getFref3: Calculate Reference Yield

Description Usage Arguments Author(s)

View source: R/popdyn.R

Description

Calculate Reference Yield

Usage

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getFref3(x, Asize, nareas, maxage, N, pyears, M_ageArray, Mat_age, Wt_age,
  V, retA, Perr, mov, SRrel, Find, Spat_targ, hs, R0a, SSBpR, aR, bR, MPA,
  maxF, SSB0, plusgroup = 0)

Arguments

x

Integer, the simulation number

Asize

A matrix (dimensions nsim by nareas) with relative size of areas

nareas

The number of spatial areas

maxage

The maximum age

N

Array of the numbers-at-age in population. Dimensions are nsim, maxage, nyears, nareas. Only values from the first year are used, which is the current N-at-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, nyears+proyears) with the proportion mature for each age-class

Wt_age

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

V

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

retA

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

Perr

A matrix (dimensions nsim, nyears+proyears) with the recruitment deviations

mov

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

SRrel

A numeric vector nsim long specifying the recruitment curve to use

Find

A matrix (dimensions nsim, nyears) with the historical fishing effort

Spat_targ

A numeric vector nsim long with the spatial targeting

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

MPA

A matrix of spatial closures by year

maxF

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

SSB0

SSB0

plusgroup

Integer. Default = 0 = no plus-group. Use 1 to include a plus-group

useCPP

logical - use the CPP code? For testing purposes only

Author(s)

A. Hordyk


DLMtool documentation built on Dec. 6, 2019, 9:06 a.m.