Assess2MOM {MSEtool} | R Documentation |
A function that develops a multiple fleet operating model (MOM) and either models a unisex or 2-sex stock from arrays of abundance, fishing mortality, and biological parameters. The user still needs to parameterize most of the observation and implementation portions of the operating model.
Assess2MOM(
Name = "MOM created by Assess2MOM",
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,
fecaa,
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 multi-OM. |
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 multiMSE, e.g., 1 = annual updates. |
CurrentYr |
Positive integer. The current year (e.g., final year of fitting to data) |
h |
The steepness of the stock-recruitment curve. Either a single numeric or a length nsim vector. |
Obs |
Either a single observation model to be used for all sexes and populations (class Obs), or a list where
|
Imp |
Either a single implementation model to be used for all sexes and populations (class Imp), or a list where
|
naa |
Numbers-at-age by sex |
faa |
Fishing mortality rate-at-age by sex and fleet |
waa |
Weight-at-age |
Mataa |
Maturity (spawning fraction)-at-age |
Maa |
Natural mortality rate-at-age |
laa |
Length-at-age |
fecaa |
Fecundity at age |
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 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 (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 MOM.
Q. Huynh