Project dynamics — project

Forward-projects population dynamics for n_proj years using either stored MCMC posterior draws (uncertainty = "mcmc") or multivariate-normal draws from a fitted fixed-effects model (uncertainty = "mvn"). Pass the assessment as data; its runtime and posterior are used internally. Use opal_project() to retain the result and its provenance in the object.

Usage

project_dynamics(
  data,
  object = NULL,
  mcmc = NULL,
  n_proj = 5,
  n_iter = 1,
  rdev_y,
  sel_fya,
  catch_ysf,
  return_hist = FALSE,
  uncertainty = NULL
)

Arguments

data: An opal_obj, legacy opal_fit, or model data list.
object: For legacy data-list calls, the fitted RTMB objective. Omit when data is an Opal object.
mcmc: Legacy data-list calls only: a SparseNUTS fit. Omit for Opal objects, which use their stored posterior. In the legacy interface, when supplied, posterior draws are used for the projection. When NULL (default), MVN draws are generated from the Hessian-derived variance-covariance matrix.
n_proj: Integer. Number of projection years.
n_iter: Integer. Number of iterations (posterior draws or MVN samples).
rdev_y: Numeric matrix [n_iter, n_proj]. Projected recruitment deviates (e.g., from project_rec_devs).
sel_fya: Numeric array [n_iter, n_fishery, n_proj, n_age]. Projected selectivity (e.g., from project_selectivity).
catch_ysf: Numeric array [n_proj, n_season, n_fishery]. Projected observed catch by year, season, and fishery.
return_hist: Logical (default FALSE). When TRUE the function returns a named list with elements dyn (the projection results) and hist_sbio, a numeric matrix [n_iter, n_year + 1] containing the full spawning-biomass trajectory from each parameter draw over the historical period. The last column of hist_sbio corresponds to the same terminal state as the proj_year = 0 bridge point in the projection, so the two can be plotted seamlessly without any join discontinuity.
uncertainty: For Opal objects, choose mcmc or mvn explicitly when a posterior exists. Random effects require complete joint posterior draws.

Value

When return_hist = FALSE (default): a list of length n_iter, each element being the named list returned by do_dynamics for that iteration. When return_hist = TRUE: a named list with elements dyn and hist_sbio.