CalcMPDynamics: Calculate population dynamics from MP recommendation

In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

Calculate population dynamics from MP recommendation

Description

An internal function to calculate the population dynamics for the next time step based on the recent MP recommendation

Usage

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()
)

Arguments

MPRecs	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).
y	The projection year
nyears	The number of historical years
proyears	The number of projection years
nsim	The number of simulations
Biomass_P	An array with dimensions nsim, maxage, proyears, and nareas with total biomass in the projection years
VBiomass_P	An array with dimensions nsim, maxage, proyears, and nareas with vulnerable biomass in the projection years
LastTAE	A vector of length nsim with the most recent TAE
LastSpatial	A matrix of nrow=nareas and ncol=nsim with the most recent spatial management arrangements
LastAllocat	A vector of length nsim with the most recent allocation
LastTAC	A vector of length nsim with the most recent TAC
TACused	A vector of length nsim with the most recent TAC
maxF	A numeric value with maximum allowed F. From OM@maxF
LR5_P	A matrix with nyears+proyears rows and nsim columns with the first length at 5 percent retention.
LFR_P	A matrix with nyears+proyears rows and nsim columns with the first length at full retention.
Rmaxlen_P	A matrix with nyears+proyears rows and nsim columns with the retention at maximum length.
retL_P	An array with dimensions nsim, nCALbins and nyears+proyears with retention at length
retA_P	An array with dimensions nsim, maxage and nyears+proyears with retention at age
retA_P_real	An array with dimensions nsim, maxage and nyears+proyears with realized retention at age. May not asymptote at one
retA_P_real_2	An array with dimensions nsim, maxage and nyears+proyears retA_P_real standardized to max 1
L5_P	A matrix with nyears+proyears rows and nsim columns with the first length at 5 percent selectivity
LFS_P	A matrix with nyears+proyears rows and nsim columns with the first length at full selectivity
Vmaxlen_P	A matrix with nyears+proyears rows and nsim columns with the selectivity at maximum length.
SLarray_P	An array with dimensions nsim, nCALbins and nyears+proyears with selectivity at length
V_P	An array with dimensions nsim, maxage and nyears+proyears with selectivity at age
V_P_real	An array with dimensions nsim, maxage and nyears+proyears with realized selectivity at age. May not asymptote at one
V_P_real_2	An array with dimensions nsim, maxage and nyears+proyears. V_P_real standardized to max 1
Fdisc_P	vector of length nsim with discard mortality. From OM@Fdisc but can be updated by MP (Rec@Fdisc)
DR_P	A matrix with nyears+proyears rows and nsim columns with the fraction discarded.
FM_P	An array with dimensions nsim, maxage, proyears, and nareas with total fishing mortality
FM_Pret	An array with dimensions nsim, maxage, proyears, and nareas with fishing mortality of the retained fish
Z_P	An array with dimensions nsim, maxage, proyears, and nareas with total mortality
CB_P	An array with dimensions nsim, maxage, proyears, and nareas with total catch
CB_Pret	An array with dimensions nsim, maxage, proyears, and nareas with retained catch
Effort_pot	A numeric vector of potential effort
StockPars	A list of stock parameters
FleetPars	A list of fleet parameters
ImpPars	A list of implementation error parameters
checks	Logical. Run internal checks? Currently not used.
control	List of control parameters used internally.

Value

A named list with updated population dynamics

Author(s)

A. Hordyk

Blue-Matter/MSEtool documentation built on Nov. 22, 2024, 8:23 p.m.