getq_multi: optimize for catchability (q)
In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

View source: R/Single_stock_multi_q_REDUNDANT.R

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

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
)

`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