers
CAL_ESSEffective sample size (independent length draws) of the multinomial catch-at-length observation error model. Uniform distribution lower and upper bounds. Positive integers
IobsObservation error in the relative abundance indices expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Positive real numbers
IbiascvNOT CURRENTLY USED Log-normal coefficient of variation controlling error in observations of relative abundance index. Uniform distribution lower and upper bounds. Positive real numbers
BtobsLog-normal coefficient of variation controlling error in observations of current stock biomass among years. Uniform distribution lower and upper bounds. Positive real numbers
BtbiascvUniform-log bounds for sampling persistent bias in current stock biomass. Uniform-log distribution lower and upper bounds. Positive real numbers
betaA 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
LenMbiascvLog-normal coefficient of variation for sampling persistent bias in length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
MbiascvLog-normal coefficient of variation for sampling persistent bias in observed natural mortality rate. Uniform distribution lower and upper bounds. Positive real numbers
KbiascvLog-normal coefficient of variation for sampling persistent bias in observed growth parameter K. Uniform distribution lower and upper bounds. Positive real numbers
t0biascvLog-normal coefficient of variation for sampling persistent bias in observed t0. Uniform distribution lower and upper bounds. Positive real numbers
LinfbiascvLog-normal coefficient of variation for sampling persistent bias in observed maximum length. Uniform distribution lower and upper bounds. Positive real numbers
LFCbiascvLog-normal coefficient of variation for sampling persistent bias in observed length at first capture. Uniform distribution lower and upper bounds. Positive real numbers
LFSbiascvLog-normal coefficient of variation for sampling persistent bias in length-at-full selection. Uniform distribution lower and upper bounds. Positive real numbers
FMSYbiascvLog-normal coefficient of variation for sampling persistent bias in FMSY. Uniform distribution lower and upper bounds. Positive real numbers
FMSY_MbiascvLog-normal coefficient of variation for sampling persistent bias in FMSY/M. Uniform distribution lower and upper bounds. Positive real numbers
BMSY_B0biascvLog-normal coefficient of variation for sampling persistent bias in BMSY relative to unfished. Uniform distribution lower and upper bounds. Positive real numbers
IrefbiascvLog-normal coefficient of variation for sampling persistent bias in relative abundance index at BMSY. Uniform distribution lower and upper bounds. Positive real numbers
BrefbiascvLog-normal coefficient of variation for sampling persistent bias in BMSY. Uniform distribution lower and upper bounds. Positive real numbers
CrefbiascvLog-normal coefficient of variation for sampling persistent bias in MSY. Uniform distribution lower and upper bounds. Positive real numbers
DbiascvLog-normal coefficient of variation for sampling persistent bias in stock depletion. Uniform distribution lower and upper bounds. Positive real numbers
DobsLog-normal coefficient of variation controlling error in observations of stock depletion among years. Uniform distribution lower and upper bounds. Positive real numbers
hbiascvLog-normal coefficient of variation for sampling persistent bias in steepness. Uniform distribution lower and upper bounds. Positive real numbers
RecbiascvLog-normal coefficient of variation for sampling persistent bias in recent recruitment strength. Uniform distribution lower and upper bounds. Positive real numbers
TACFracMean fraction of TAC taken. Uniform distribution lower and upper bounds. Positive real number.
TACSDLog-normal coefficient of variation in the fraction of Total Allowable Catch (TAC) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.
TAEFracMean fraction of TAE taken. Uniform distribution lower and upper bounds. Positive real number.
TAESDLog-normal coefficient of variation in the fraction of Total Allowable Effort (TAE) taken. Uniform distribution lower and upper bounds. Non-negative real numbers.
SizeLimFracThe real minimum size that is retained expressed as a fraction of the size. Uniform distribution lower and upper bounds. Positive real number.
SizeLimSDLog-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 can be created by calls of the form
new('OM', Stock, Fleet, Obs, Imp).
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.