MSEtool (version 3.7.3)

validcpars: Valid custom parameters (cpars)

Description

Valid custom parameters (cpars)

Usage

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

Value

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

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?

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) {
validcpars() # all valid cpars

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