Function optimizes catchability (q, where F=qE) required to get to user-specified stock depletion
getq3(x, D, SSB0, nareas, maxage, N, pyears, M_ageArray, Mat_age, Asize, Wt_age,
V, retA, Perr, mov, SRrel, Find, Spat_targ, hs, R0a, SSBpR, aR, bR,
bounds = c(1e-05, 15), maxF, MPA, useCPP = TRUE)Integer, the simulation number
A numeric vector nsim long of sampled depletion
A numeric vector nsim long of total unfished spawning biomass
The number of spatial areas
The maximum age
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.
The number of years to project forward. Equal to 'nyears' for optimizing for q.
An array (dimensions nsim, maxage, nyears+proyears) with the natural mortality-at-age and year
An array (dimensions nsim, maxage, proyears+nyears) with the proportion mature for each age-class
A matrix (dimensions nsim, nareas) with size of each area
An array (dimensions nsim, maxage, nyears+proyears) with the weight-at-age and year
An array (dimensions nsim, maxage, nyears+proyears) with the vulnerability-at-age and year
An array (dimensions nsim, maxage, nyears+proyears) with the probability retained-at-age and year
A matrix (dimensions nsim, nyears+proyears) with the recruitment deviations
An array (dimensions nsim, nareas, nareas) with the movement matrix
A numeric vector nsim long specifying the recruitment curve to use
A matrix (dimensions nsim, nyears) with the historical fishing effort
A numeric vector nsim long with the spatial targeting
A numeric vector nsim long with the steepness values for each simulation
A matrix (dimensions nsim, nareas) with the unfished recruitment by area
A matrix (dimensions nsim, nareas) with the unfished spawning-per-recruit by area
A numeric vector nareas long with the Ricker SRR a values
A numeric vector nareas long with the Ricker SRR b values
A numeric vector of length 2 with bounds for the optimizer
A numeric value specifying the maximum fishing mortality for any single age class
A matrix of spatial closures by year
logical - use the CPP code? For testing purposes only