Simulation specific values for all Stock parameters can be set with a vector of length OM@nsim in OM@cpars$SLOT.
Some (silly) examples:
# assuming nsim = 3
OM@cpars$M <- c(0.1, 0.2, 0.3)
OM@cpars$Linf <- c(100, 200, 300)
OM@cpars$K <- c(0.3, 0.2, 0.1)The correlations are maintained when the custom parameters are sampled. See Generating Correlated Life-History Parameters for more examples.
Natural Mortality
For simulation-, age- and year-specific values, use OM@cpars$M_ageArray with dimensions: numeric array dim = c(nsim, maxage+1, nyears+proyears).
Discard Mortality
For simulation-, age- and year-specific discard mortality use OM@cpars$Fdisc_array1 with dimensions: numeric array dim=c(nsim, maxage+1, nyears+proyears).
For simulation-, length- and year-specific discard mortality use OM@cpars$Fdisc_array2 with dimensions: numeric array dim=c(nsim, nLengthBins, nyears+proyears). Note that you must supply OM@cpars$CAL_bins or OM@cpars$CAL_binsmid as well.
Virgin Recruitment (R0)
By default OM@R0 is a single value that applies to all simulations.
Simulation-specific values for R0 can be set with OM@cpars$R0, e.g., OM@cpars$R0 <- c(1000, 2000, 1000).
Recruitment Deviations
For simulation- and year-specific recruitment deviations, use OM@cpars$Perr_y with dimensions: numeric matrix dim = c(nsim, maxage+proyears+nyears).
The first maxage values are the recruitment deviations for the age-classes in the initial year.
Note that when OM@cpars$Perr_y is populated, OM@Perr and OM@AC are ignored.
Size-at-Age
For simulation-, age- and year-specific values for mean length-at-age, use OM@cpars$Len_age with dimensions: numeric array dim = c(nsim, maxage+1, nyears+proyears).
For simulation-, age- and year-specific values for standard deviation of length-at-age, use OM@cpars$LatASD with dimensions: numeric array dim = c(nsim, maxage+1, nyears+proyears).
For simulation-, age- and year-specific values for mean weight-at-age, use OM@cpars$Wt_age with dimensions: numeric array dim = c(nsim, maxage+1, nyears+proyears).
Maturity-at-Age
For simulation-, age- and year-specific values for maturity-at-age, use OM@cpars$Mat_age with dimensions: numeric array dim = c(nsim, maxage+1, nyears+proyears).
Depletion & Initial Depletion
Simulation specific values for depletion can be set as a numeric vector of length OM@nsim in OM@cpars$D.
Initial depletion (depletion in first year) can be set with OM@cpars$initD.
Spatial & Movement
Custom movement matrix can be included with OM@cpars$mov with dimensions: numeric array dim = c(nsim, maxage+1, narea, narea) OR dim = c(nsim, maxage+1, narea, narea, nyears+proyears).
Custom area size (for more than 2 areas) can be set with OM@cpars$Asize with dimensions: numeric matrix dim = c(nsim, narea).