Custom Fleet Parameters

Simulation specific values for all Fleet parameters can be set with a vector of length OM@nsim in OM@cpars$SLOT. Some (silly) examples: # assuming nsim = 3 OM@cpars$LFS <- c(100, 200, 300)
OM@cpars$qcv <- c(0.1, 0.2, 0.3) The correlations are maintained when the custom parameters are sampled. See Generating Correlated Life-History Parameters for more examples. Fishing Effort Simulation and year-specific values for historical fishing effort/mortality can be set with OM@cpars$Find with dimensions numeric matrix dim = c(nsim, nyears).

Note that is OM@cpars$Find contains actual apical F values (rather than scaled F), OM@cpars$q <- rep(1,OM@nsim) will skip the optimization for depletion (not necessary as depletion is simply calculated from the selectivity and pattern in F).

Selectivity and Retention

Simulation-, age-, and year- specific selectivity pattern can be set with OM@cpars$V with dimensions numeric array dim = c(nsim, maxage+1, nyears+proyears). Simulation-, length-, and year- specific selectivity pattern can be set with OM@cpars$SLarray with dimensions numeric array dim = c(nsim, nCALbins, nyears+proyears). Note that you must supply OM@cpars$CAL_bins or OM@cpars$CAL_binsmid as well.

Simulation-, age-, and year- specific retention pattern can be set with OM@cpars$retA with dimensions numeric array dim = c(nsim, maxage+1, nyears+proyears). Simulation-, length-, and year- specific retention pattern can be set with OM@cpars$retL with dimensions numeric array dim = c(nsim, nCALbins, nyears+proyears). Note that you must supply OM@cpars$CAL_bins or OM@cpars$CAL_binsmid as well.

Simulation- and year-specific discard ratio can be set with OM@cpars$DR_y with dimensions: numeric matrix nrow=nsim, ncol=nyears+proyears. MPAs and Spatial Closures Time-varying spatial closures can be modeled with OM@cpars$MPA with dimensions numeric matrix dim=c(nyears+proyears, nareas).

If more than two areas are modeled, OM@cpars\$mov must also be specified. See Spatial & Movement for details.