VPA2OM: Reads bootstrap estimates from a VPA stock assessment into an...
In tcarruth/MSEtool: Management Strategy Evaluation Toolkit

Description Usage Arguments Value Author(s) See Also

A function that uses a set of VPA bootstrap estimates of numbers-at-age, fishing mortality rate-at-age, M-at-age, weight-at-age, length-at-age and Maturity-at-age to define a fully described DLMtool / MSEtool operating model. The user still needs to parameterize most of the observation and implementation portions of the operating model.

VPA2OM(
  Name = "A fishery made by VPA2OM",
  proyears = 50,
  interval = 2,
  CurrentYr = 2019,
  h = 0.999,
  Obs = DLMtool::Imprecise_Unbiased,
  Imp = DLMtool::Perfect_Imp,
  naa,
  faa,
  waa,
  Mataa,
  Maa,
  laa,
  nyr_par_mu = 3,
  LowerTri = 1,
  recind = 2,
  plusgroup = TRUE,
  altinit = 0,
  fixq1 = TRUE,
  report = FALSE,
  silent = FALSE
)

`Name`	Character string. The name of the operating model.
`proyears`	Positive integer. The number of projection years for MSE.
`interval`	Positive integer. The interval at which management procedures will update the management advice in runMSE, e.g., 1 = annual updates.
`CurrentYr`	Positive integer. The current year (final year of VPA fitting to data)
`h`	Numeric value greater than 0.2 and less than 1. The steepness of the stock-recruitment curve (assumed to be close to 1 to match VPA assumption).
`Obs`	The observation model (class Obs). This function only updates the catch and index observation error.
`Imp`	The implementation model (class Imp). This function does not update implementation parameters.
`naa`	Numeric array [sim, ages, year]. Numbers-at-age [first age is age zero].
`faa`	Numeric array [sim, ages, year]. Fishing mortality rate-at-age [first age is age zero].
`waa`	Numeric array [sim, ages, year]. Weight-at-age [first age is age zero].
`Mataa`	Numeric array [sim, ages, year]. Maturity (spawning fraction)-at-age [first age is age zero].
`Maa`	Numeric array [sim, ages, year]. Natural mortality rate-at-age [first age is age zero].
`laa`	Numeric array [sim, ages, year]. Length-at-age [first age is age zero].
`nyr_par_mu`	Positive integer. The number of recent years that natural mortality, age vulnerability, weight, length and maturity parameters are averaged over for defining future projection conditions.
`LowerTri`	Integer. The number of recent years for which model estimates of recruitment are ignored (not reliably estimated by the VPA)
`recind`	Positive integer. The first age class that fish 'recruit to the fishery'. The default is 2 - ie the first position in the age dimension of naa is age zero
`plusgroup`	Logical. Does the VPA assume that the oldes age class is a plusgroup?
`altinit`	Integer. Various assumptions for how VPAs set up the initial numbers. 0: standard, 1: no plus group, 2: temporary fix for DLMtool plus group initialization
`fixq1`	Logical. Should q be fixed (ie assume the F-at-age array faa is accurate?
`report`	Logical, if TRUE, a diagnostic will be reported showing the matching of the OM reconstructed numbers at age vs the VPA assessment.
`silent`	Whether to silence messages to the console.