validcpars {MSEtool} | R Documentation |
Valid custom parameters (cpars)
Description
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$control <- list(TAC = "removals", CAL = "removals")
, can be
specified to override default settings in the MSE simulation. Possible names in the control
list are:
-
TAC
Character, set to"removals"
so that the TAC is applied to the sum of retained + discarded catch. Default only applies the TAC to the retained catch. -
CAL
Character, set to"removals"
to sample the catch-at-length from retained + discarded catch. Default only samples from retained catch. -
D
Character, set to"VB"
so that historical depletionOM@D
corresponds to vulnerable biomass depletion (only used whenOM@cpars$qs = NULL
). -
optVB
Logical, set toTRUE
so that historical depletionOM@D
corresponds to vulnerable biomass depletion. Default sets depletion according to spawning biomasss whenOM@cpars$qs = NULL
. -
optSBMSY
Logical, set toTRUE
such thatOM@D
corresponds to the ratio of spawning biomass to MSY. Default uses according to spawning biomass depletion (biomass relative to unfished levels). -
Depletion
Character, set to"end"
such that historical depletionOM@D
corresponds to the biomass at the end of the last projection year. Default corresponds to the value at the beginning of the last projection year. -
ntrials
Integer, set the number of iterations to sample the operating model to match the depletion toOM@D
. Default is 50. -
fracD
Numeric, the maximum allowable proportion of simulations allowed to hit the bounds of the depletion parameter (simulation returns an error if exceeded). Default is 0.05. -
checks
Logical. IfTRUE
, plots depletion and SB/SBMSY figures and prints values to the R console to diagnose issues with operating model configuration with regards to depletion. -
unfished
Logical. IfTRUE
, returns historical simulations with F = 0. -
progress
Logical. IfTRUE
, updates progress bar throughshiny::incProgress
. Used in conjunction with Shiny apps. -
maxiterF
Integer, the number of iterations to solve for F in the projections from the specified TAC. Default is 300. -
tolF
Numeric, the tolerance for the catch relative to the TAC when solving for F in the projections. Default is 1e-4. -
HZN
Integer, the number of generations to solve for B_low. Default is 2. SeegetBlow()
. -
Bfrac
Numeric, proportion of SBMSY to solve for B_low. Default is 0.5. SeegetBlow()
. -
skipdata
Logical. IfTRUE
, skips conditioning on data inMOM@cpars[[p]][[f]]$Data
. Only used inmultiMSE()
. -
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 inmultiMSE()
. -
HistRel
Logical, whether to perform the historical reconstruction with inter-stock relationships inMOM@Rel
. Default is TRUE. Only used inmultiMSE()
.
Examples
## Not run:
validcpars() # all valid cpars
validcpars("Obs", FALSE) # invalid Obs cpars
## End(Not run)