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.
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,
...
)An object of class OM.
a SAM output object
Positive integer. The number of simulations.
Positive integer. The number of projection years for MSE.
Positive integer. The interval at which management procedures will update the management advice in runMSE, e.g., 1 = annual updates.
Character string. The name of the operating model.
positive real number or array [sim, ages, year]. The default weight-length parameter a (W=aL^b)
positive real number or array [sim, ages, year]. The default weight-length parameter b (W=aL^b)
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
The observation model (class Obs). This function only updates the catch and index observation error.
The implementation model (class Imp). This function does not update implementation parameters.
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.
Integer. The number of recent years for which model estimates of recruitment are ignored (not reliably estimated by the assessment)
Logical. Does the assessment assume that the oldest age class is a plusgroup?
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
Logical. Should q be fixed (ie assume the F-at-age array faa is accurate?
Logical, if TRUE, a diagnostic will be reported showing the matching of the OM reconstructed numbers at age vs the assessment.
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),
T. Carruthers
Use a seed for the random number generator to sample future recruitment.
Assess2OM