Import an MSEtool OM from IOTC Albacore conditioning output

Constructs a multi-stock, multi-fleet MSEtool MSEtool::OM() from the MCMC posterior samples produced by the IOTC Albacore conditioning model. The OM is quarterly (4 seasons) with two sexes (Female, Male; from StockObjectList) and six fleets.

Usage

ImportOM(OMName = "OM5b")

Arguments

OMName

Character scalar. Suffix identifying which conditioning dataset to load, via get(paste0('CondData_', OMName)) (e.g. 'OM5b' loads CondData_OM5b). Also used as the Name of the returned OM.

Value

An MSEtool::OM() object with stocks and fleets fully populated from the MCMC posterior, ready to pass to MSEtool::Simulate().

Details

Natural mortality and stock-recruit parameters are drawn directly from CondData_<OMName> (e.g. CondData_OM5b). object$R0 is total (both-sex) unfished recruitment and is split evenly between the two stocks; recruitment is restricted to the recruitment season (season 4) via a mask on R0, and RecDevInit/RecDevHist are derived from the conditioning model's own numbers-at-age and recruitment deviations. R0 is passed to MSEtool::SRR() in thousands (Units = 1000), so MSEtool::Simulate() output (e.g. Hist@Number) is in thousands of fish, not the raw individual counts used by CondData_<OMName>.

Historical fishing mortality is recovered from the MCMC harvest rates (object$H), and fleet selectivity from object$sela.