Red Drum: a NOAA Operating model
A DLMtool case study of a U.S. Gulf of Mexico data-limited stock
Skyler Sagarese [email protected]
October 2018
Introduction
During the SEDAR 49 stock assessment for US Gulf of Mexico data-limited species (2016), management procedures were evaluated and tested (via management strategy evaluation) for their feasibility in providing catch advice for eight stocks.
This operating model was based on parameters and data reported in Sagarese et al. (2016) and SEDAR (2016).
Figure 1. The U.S. EEZ and Gulf of Mexico Fishery Management Council boundaries (image taken from SEDAR 2016)
Figure 2. Red Drum (image courtesy of the NOAA Photo Library)
Operating Model
The OM rdata file can be downloaded from here
Download and import into R using myOM <- readRDS('OM.rdata')
Species Information
Species: Sciaenops ocellatus
Common Name: Red Drum
Management Agency: NOAA
Region: Gulf of Mexico
Sponsor: NOAA
Latitude: 29.5, 30, 25.1, 25.9
Longitude: -94.3, -83.8, -81.3, -96.9
OM Parameters
OM Name: Name of the operating model: U.S. Gulf of Mexico Red Drum
nsim: The number of simulations: 192
proyears: The number of projected years: 40
interval: The assessment interval - how often would you like to update the management system? 10
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
SEDAR (2016)
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): 42
Based on Sagarese et al. (2016).
R0: The magnitude of unfished recruitment. Single value. Positive real number
Specified Value(s): 1000
Arbitrary value chosen for scaling population size.
M: Natural mortality rate. Uniform distribution lower and upper bounds. Positive real number
Specified Value(s): 0.16, 0.18
Based on Sagarese et al. (2016).
M2: (Optional) Natural mortality rate at age. Vector of length maxage . Positive real number
Slot not used.
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
Slot not used. Age-constant M was assumed.
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
Slot not used.
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, 1
Based on Sagarese et al. (2016).
SRrel: Type of stock-recruit relationship. Single value, switch (1) Beverton-Holt (2) Ricker. Integer
Specified Value(s): 1
Based on Sagarese et al. (2016).
Perr: Process error, the CV of lognormal recruitment deviations. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.6, 0.76
Based on Sagarese et al. (2016).
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): 0.19, 0.36
Based on Sagarese et al. (2016).
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): 87.8, 88.3
Based on Sagarese et al. (2016).
K: von Bertalanffy growth parameter k. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.31, 0.32
Based on Sagarese et al. (2016).
t0: von Bertalanffy theoretical age at length zero. Uniform distribution lower and upper bounds. Non-positive real numbers
Specified Value(s): -1.33, -1.25
Based on Sagarese et al. (2016).
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
No value was reported, default values were used instead.
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
Slot not used.
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
Slot not used.
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): 66.5, 69.5
Based on Sagarese et al. (2016).
L50_95: Length increment from 50 percent to 95 percent maturity. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 9, 14.5
Based on Sagarese et al. (2016).
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): 0.05, 0.55
Based on Sagarese et al. (2016).
Fdisc: Fraction of discarded fish that die. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0.05, 0.08
Low discard mortality reported and substantiated in the literature and by fishermen (SEDAR 2016).
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
Based on Sagarese et al. (2016).
b: Length-weight parameter beta. Single value. Positive real number
Specified Value(s): 3.15
Based on Sagarese et al. (2016).
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): 0.1, 0.1
Based on Sagarese et al. (2016).
Frac_area_1: The fraction of the unfished biomass in stock 1. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.1, 0.1
Based on Sagarese et al. (2016).
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, 0.6
Based on Sagarese et al. (2016).
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): 135
Based on Sagarese et al. (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
Based on Sagarese et al. (2016).
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
Based on effort estimates in SEDAR (2016).
EffLower: Lower bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
Based on effort estimates in SEDAR (2016).
EffUpper: Upper bound on relative effort corresponding to EffYears. Vector. Non-negative real numbers
Based on effort estimates in SEDAR (2016).
| EffYears | EffLower | EffUpper |
|---|---|---|
| 1880 | 0.000 | 0.610 |
| 1881 | 0.000 | 0.610 |
| 1882 | 0.000 | 0.610 |
| 1883 | 0.000 | 0.610 |
| 1884 | 0.000 | 0.610 |
| 1885 | 0.000 | 0.610 |
| 1886 | 0.000 | 0.610 |
| 1887 | 0.000 | 0.610 |
| 1888 | 0.000 | 0.610 |
| 1889 | 0.000 | 0.610 |
| 1890 | 0.000 | 0.610 |
| 1891 | 0.000 | 0.610 |
| 1892 | 0.000 | 0.610 |
| 1893 | 0.000 | 0.610 |
| 1894 | 0.000 | 0.610 |
| 1895 | 0.000 | 0.610 |
| 1896 | 0.000 | 0.610 |
| 1897 | 0.000 | 0.610 |
| 1898 | 0.000 | 0.610 |
| 1899 | 0.000 | 0.610 |
| 1900 | 0.000 | 0.610 |
| 1901 | 0.000 | 0.610 |
| 1902 | 0.000 | 0.610 |
| 1903 | 0.000 | 0.610 |
| 1904 | 0.000 | 0.610 |
| 1905 | 0.000 | 0.610 |
| 1906 | 0.000 | 0.610 |
| 1907 | 0.000 | 0.610 |
| 1908 | 0.000 | 0.610 |
| 1909 | 0.000 | 0.610 |
| 1910 | 0.000 | 0.610 |
| 1911 | 0.000 | 0.610 |
| 1912 | 0.000 | 0.610 |
| 1913 | 0.000 | 0.610 |
| 1914 | 0.000 | 0.610 |
| 1915 | 0.000 | 0.610 |
| 1916 | 0.000 | 0.610 |
| 1917 | 0.000 | 0.610 |
| 1918 | 0.000 | 0.610 |
| 1919 | 0.000 | 0.610 |
| 1920 | 0.000 | 0.610 |
| 1921 | 0.000 | 0.610 |
| 1922 | 0.000 | 0.610 |
| 1923 | 0.000 | 0.610 |
| 1924 | 0.000 | 0.610 |
| 1925 | 0.000 | 0.610 |
| 1926 | 0.000 | 0.610 |
| 1927 | 0.000 | 0.610 |
| 1928 | 0.000 | 0.610 |
| 1929 | 0.000 | 0.610 |
| 1930 | 0.000 | 0.610 |
| 1931 | 0.000 | 0.610 |
| 1932 | 0.000 | 0.610 |
| 1933 | 0.000 | 0.610 |
| 1934 | 0.000 | 0.610 |
| 1935 | 0.000 | 0.610 |
| 1936 | 0.000 | 0.610 |
| 1937 | 0.000 | 0.610 |
| 1938 | 0.000 | 0.610 |
| 1939 | 0.000 | 0.610 |
| 1940 | 0.000 | 0.610 |
| 1941 | 0.000 | 0.610 |
| 1942 | 0.000 | 0.610 |
| 1943 | 0.000 | 0.610 |
| 1944 | 0.000 | 0.610 |
| 1945 | 0.000 | 0.610 |
| 1946 | 0.000 | 0.610 |
| 1947 | 0.000 | 0.610 |
| 1948 | 0.000 | 0.610 |
| 1949 | 0.000 | 0.610 |
| 1950 | 0.000 | 0.610 |
| 1951 | 0.000 | 0.610 |
| 1952 | 0.000 | 0.610 |
| 1953 | 0.000 | 0.610 |
| 1954 | 0.000 | 0.610 |
| 1955 | 0.000 | 0.610 |
| 1956 | 0.000 | 0.610 |
| 1957 | 0.000 | 0.610 |
| 1958 | 0.000 | 0.610 |
| 1959 | 0.000 | 0.610 |
| 1960 | 0.000 | 0.610 |
| 1961 | 0.000 | 0.610 |
| 1962 | 0.000 | 0.610 |
| 1963 | 0.000 | 0.610 |
| 1964 | 0.000 | 0.610 |
| 1965 | 0.000 | 0.610 |
| 1966 | 0.000 | 0.610 |
| 1967 | 0.000 | 0.610 |
| 1968 | 0.000 | 0.610 |
| 1969 | 0.000 | 0.610 |
| 1970 | 0.000 | 0.610 |
| 1971 | 0.000 | 0.610 |
| 1972 | 0.000 | 0.610 |
| 1973 | 0.000 | 0.610 |
| 1974 | 0.000 | 0.610 |
| 1975 | 0.000 | 0.610 |
| 1976 | 0.000 | 0.610 |
| 1977 | 0.000 | 0.610 |
| 1978 | 0.000 | 0.610 |
| 1979 | 0.000 | 0.610 |
| 1980 | 0.000 | 0.610 |
| 1981 | 0.273 | 0.614 |
| 1982 | 0.271 | 0.351 |
| 1983 | 0.364 | 0.464 |
| 1984 | 0.404 | 0.535 |
| 1985 | 0.367 | 0.521 |
| 1986 | 0.468 | 0.564 |
| 1987 | 0.512 | 0.587 |
| 1988 | 0.637 | 0.705 |
| 1989 | 0.513 | 0.587 |
| 1990 | 0.433 | 0.487 |
| 1991 | 0.535 | 0.600 |
| 1992 | 0.570 | 0.613 |
| 1993 | 0.553 | 0.593 |
| 1994 | 0.579 | 0.618 |
| 1995 | 0.588 | 0.628 |
| 1996 | 0.576 | 0.617 |
| 1997 | 0.617 | 0.662 |
| 1998 | 0.545 | 0.587 |
| 1999 | 0.567 | 0.610 |
| 2000 | 0.708 | 0.764 |
| 2001 | 0.735 | 0.791 |
| 2002 | 0.694 | 0.745 |
| 2003 | 0.831 | 0.896 |
| 2004 | 0.902 | 1.000 |
| 2005 | 0.784 | 0.877 |
| 2006 | 0.789 | 0.880 |
| 2007 | 0.858 | 0.957 |
| 2008 | 0.871 | 0.969 |
| 2009 | 0.774 | 0.867 |
| 2010 | 0.731 | 0.818 |
| 2011 | 0.755 | 0.830 |
| 2012 | 0.743 | 0.823 |
| 2013 | 0.782 | 0.876 |
| 2014 | 0.722 | 0.823 |
Esd: Additional inter-annual variability in fishing mortality rate. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0.71
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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): 0.62, 0.65
Based on Sagarese et al. (2016).
LFS: Shortest length that is fully vulnerable to fishing. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.75, 0.78
Based on Sagarese et al. (2016).
Vmaxlen: The vulnerability of fish at Stock@Linf . Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0, 0
Based on Sagarese et al. (2016).
isRel: Selectivity parameters in units of size-of-maturity (or absolute eg cm). Single value. Boolean.
Specified Value(s): TRUE
L5 and LFS are specified as fractions of length at 50% 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 follows selectivity. It was repoted that “the average weight of a released Red Drum was assumed to be the same as the average weight of landed Red Drum” (SEDAR 2016).
LFR: Shortest length that is fully retained. Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 0, 0
Retention follows selectivity.
Rmaxlen: The retention of fish at Stock@Linf . Uniform distribution lower and upper bounds. Non-negative real numbers
Specified Value(s): 1, 1
Retention follows selectivity.
DR: Discard rate - the fraction of caught fish that are discarded. Uniform distribution lower and upper bounds. Fraction
Specified Value(s): 0.5, 0.7
This is a recreational fishery with high discarding (up to 62%) (SEDAR 2016).
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): 2014
The most recent year of data for the SEDAR process.
Existing Spatial Closures: MPA
MPA: (Optional) Matrix specifying spatial closures for historical years.
Slot not used.
Obs Parameters
Overall, the observation model parameter are taken from the Imprecise_Biased model subject to a few additional changes.
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): 0.05, 0.05
Based on Sagarese et al. (2016).
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): 0.05
Based on Sagarese et al. (2016).
CAA_nsamp: Number of catch-at-age observation per time step. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 150, 200
Based on Sagarese et al. (2016).
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): 10, 20
Based on Sagarese et al. (2016).
CAL_nsamp: Number of catch-at-length observation per time step. Uniform distribution lower and upper bounds. Positive integers
Specified Value(s): 150, 200
Based on Sagarese et al. (2016).
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): 10, 20
Based on Sagarese et al. (2016).
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): 1.18, 1.18
Based on Sagarese et al. (2016).
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): 1.18
This parameter is not used in this version of DLMtool.
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
Based on Sagarese et al. (2016).
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): 0.2, 5
Based on Sagarese et al. (2016).
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): 0.33, 3
Based on Sagarese et al. (2016).
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): 0.2
Based on Sagarese et al. (2016).
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): 0.32
Based on Sagarese et al. (2016).
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): 0.01
Based on Sagarese et al. (2016).
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): 0.03
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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): 0.65
Based on Sagarese et al. (2016).
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): 0.12
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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): 0.11
Based on Sagarese et al. (2016).
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): 0.14
Based on Sagarese et al. (2016).
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): 0.3
Based on Sagarese et al. (2016).
Crefbiascv: Log-normal coefficient of variation for sampling persistent bias in MSY. Uniform distribution lower and upper bounds. Positive real numbers
Specified Value(s): 0.3
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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): 1
Based on Sagarese et al. (2016).
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, 0.2
Based on Sagarese et al. (2016).
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): 0.11
Based on Sagarese et al. (2016).
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
Based on Sagarese et al. (2016).
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
Output Control Implementation Error: TACFrac, TACSD
TACFrac: Mean fraction of TAC taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 0.9, 1.1
Here we assume that the actual catches can be 90-110% of the recommended TAC.
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, 0.05
We assume some inter-annual variability in following the recommended TAC.
Effort Control Implementation Error: TAEFrac, TAESD
TAEFrac: Mean fraction of TAE taken. Uniform distribution lower and upper bounds. Positive real number.
Specified Value(s): 0.9, 1.1
We have little information to inform this parameter, and set the implementation error in effort equal to the TAC implementation error.
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, 0.05
We assume some inter-annual variability in following the recommended TAE.
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): 0.95, 1
We assume that some undersized-fish are caught but otherwise, a size limit would be well-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
We assume that the implementation of the size limit is consistent between years.
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
References
Sagarese, S. R., J. J. Isely, and M. W. Smith. 2016. Review of Operating Model Parameters for SEDAR 49: Red Drum. SEDAR 49-AW-04. SEDAR, North Charleston, SC. 17 pp.
Southeast Data Assessment and Review (SEDAR). 2016. Stock Assessment Report: Gulf of Mexico Data-limited Species. SEDAR, North Charleston, SC. 618 pp.