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.
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.
Name of the operating model
Name of the agency responsible for the management of the fishery. Character string
Name of the general geographic region of the fishery. Character string
Name of the organization who sponsored the OM. Character string
Latitude (decimal degrees). Negative values represent the South of the Equator. Numeric. Single value
Longitude (decimal degrees). Negative values represent the West of the Prime Meridian. Numeric. Single value
The number of simulations
The number of projected years
The assessment interval - how often would you like to update the management system?
The percentile of the sample of the management recommendation for each method
Maximum instantaneous fishing mortality rate that may be simulated for any given age class
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.
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
A random seed to ensure users can reproduce results exactly
A reference to a website or article from which parameters were taken to define the operating model
List of stock objects
List of Fleet objects
Hierarchical List of Observation model objects Level 1 is stock, level 2 is fleet
Hierarchical List of Implementation model objects Level 1 is stock, level 2 is fleet
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)
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).
A list nstock long, of current effort factors by fleet (default is 1 - same as current effort)
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
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.
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 can be created by calls of the form
new('MOM', Stock_list, Fleet_list, Obs_list, Imp_list).
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.