getFref3: Calculate Reference Yield
In DLMtool/DLMtool: Data-Limited Methods Toolkit

Calculate Reference Yield

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
)

`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