Description
An object containing all the parameters needed to control the MSE which can
be build from component Stock, Fleet and Observation 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.Slots
Name- Name of the operating model
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)
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)
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)
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
Source- A reference to a website or article form which parameters were taken to define the operating model
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)
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)
Fsd- 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)
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)
Objects from the Class
Objects can be created by calls of the form
new('OM', Stock, Fleet, Observation).