An internal function to calculate the population dynamics for the next time step based on the recent MP recommendation
CalcMPDynamics(
MPRecs,
y,
nyears,
proyears,
nsim,
Biomass_P,
VBiomass_P,
LastTAE,
histTAE,
LastSpatial,
LastAllocat,
LastTAC,
TACused,
maxF,
LR5_P,
LFR_P,
Rmaxlen_P,
retL_P,
retA_P,
retA_P_real,
retA_P_real_2,
L5_P,
LFS_P,
Vmaxlen_P,
SLarray_P,
V_P,
V_P_real,
V_P_real_2,
Fdisc_P,
DR_P,
FM_P,
FM_Pret,
Z_P,
CB_P,
CB_Pret,
Effort_pot,
StockPars,
FleetPars,
ImpPars,
checks = FALSE,
control = list()
)A named list with updated population dynamics
A named list of MP recommendations. The names are the same as slotNames('Rec'), except
for Misc. Each element in the list is a matrix. With the exception of Spatial, all elements in list
have nrow=1 and ncol=nsim. Spatial has nrow=nareas. Matrices can be empty matrix, populated with all NAs
(both mean no change in management with respect to this element (e.g. Effort)), or populated with a recommendation.
MPs must either return a recommendation or no recommendation for every simulation for a particular slot (i.e. cannot have some NA and some values).
The projection year
The number of historical years
The number of projection years
The number of simulations
An array with dimensions nsim, maxage, proyears, and nareas with total biomass in the projection years
An array with dimensions nsim, maxage, proyears, and nareas with vulnerable biomass in the projection years
A vector of length nsim with the most recent TAE
A matrix of nrow=nareas and ncol=nsim with the most recent spatial management arrangements
A vector of length nsim with the most recent allocation
A vector of length nsim with the most recent TAC
A vector of length nsim with the most recent TAC
A numeric value with maximum allowed F. From OM@maxF
A matrix with nyears+proyears rows and nsim columns with the first length at 5 percent retention.
A matrix with nyears+proyears rows and nsim columns with the first length at full retention.
A matrix with nyears+proyears rows and nsim columns with the retention at maximum length.
An array with dimensions nsim, nCALbins and nyears+proyears with retention at length
An array with dimensions nsim, maxage and nyears+proyears with retention at age
An array with dimensions nsim, maxage and nyears+proyears with realized retention at age. May not asymptote at one
An array with dimensions nsim, maxage and nyears+proyears retA_P_real standardized to max 1
A matrix with nyears+proyears rows and nsim columns with the first length at 5 percent selectivity
A matrix with nyears+proyears rows and nsim columns with the first length at full selectivity
A matrix with nyears+proyears rows and nsim columns with the selectivity at maximum length.
An array with dimensions nsim, nCALbins and nyears+proyears with selectivity at length
An array with dimensions nsim, maxage and nyears+proyears with selectivity at age
An array with dimensions nsim, maxage and nyears+proyears with realized selectivity at age. May not asymptote at one
An array with dimensions nsim, maxage and nyears+proyears. V_P_real standardized to max 1
vector of length nsim with discard mortality. From OM@Fdisc but can be updated by MP (Rec@Fdisc)
A matrix with nyears+proyears rows and nsim columns with the fraction discarded.
An array with dimensions nsim, maxage, proyears, and nareas with total fishing mortality
An array with dimensions nsim, maxage, proyears, and nareas with fishing mortality of the retained fish
An array with dimensions nsim, maxage, proyears, and nareas with total mortality
An array with dimensions nsim, maxage, proyears, and nareas with total catch
An array with dimensions nsim, maxage, proyears, and nareas with retained catch
A numeric vector of potential effort
A list of stock parameters
A list of fleet parameters
A list of implementation error parameters
Logical. Run internal checks? Currently not used.
List of control parameters used internally.
A. Hordyk