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,
L5_P,
LFS_P,
Vmaxlen_P,
SLarray_P,
V_P,
Fdisc_P,
DR_P,
M_ageArray,
FM_P,
FM_Pret,
Z_P,
CB_P,
CB_Pret,
TAC_f,
E_f,
SizeLim_f,
FinF,
Spat_targ,
CAL_binsmid,
Linf,
Len_age,
maxage,
nareas,
Asize,
nCALbins,
qs,
qvar,
qinc,
Effort_pot,
checks = FALSE
)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 expection 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
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
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 and nyears+proyears with natural mortality at age
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 matrix with nsim rows and proyears columns with the TAC implementation error
A matrix with nsim rows and proyears columns with the effort implementation error
A matrix with nsim rows and proyears columns with the size limit implementation error
A numeric vector of length nsim with fishing mortality in the last historical year
A numeric vector of length nsim with spatial targeting
A numeric vector of length nCALbins with mid-points of the CAL bins
A numeric vector of length nsim with Linf (from Stock@Linf)
An array with dimensions nsim, maxage, and nyears+proyears with length-at-age
A numeric value with maximum age from Stock@maxage
A numeric value with number of areas
A matrix with nsim rows and nareas columns with the relative size of each area
The number of CAL bins. Should be the same as length(CAL_binsmid)
A numeric vector of length nsim with catchability coefficient
A matrix with nsim rows and proyears columns with catchability variability
A numeric vector of length nsim with average annual change in catchability
A numeric vector of potential effort
Logical. Run internal checks? Currently not used.
A named list with updated population dynamics