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Valid custom parameters (cpars)

Source: R/SampleOM.R
validcpars.Rd

Valid custom parameters (cpars)

Usage

validcpars(
  type = c("all", "Stock", "Fleet", "Obs", "Imp", "internal"),
  valid = TRUE,
  show = TRUE
)

Arguments

type

What cpars to show? 'all', 'Stock', 'Fleet', 'Obs', 'Imp', or 'internal'

valid

Logical. Show valid cpars?

show

Logical. Display the table in the Viewer?

Value

a HTML datatable with variable name, description and type of valid cpars

Control list

A named list for control, for example, OM@cpars$control <- list(TAC = "removals", CAL = "removals"), can be specified to override default settings in the MSE simulation. Possible names in the control list are:

  • TAC Character, set to "removals" so that the TAC is applied to the sum of retained + discarded catch. Default only applies the TAC to the retained catch.

  • CAL Character, set to "removals" to sample the catch-at-length from retained + discarded catch. Default only samples from retained catch.

  • D Character, set to "VB" so that historical depletion OM@D corresponds to vulnerable biomass depletion (only used when OM@cpars$qs = NULL).

  • optVB Logical, set to TRUE so that historical depletion OM@D corresponds to vulnerable biomass depletion. Default sets depletion according to spawning biomasss when OM@cpars$qs = NULL.

  • optSBMSY Logical, set to TRUE such that OM@D corresponds to the ratio of spawning biomass to MSY. Default uses according to spawning biomass depletion (biomass relative to unfished levels).

  • Depletion Character, set to "end" such that historical depletion OM@D corresponds to the biomass at the end of the last projection year. Default corresponds to the value at the beginning of the last projection year.

  • ntrials Integer, set the number of iterations to sample the operating model to match the depletion to OM@D. Default is 50.

  • fracD Numeric, the maximum allowable proportion of simulations allowed to hit the bounds of the depletion parameter (simulation returns an error if exceeded). Default is 0.05.

  • checks Logical. If TRUE, plots depletion and SB/SBMSY figures and prints values to the R console to diagnose issues with operating model configuration with regards to depletion.

  • unfished Logical. If TRUE, returns historical simulations with F = 0.

  • progress Logical. If TRUE, updates progress bar through shiny::incProgress. Used in conjunction with Shiny apps.

  • maxiterF Integer, the number of iterations to solve for F in the projections from the specified TAC. Default is 300.

  • tolF Numeric, the tolerance for the catch relative to the TAC when solving for F in the projections. Default is 1e-4.

  • HZN Integer, the number of generations to solve for B_low. Default is 2. See getBlow().

  • Bfrac Numeric, proportion of SBMSY to solve for B_low. Default is 0.5. See getBlow().

  • skipdata Logical. If TRUE, skips conditioning on data in MOM@cpars[[p]][[f]]$Data. Only used in multiMSE().

  • HermEq Logical, whether the equilibrium population age structures in the multi-OM is generated from the hermaphroditism vector (intended for use in salmonMSE). Default is TRUE. Only used in multiMSE().

  • HistRel Logical, whether to perform the historical reconstruction with inter-stock relationships in MOM@Rel. Default is TRUE. Only used in multiMSE().

Examples

if (FALSE) { # \dontrun{
validcpars() # all valid cpars

validcpars("Obs", FALSE) # invalid Obs cpars
} # }