R: Class "MOM"

MOM-class {MSEtool}

R Documentation

Class `'MOM'`

Description

An object containing all the parameters needed to control a multi-stock, multi-fleet MSE which can be build from component Stock, Fleet, Obs, and Imp objects.

Details

Almost all of these inputs are a vector of length 2 which describes the upper and lower bounds of a uniform distribution from which to sample the parameter.

Slots

Name: Name of the operating model
Agency: Name of the agency responsible for the management of the fishery. Character string
Region: Name of the general geographic region of the fishery. Character string
Sponsor: Name of the organization who sponsored the OM. Character string
Latitude: Latitude (decimal degrees). Negative values represent the South of the Equator. Numeric. Single value
Longitude: Longitude (decimal degrees). Negative values represent the West of the Prime Meridian. Numeric. Single value
nsim: The number of simulations
proyears: The number of projected years
interval: The assessment interval - how often would you like to update the management system?
pstar: The percentile of the sample of the management recommendation for each method
maxF: Maximum instantaneous fishing mortality rate that may be simulated for any given age class
reps: Number of samples of the management recommendation for each method. Note that when this is set to 1, the mean value of the data inputs is used.
cpars: A hierarchical list nstock then nfleet long of custom parameters. Time series are a matrix nsim rows by nyears columns. Single parameters are a vector nsim long
seed: A random seed to ensure users can reproduce results exactly
Source: A reference to a website or article from which parameters were taken to define the operating model
Stocks: List of stock objects
Fleets: List of Fleet objects
Obs: Hierarchical List of Observation model objects Level 1 is stock, level 2 is fleet
Imps: Hierarchical List of Implementation model objects Level 1 is stock, level 2 is fleet
CatchFrac: A list nstock long, of matrices nsim x nfleet representing the fraction of current catches of the various fleets to each stock (each matrix is nsim by nfleet long and rows sum to 1 for each stock)
Allocation: A list nstock long, of matrices nsim x nfleet representing the fraction of future TACs of the various fleets to each stock (each matrix is nsim by nfleet long and rows sum to 1 for each stock).
Efactor: A list nstock long, of current effort factors by fleet (default is 1 - same as current effort)
Complexes: A list of stock complexes. Each position is a vector of stock numbers (as they appear in StockPars) for which data should be aggregated and TAC recommendations split among stocks according to vulnerable biomass
SexPars: A list of slots that control sex-specific dynamics, i.e., sex-specific spawning and hermaphroditism. More generally, controls spawning and moving abundance between stocks. See details.
Rel: A list of biological / ecological relationships among stocks over-ridden if an MP of class 'MP_F" is supplied that is a multi-fleet MP.

Objects from the Class

Objects can be created by calls of the form new('MOM', Stock_list, Fleet_list, Obs_list, Imp_list).

SexPars

SSBfrom A nstock x nstock matrix that specifies the proportion of the spawning output of the row p stock for the column p' stock. A diagonal matrix means each stock is responsible for its own recruitment.
Herm A list with each entry containing a matrix (nsim x maxage + 1) that specifies the proportion at age that moves from stock p to p' (sequential hermaphroditism). The names of the list should be of the form "H_p'_p" where p and p' are integers that identify the stock.
share_par Optional. Logical to indicate whether stock-recruit, depletion, and observation/implementation parameters are mirrored between stocks. By default, TRUE.

Author(s)

T. Carruthers and A. Hordyk

Class 'MOM'