Project dynamics

Usage

project_dynamics(
  data,
  object,
  mcmc = NULL,
  first_yr,
  last_yr,
  n_iter = 1,
  rdev_y,
  sel_fya,
  catch_ysf
)

Arguments

data: A list containing model data including dimensions, observations, and biological parameters.
object: A TMB model object returned from MakeADFun.
mcmc: Optional MCMC fit object from SparseNUTS. If NULL, uses MLE parameters.
first_yr: An integer specifying the first projection year.
last_yr: An integer specifying the last projection year.
n_iter: An integer specifying the number of simulation iterations.
rdev_y: A matrix of recruitment deviates with dimensions \[n_iter, n_years\].
sel_fya: An array of selectivity values with dimensions \[n_iter, n_fishery, n_years, n_age\].
catch_ysf: An array of catch data with dimensions \[n_years, n_season, n_fishery\].

Value

A list of length n_iter, each element containing projected population dynamics including abundance, biomass, CPUE, genetic tags, and HSP observations.