Assess2OM  R Documentation 
Assess2OM
is identical to VPA2OM
.A function that uses a set of bootstrap estimates of numbersatage, fishing mortality rateatage, Matage, weightatage, lengthatage and Maturityatage 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.
Assess2OM(
Name = "A fishery made by VPA2OM",
proyears = 50,
interval = 2,
CurrentYr = as.numeric(format(Sys.Date(), "%Y")),
h = 0.999,
Obs = MSEtool::Imprecise_Unbiased,
Imp = MSEtool::Perfect_Imp,
naa,
faa,
waa,
Mataa,
Maa,
laa,
nyr_par_mu = 3,
LowerTri = 1,
recind = 0,
plusgroup = TRUE,
altinit = 0,
fixq1 = TRUE,
report = FALSE,
silent = FALSE,
...
)
VPA2OM(
Name = "A fishery made by VPA2OM",
proyears = 50,
interval = 2,
CurrentYr = as.numeric(format(Sys.Date(), "%Y")),
h = 0.999,
Obs = MSEtool::Imprecise_Unbiased,
Imp = MSEtool::Perfect_Imp,
naa,
faa,
waa,
Mataa,
Maa,
laa,
nyr_par_mu = 3,
LowerTri = 1,
recind = 0,
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 fitting to data) 
h 
The steepness of the stockrecruitment curve (greater than 0.2 and less than 1, assumed to be close to 1 to match VPA assumption). Either a single numeric or a length nsim vector. 
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 
faa 
Numeric array 
waa 
Numeric array 
Mataa 
Numeric array 
Maa 
Numeric array 
laa 
Numeric array 
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) 
recind 
Positive integer. The first age class that fish 'recruit to the fishery'. The default is 0  ie the first position in the age dimension of naa is age zero 
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 Fatage 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 (for all, either a numeric or a length nsim vector):

Use a seed for the random number generator to sample future recruitment.
An object of class OM.
T. Carruthers
SS2OM iSCAM2OM WHAM2OM ASAP2OM
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