Takes a fitted WHAM (Wood's Hole Assessment Model) and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.

Takes a fitted WHAM (Wood's Hole Assessment Model) and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix. Maturity-at-age-year, Mortality-at-age-year and weight-at-age-year are identical among simulations and are a direct copy of the matrices in the WHAM fitting object.

Usage

WHAM2OM(
  obj,
  nsim = 3,
  proyears = 30,
  interval = 2,
  Name = NULL,
  WLa = 1,
  WLb = 3,
  WAAind = 1,
  Obs = MSEtool::Imprecise_Unbiased,
  Imp = MSEtool::Perfect_Imp,
  nyr_par_mu = 3,
  LowerTri = 2,
  plusgroup = T,
  altinit = 0,
  fixq1 = T,
  report = FALSE,
  silent = FALSE,
  ...
)

Arguments

obj: a list object created by fit_wham().
nsim: Positive integer. The number of simulations.
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.
Name: Character string. The name of the operating model.
WLa: positive real number or array [sim, ages, year]. The default weight-length parameter a (W=aL^b)
WLb: positive real number or array [sim, ages, year]. The default weight-length parameter b (W=aL^b)
WAAind: positive integer. The index of the WHAM weight-at-age array input$data$waa to be assumed as the weight-at-age for the operating model
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.
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 assessment)
plusgroup: Logical. Does the assessment assume that the oldest age class is a plusgroup?
altinit: Integer. Various assumptions for how to set up the initial numbers. 0: standard, 1: no plus group, 2: temporary fix for MSEtool 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 assessment.
silent: Whether to silence messages to the console.
...: Additional arguments, including R0 (unfished recruitment), phi0 (unfished spawners per recruit associated with R0 and h for calculating stock recruit parameters),

Value

An object of class OM.

Details

Use a seed for the random number generator to sample future recruitment.

Author

T. Carruthers