Reference points for conditioning model

Internal functions that calculate productivity (.CM_prod()) and reference points (.CM_MSY()) from the conditioning model. These functions can be used to calculate values for a subset of years (productivity can vary in time with natural mortality and maturity), or from average biological parameters in a subset of years.

Usage

.CM_prod(report, d, index = NULL, mean_bio = FALSE)

.CM_Srep(report, d, index = NULL, mean_bio = FALSE, type = c("spawner", "egg"))

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

Arguments

report

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

d

List of data variables, obtained with get_CMdata()

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

simple

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

AEQ

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

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

ncores

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

Value

Matrix, dimension [length(index), length(report)]. If mean_bio = TRUE, matrix has 1 row.

See also

CM_MSY()