CalcMPDynamics: Calculate population dynamics from MP recommendation

In DLMtool/DLMtool: Data-Limited Methods Toolkit

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,
  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
)

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

Value

A named list with updated population dynamics

Author(s)

A. Hordyk

DLMtool/DLMtool documentation built on June 20, 2021, 5:20 p.m.