Plot reference points from conditioning model

Plots time series of MSY reference points. Not used in automated reporting as they can be computationally expensive and individual case studies may require specific assumptions.

Usage

CM_MSY(
  report,
  d,
  year1 = 1,
  simple = FALSE,
  index = NULL,
  mean_bio = FALSE,
  type = c("spawner", "egg", "u"),
  maximize = c("MSY", "MER"),
  AEQ = TRUE,
  ncores = 1,
  na.rm = FALSE
)

CM_Sgen(
  report,
  d,
  year1 = 1,
  simple = FALSE,
  index = NULL,
  mean_bio = FALSE,
  ncores = 1,
  na.rm = FALSE
)

Arguments

report

List, output of state variables from individual MCMC samples, obtained with get_report()

d

List of data variables, obtained with get_CMdata()

year1

Numeric, first year of model

simple

Logical, whether to use Ricker lambert equations for MSY reference points (TRUE) or age-structured optimization (FALSE)

index

Integer vector to subset years with which to calculate reference points. Can be used to reduce computation or average biological parameters from a subset of years, see mean_bio argument. If NULL, uses all years of model.

mean_bio

Logical, whether to average the natural mortality and maturity parameters across years indicated in index

type

Character, the type of reference point to calculate

maximize

Character, whether the numerical optimization maximizes catch (MSY) or excess recruitment (MER). For testing only, should not impact results. Only used if simple = FALSE

AEQ

Logical, whether to use adult equivalents when calculating MSY for preterminal fisheries#' Only used if simple = FALSE. Should always be TRUE

ncores

Numeric, number of processors for parallel computation. Useful if calculating numerically for many MCMC samples

na.rm

Logical, whether to exclude negative values from the median in figures

Value

ggplot object

See also

CM_prod() CM_Srep() .CM_MSY()