CalcMPDynamics: Calculate population dynamics from MP recommendation

View source: R/popdyn.R

CalcMPDynamicsR Documentation

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 Feb. 12, 2024, 3:34 p.m.