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 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 = MSEtool::Imprecise_Unbiased,
Imp = MSEtool::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
)Character string. The name of the operating model.
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.
Positive integer. The current year (final year of VPA fitting to data)
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).
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.
Numeric array [sim, ages, year]. Numbers-at-age [first age is age zero].
Numeric array [sim, ages, year]. Fishing mortality rate-at-age [first age is age zero].
Numeric array [sim, ages, year]. Weight-at-age [first age is age zero].
Numeric array [sim, ages, year]. Maturity (spawning fraction)-at-age [first age is age zero].
Numeric array [sim, ages, year]. Natural mortality rate-at-age [first age is age zero].
Numeric array [sim, ages, year]. Length-at-age [first age is age zero].
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 VPA)
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
Logical. Does the VPA assume that the oldes age class is a plusgroup?
Integer. Various assumptions for how VPAs 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 VPA assessment.
Whether to silence messages to the console.