getq_multi: optimize for catchability (q)

Description Usage Arguments Author(s)

View source: R/Single_stock_multi_q_REDUNDANT.R

Description

Function optimizes catchability (q, where F=qE) required to get to user-specified stock depletion

Usage

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getq_multi(
  x,
  D,
  SSB0,
  nareas,
  maxage,
  Np,
  pyears,
  M_ageArray,
  Mat_age,
  Asize,
  Wt_age,
  FleetP,
  Perr,
  mov,
  SRrel,
  hs,
  R0a,
  SSBpR,
  aR,
  bR,
  bounds = c(1e-05, 15),
  maxF,
  MPAc,
  CFp,
  useCPP = TRUE
)

Arguments

x

Integer, the simulation number

D

A numeric vector nsim long of sampled depletion

SSB0

A numeric vector nsim long of total unfished spawning biomass

nareas

The number of spatial areas

maxage

The maximum age

pyears

The number of years to project forward. Equal to 'nyears' for optimizing for q.

M_ageArray

An array (dimensions nsim, maxage, nyears+proyears) with the natural mortality-at-age and year

Mat_age

An array (dimensions nsim, maxage, proyears+nyears) with the proportion mature for each age-class

Asize

A matrix (dimensions nsim, nareas) with size of each area

Wt_age

An array (dimensions nsim, maxage, nyears+proyears) with the weight-at-age and year

FleetP

A list of Fleets containing entries for V, retA, Find and Spat_targ

mov

An array (dimensions nsim, nareas, nareas) with the movement matrix

SRrel

A numeric vector nsim long specifying the recruitment curve to use

hs

A numeric vector nsim long with the steepness values for each simulation

R0a

A matrix (dimensions nsim, nareas) with the unfished recruitment by area

SSBpR

A matrix (dimensions nsim, nareas) with the unfished spawning-per-recruit by area

aR

A numeric vector nareas long with the Ricker SRR a values

bR

A numeric vector nareas long with the Ricker SRR b values

bounds

A numeric vector of length 2 with bounds for the optimizer

maxF

A numeric value specifying the maximum fishing mortality for any single age class

useCPP

logical - use the CPP code? For testing purposes only

N

Array of the numbers-at-age in population. Dimensions are nsim, maxage, nyears, nareas. Only values from the first year (i.e 'N[,,1,]') are used, which is the current N-at-age.

MPA

A matrix of spatial closures by year

Author(s)

T.Carruthers and A. Hordyk


tcarruth/MSEtool documentation built on Sept. 16, 2020, 5:59 a.m.