Operating Model Indian Ocean Skipjack (Katsuwonus pelamis)
Based on the 2017 IOTC Report
Adrian Hordyk, University of British Columbia [email protected]
August 2019
Introduction
The principal document for populating this operating model was the Stock Synthesis assessment and
The operating model is specified based on the MLE estimates from the SS3 assessment. No additional
uncertainty in life-history or exploitation parameters has been added to the operating model.
Operating Model
The OM rdata file can be downloaded from here
Download and import into R using myOM <- readRDS('OM.rdata')
Species Information
Species: Katsuwonus pelamis
Common Name: Skipjack
Management Agency: IOTC
Region: Indian Ocean
OM Parameters
OM Name: Name of the operating model: Skipjack OM
nsim: The number of simulations: 192
proyears: The number of projected years: 50
interval: The assessment interval - how often would you like to update the management system? 1
pstar: The percentile of the sample of the management recommendation for each method: 0.5
maxF: Maximum instantaneous fishing mortality rate that may be simulated for any given age class: 3
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. 1
Source: A reference to a website or article from which parameters were taken to define the operating model
No source provided. Author: No author provided.
Custom Parameters
Length-at-age, weight-at-age, maturity-at-age, and vulnerability-at-age schedules for each
year were imported directly from SS3 output and provided to the operating model through
the custom parameters feature.
The historical pattern in fishing effort (Find) was also provided in cpars.
Stock Parameters
Mortality and age: maxage, R0, M, M2, Mexp, Msd
maxage: The maximum age of individuals that is simulated (there is no plus group ). Single value. Positive integer
Specified Value(s): 8
From SS3
R0: The magnitude of unfished recruitment. Single value. Positive real number
Specified Value(s): 423779
From SS3 MLE estimate.
M: Natural mortality rate. Uniform distribution lower and upper bounds. Positive real number
Specified Value(s): 0.86, 0.6, 0.85, 1.16, 1.23, 1.23, 1.23, 1.23
Natural-mortality-at-age was imported from the SS3 assessment.
M2: (Optional) Natural mortality rate at age. Vector of length maxage . Positive real number
Specified Value(s): 0.86, 0.6, 0.85, 1.16, 1.23, 1.23, 1.23, 1.23
Natural-mortality-at-age was imported from the SS3 assessment.
Mexp: Exponent of the Lorenzen function assuming an inverse relationship between M and weight. Uniform distribution lower and upper bounds. Real numbers <= 0.
Specified Value(s): 0, 0
Not used.
Msd: Inter-annual variability in natural mortality rate expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Following the SS assessment, no inter-annual variability in life-history parameters was assumed in the life-history parameters.
Natural Mortality Parameters
Sampled Parameters
Histograms of 48 simulations of M, Mexp, and Msd parameters, with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
The average natural mortality rate by year for adult fish for 3 simulations. The vertical dashed line indicates the end of the historical period:
M-at-Age
Natural mortality-at-age for 3 simulations in the first historical year, the last historical year (i.e., current year), and the last projected year:
M-at-Length
Natural mortality-at-length for 3 simulations in the first historical year, the last historical year (i.e., current year), and the last projected year:
Recruitment: h, SRrel, Perr, AC
h: Steepness of the stock recruit relationship. Uniform distribution lower and upper bounds. Values from 1/5 to 1
Specified Value(s): 0.8, 0.8
Following the assessment, steepness was fixed.
SRrel: Type of stock-recruit relationship. Single value, switch (1) Beverton-Holt (2) Ricker. Integer
Specified Value(s): 1
Following the assessment, a Beverton-Holt stock recruitment model.
Perr: Process error, the CV of lognormal recruitment deviations. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.28, 0.28
From the SS assessment.
AC: Autocorrelation in recruitment deviations rec(t)=ACrec(t-1)+(1-AC)sigma(t). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): -0.06, -0.06
From the SS assessment.
Recruitment Parameters
Sampled Parameters
Histograms of 48 simulations of steepness (h), recruitment process error (Perr) and auto-correlation (AC) for the Beverton-Holt stock-recruitment relationship, with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Non-stationarity in stock productivity: Period, Amplitude
Period: (Optional) Period for cyclical recruitment pattern in years. Uniform distribution lower and upper bounds. Non-negative real numbers
Slot not used.
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
Slot not used.
Growth: Linf, K, t0, LenCV, Ksd, Linfsd
Linf: Maximum length. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
Length-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Len_age)
K: von Bertalanffy growth parameter k. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
Length-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Len_age)
t0: von Bertalanffy theoretical age at length zero. Uniform distribution lower and upper bounds. Non-positive real numbers
Specified Value(s): 0, 0
Length-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Len_age)
LenCV: Coefficient of variation of length-at-age (assumed constant for all age classes). Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.1
Fixed at a default value.
Ksd: Inter-annual variability in growth parameter k expressed as coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Following the SS assessment, no inter-annual variability in life-history parameters was assumed in the life-history parameters.
Linfsd: Inter-annual variability in maximum length expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Following the SS assessment, no inter-annual variability in life-history parameters was assumed in the life-history parameters.
Growth Parameters
Sampled Parameters
Histograms of 48 simulations of von Bertalanffy growth parameters Linf, K, and t0, and inter-annual variability in Linf and K (Linfsd and Ksd), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
The Linf and K parameters in each year for 3 simulations. The vertical dashed line indicates the end of the historical period:
Growth Curves
Sampled length-at-age curves for 3 simulations in the first historical year, the last historical year, and the last projection year. 
Maturity: L50, L50_95
L50: Length at 50 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
Maturity-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Mat_age)
L50_95: Length increment from 50 percent to 95 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
Maturity-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Mat_age)
Maturity Parameters
Sampled Parameters
Histograms of 48 simulations of L50 (length at 50% maturity), L95 (length at 95% maturity), and corresponding derived age at maturity parameters (A50 and A95), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Maturity at Age and Length
Maturity-at-age and -length for 3 simulations in the first historical year, the last historical year (i.e., current year), and the last projected year:
Stock depletion and Discard Mortality: D, Fdisc
D: Current level of stock depletion SSB(current)/SSB(unfished). Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0.42, 0.42
Fixed at the SS3 MLE estimate.
Fdisc: Fraction of discarded fish that die. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No discard mortality was assumed.
Depletion and Discard Mortality
Sampled Parameters
Histograms of 48 simulations of depletion (spawning biomass in the last historical year over average unfished spawning biomass; D) and the fraction of discarded fish that are killed by fishing mortality (Fdisc), with vertical colored lines indicating 3 randomly drawn values.
Length-weight conversion parameters: a, b
a: Length-weight parameter alpha. Single value. Positive real number
Specified Value(s): 0
Weight-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Wt_age)
b: Length-weight parameter beta. Single value. Positive real number
Specified Value(s): 3.39
Weight-at-age from the assessment was provided directly to the OM with custom parameters (OM@cpars$Wt_age)
Spatial distribution and movement: Size_area_1, Frac_area_1, Prob_staying
Size_area_1: The size of area 1 relative to area 2. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5, 0.5
A mixed stock is assumed
Frac_area_1: The fraction of the unfished biomass in stock 1. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5, 0.5
A mixed stock is assumed
Prob_staying: The probability of inviduals in area 1 remaining in area 1 over the course of one year. Uniform distribution lower and upper bounds. Positive fraction.
Specified Value(s): 0.5, 0.5
A mixed stock is assumed
Spatial & Movement
Sampled Parameters
Histograms of 48 simulations of size of area 1 (Size_area_1), fraction of unfished biomass in area 1 (Frac_area_1), and the probability of staying in area 1 in a year (Frac_area_1), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Fleet Parameters
Historical years of fishing, spatial targeting: nyears, Spat_targ
nyears: The number of years for the historical spool-up simulation. Single value. Positive integer
Specified Value(s): 67
The assessment is from 1950 - 2016.
Spat_targ: Distribution of fishing in relation to spatial biomass: fishing distribution is proportional to B^Spat_targ. Uniform distribution lower and upper bounds. Real numbers
Specified Value(s): 1, 1
Default assumption that effort distributed in proportion to density.
Trend in historical fishing effort (exploitation rate), interannual variability in fishing effort: EffYears, EffLower, EffUpper, Esd
EffYears: Years representing join-points (vertices) of time-varying effort. Vector. Non-negative real numbers
From the SS assessment (OM@cpars$Find).
EffLower: Lower bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
From the SS assessment (OM@cpars$Find).
EffUpper: Upper bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
From the SS assessment (OM@cpars$Find).
| EffYears | EffLower | EffUpper |
|---|---|---|
| 1950 | 0.00685 | 0.00685 |
| 1951 | 0.00859 | 0.00859 |
| 1952 | 0.00848 | 0.00848 |
| 1953 | 0.00906 | 0.00906 |
| 1954 | 0.00952 | 0.00952 |
| 1955 | 0.00969 | 0.00969 |
| 1956 | 0.01010 | 0.01010 |
| 1957 | 0.01110 | 0.01110 |
| 1958 | 0.01060 | 0.01060 |
| 1959 | 0.01070 | 0.01070 |
| 1960 | 0.01050 | 0.01050 |
| 1961 | 0.01040 | 0.01040 |
| 1962 | 0.01180 | 0.01180 |
| 1963 | 0.01330 | 0.01330 |
| 1964 | 0.01390 | 0.01390 |
| 1965 | 0.01800 | 0.01800 |
| 1966 | 0.02130 | 0.02130 |
| 1967 | 0.02310 | 0.02310 |
| 1968 | 0.02290 | 0.02290 |
| 1969 | 0.02460 | 0.02460 |
| 1970 | 0.02860 | 0.02860 |
| 1971 | 0.02770 | 0.02770 |
| 1972 | 0.02340 | 0.02340 |
| 1973 | 0.02970 | 0.02970 |
| 1974 | 0.03630 | 0.03630 |
| 1975 | 0.02850 | 0.02850 |
| 1976 | 0.03340 | 0.03340 |
| 1977 | 0.03160 | 0.03160 |
| 1978 | 0.02880 | 0.02880 |
| 1979 | 0.03160 | 0.03160 |
| 1980 | 0.03570 | 0.03570 |
| 1981 | 0.03760 | 0.03760 |
| 1982 | 0.03960 | 0.03960 |
| 1983 | 0.04210 | 0.04210 |
| 1984 | 0.05880 | 0.05880 |
| 1985 | 0.06820 | 0.06820 |
| 1986 | 0.08280 | 0.08280 |
| 1987 | 0.10200 | 0.10200 |
| 1988 | 0.11200 | 0.11200 |
| 1989 | 0.14500 | 0.14500 |
| 1990 | 0.13800 | 0.13800 |
| 1991 | 0.14100 | 0.14100 |
| 1992 | 0.16300 | 0.16300 |
| 1993 | 0.19000 | 0.19000 |
| 1994 | 0.21600 | 0.21600 |
| 1995 | 0.23100 | 0.23100 |
| 1996 | 0.23700 | 0.23700 |
| 1997 | 0.28000 | 0.28000 |
| 1998 | 0.29300 | 0.29300 |
| 1999 | 0.29400 | 0.29400 |
| 2000 | 0.28300 | 0.28300 |
| 2001 | 0.28800 | 0.28800 |
| 2002 | 0.31600 | 0.31600 |
| 2003 | 0.34500 | 0.34500 |
| 2004 | 0.34800 | 0.34800 |
| 2005 | 0.39700 | 0.39700 |
| 2006 | 0.49400 | 0.49400 |
| 2007 | 0.55000 | 0.55000 |
| 2008 | 0.54300 | 0.54300 |
| 2009 | 0.48700 | 0.48700 |
| 2010 | 0.46400 | 0.46400 |
| 2011 | 0.47500 | 0.47500 |
| 2012 | 0.51600 | 0.51600 |
| 2013 | 0.62700 | 0.62700 |
| 2014 | 0.59300 | 0.59300 |
| 2015 | 0.57700 | 0.57700 |
| 2016 | 0.56300 | 0.56300 |
Esd: Additional inter-annual variability in fishing mortality rate. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No additional variability was added to historical effort.
Historical Effort
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in historical fishing mortality (Esd), with vertical colored lines indicating 3 randomly drawn values used in the time-series plot:
Time-Series
Time-series plot showing 3 trends in historical fishing mortality (OM@EffUpper and OM@EffLower or OM@cpars$Find):
Annual increase in catchability, interannual variability in catchability: qinc, qcv
qinc: Average percentage change in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No systematic changes in future fishing efficiency were assumed.
qcv: Inter-annual variability in fishing efficiency (applicable only to forward projection and input controls). Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
No variability in changes in future fishing efficiency were assumed.
Future Catchability
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in fishing efficiency (qcv) and average annual change in fishing efficiency (qinc), with vertical colored lines indicating 3 randomly drawn values used in the time-series plot:
Time-Series
Time-series plot showing 3 trends in future fishing efficiency (catchability): 
Fishery gear length selectivity: L5, LFS, Vmaxlen, isRel
L5: Shortest length corresponding to 5 percent vulnerability. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
From the SS assessment (OM@cpars$V).
LFS: Shortest length that is fully vulnerable to fishing. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0, 0
From the SS assessment (OM@cpars$V).
Vmaxlen: The vulnerability of fish at Stock@Linf . Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0, 0
From the SS assessment (OM@cpars$V).
isRel: Selectivity parameters in units of size-of-maturity (or absolute eg cm). Single value. Boolean.
Specified Value(s): FALSE
The selectivity parameters are set as absolute sizes (not relative to the size of maturity)
Fishery length retention: LR5, LFR, Rmaxlen, DR
LR5: Shortest length corresponding ot 5 percent retention. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Retention is assumed to follow selectivity curve.
LFR: Shortest length that is fully retained. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Retention is assumed to follow selectivity curve.
Rmaxlen: The retention of fish at Stock@Linf . Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 1, 1
Retention is assumed to follow selectivity curve.
DR: Discard rate - the fraction of caught fish that are discarded. Uniform distribution lower and upper bounds. Fraction
Slot not used.
Time-varying selectivity: SelYears, AbsSelYears, L5Lower, L5Upper, LFSLower, LFSUpper, VmaxLower, VmaxUpper
SelYears: (Optional) Years representing join-points (vertices) at which historical selectivity pattern changes. Vector. Positive real numbers
Slot not used.
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
Slot not used.
L5Lower: (Optional) Lower bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
L5Upper: (Optional) Upper bound of L5 (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
LFSLower: (Optional) Lower bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
LFSUpper: (Optional) Upper bound of LFS (use ChooseSelect function to set these). Vector. Non-negative real numbers
Slot not used.
VmaxLower: (Optional) Lower bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction
Slot not used.
VmaxUpper: (Optional) Upper bound of Vmaxlen (use ChooseSelect function to set these). Vector. Fraction
Slot not used.
Current Year: CurrentYr
CurrentYr: The current calendar year (final year) of the historical simulations (eg 2011). Single value. Positive integer.
Specified Value(s): 2016
The most recent fishery data is from 2016.
Existing Spatial Closures: MPA
MPA: (Optional) Matrix specifying spatial closures for historical years.
Slot not used.
Obs Parameters
In general, the observation model parameters are taken from the Generic_Obs model in DLMtool.
Catch statistics: Cobs, Cbiascv, CAA_nsamp, CAA_ESS, CAL_nsamp, CAL_ESS
Cobs: Log-normal catch observation error expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.01, 0.01
Catch observation error was estimated from SS assessment.
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
Specified Value(s): 0.1
Borrowed from Generic_Obs
CAA_nsamp: Number of catch-at-age observation per time step. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 100, 200
Borrowed from Generic_Obs
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
Specified Value(s): 25, 50
Borrowed from Generic_Obs
CAL_nsamp: Number of catch-at-length observation per time step. Uniform distribution lower and upper bounds. Positive integers
Specified Value(s): 100, 200
Borrowed from Generic_Obs
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
Specified Value(s): 25, 50
Borrowed from Generic_Obs
Index imprecision, bias and hyperstability: Iobs, Ibiascv, Btobs, Btbiascv, beta
Iobs: Observation error in the relative abundance indices expressed as a coefficient of variation. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.1
Index observation error was estimated from SS assessment.
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
Specified Value(s): 0.2
Borrowed from Generic_Obs
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
Specified Value(s): 0.2, 0.5
Borrowed from Generic_Obs
Btbiascv: Uniform-log bounds for sampling persistent bias in current stock biomass. Uniform-log distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.33, 3
Borrowed from Generic_Obs
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
Specified Value(s): 0.5, 2
Borrowed from Generic_Obs
Bias in maturity, natural mortality rate and growth parameters: LenMbiascv, Mbiascv, Kbiascv,t0biascv, Linfbiascv
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
Specified Value(s): 0.1
Borrowed from Generic_Obs
Mbiascv: Log-normal coefficient of variation for sampling persistent bias in observed natural mortality rate. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
Borrowed from Generic_Obs
Kbiascv: Log-normal coefficient of variation for sampling persistent bias in observed growth parameter K. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
Borrowed from Generic_Obs
t0biascv: Log-normal coefficient of variation for sampling persistent bias in observed t0. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1
Borrowed from Generic_Obs
Linfbiascv: Log-normal coefficient of variation for sampling persistent bias in observed maximum length. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.05
Borrowed from Generic_Obs
Bias in length at first capture, length at full selection: LFCbiascv, LFSbiascv
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
Specified Value(s): 0.05
Borrowed from Generic_Obs
LFSbiascv: Log-normal coefficient of variation for sampling persistent bias in length-at-full selection. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.05
Borrowed from Generic_Obs
Bias in fishery reference points, unfished biomass, FMSY, FMSY/M ratio, biomass at MSY relative to unfished: FMSYbiascv, FMSY_Mbiascv, BMSY_B0biascv
FMSYbiascv: Not used. Log-normal coefficient of variation for sampling persistent bias in FMSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
Borrowed from Generic_Obs
FMSY_Mbiascv: Log-normal coefficient of variation for sampling persistent bias in FMSY/M. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
Borrowed from Generic_Obs
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
Specified Value(s): 0.2
Borrowed from Generic_Obs
Management targets in terms of the index (i.e., model free), the total annual catches and absolute biomass levels: Irefbiascv, Crefbiascv, Brefbiascv
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
Specified Value(s): 0.2
Borrowed from Generic_Obs
Crefbiascv: Log-normal coefficient of variation for sampling persistent bias in MSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
Borrowed from Generic_Obs
Brefbiascv: Log-normal coefficient of variation for sampling persistent bias in BMSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
Borrowed from Generic_Obs
Depletion bias and imprecision: Dbiascv, Dobs
Dbiascv: Log-normal coefficient of variation for sampling persistent bias in stock depletion. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.5
Borrowed from Generic_Obs
Dobs: Log-normal coefficient of variation controlling error in observations of stock depletion among years. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.05, 0.1
Borrowed from Generic_Obs
Recruitment compensation and trend: hbiascv, Recbiascv
hbiascv: Log-normal coefficient of variation for sampling persistent bias in steepness. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.2
Borrowed from Generic_Obs
Recbiascv: Log-normal coefficient of variation for sampling persistent bias in recent recruitment strength. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.3
Borrowed from Generic_Obs
Obs Plots
Observation Parameters
Catch Observations
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in catch observations (Csd) and persistent bias in observed catch (Cbias), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Depletion Observations
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in depletion observations (Dobs) and persistent bias in observed depletion (Dbias), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Abundance Observations
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in abundance observations (Btobs) and persistent bias in observed abundance (Btbias), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Index Observations
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in index observations (Iobs) and hyper-stability/depletion in observed index (beta), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Time-series plot of 3 samples of index observation error:
Plot showing an example true abundance index (blue) with 3 samples of index observation error and the hyper-stability/depletion parameter (beta):
Recruitment Observations
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in index observations (Recsd) , with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Composition Observations
Sampled Parameters
Histograms of 48 simulations of catch-at-age effective sample size (CAA_ESS) and sample size (CAA_nsamp) and catch-at-length effective (CAL_ESS) and actual sample size (CAL_nsamp) with vertical colored lines indicating 3 randomly drawn values:
Parameter Observations
Sampled Parameters
Histograms of 48 simulations of bias in observed natural mortality (Mbias), von Bertalanffy growth function parameters (Linfbias, Kbias, and t0bias), length-at-maturity (lenMbias), and bias in observed length at first capture (LFCbias) and first length at full capture (LFSbias) with vertical colored lines indicating 3 randomly drawn values:
Reference Point Observations
Sampled Parameters
Histograms of 48 simulations of bias in observed FMSY/M (FMSY_Mbias), BMSY/B0 (BMSY_B0bias), reference index (Irefbias), reference abundance (Brefbias) and reference catch (Crefbias), with vertical colored lines indicating 3 randomly drawn values:
Imp Parameters
No implementation error was assumed in the operating model.
Output Control Implementation Error: TACFrac, TACSD
TACFrac: Mean fraction of TAC taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 1, 1
TACs were assumed to be perfectly implemented.
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.
Specified Value(s): 0, 0
TACs were assumed to be perfectly implemented.
Effort Control Implementation Error: TAEFrac, TAESD
TAEFrac: Mean fraction of TAE taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 1, 1
TAEs were assumed to be perfectly implemented.
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.
Specified Value(s): 0, 0
TAEs were assumed to be perfectly implemented.
Size Limit Control Implementation Error: SizeLimFrac, SizeLimSD
SizeLimFrac: The real minimum size that is retained expressed as a fraction of the size. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 1, 1
Size limits were assumed to be perfectly implemented
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.
Specified Value(s): 0, 0
Size limits were assumed to be perfectly implemented
Imp Plots
Implementation Parameters
TAC Implementation
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in TAC implementation error (TACSD) and persistent bias in TAC implementation (TACFrac), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
TAE Implementation
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in TAE implementation error (TAESD) and persistent bias in TAC implementation (TAEFrac), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Size Limit Implementation
Sampled Parameters
Histograms of 48 simulations of inter-annual variability in size limit implementation error (SizeLimSD) and persistent bias in size limit implementation (SizeLimFrac), with vertical colored lines indicating 3 randomly drawn values used in other plots:
Time-Series
Historical Simulation Plots
Historical Time-Series
Spawning Biomass
Depletion
Absolute
Vulnerable Biomass
Depletion
Absolute
Total Biomass
Depletion
Absolute
Recruitment
Relative
Absolute
Catch
Relative
Absolute
Historical Fishing Mortality
Historical Time-Series
