WHAM2OM: Takes a fitted SAM model and samples historical population...

In Blue-Matter/MSEtool: Management Strategy Evaluation Toolkit

Takes a fitted SAM model and samples historical population and fishing dynamics from the MLE fit and variance-covariance matrix.

Description

Takes a fitted SAM 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 SAM output object
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),

Details

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

Value

An object of class OM.

Author(s)

T. Carruthers

See Also

Assess2OM

Blue-Matter/MSEtool documentation built on Nov. 22, 2024, 8:23 p.m.