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Run Iterative Francis Reweighting Procedure

run_francis.Rd

Runs an iterative Francis reweighting procedure for composition data (fishery and survey age- and length-compositions). The function reweights input data, repeatedly fits the model, and computes updated Francis weights.

Usage

run_francis(
  data,
  parameters,
  mapping,
  random = NULL,
  n_francis_iter = 10,
  newton_loops = 0
)

Arguments

data

A list of model input data, including at least observed compositions (`ObsFishAgeComps`, `ObsFishLenComps`, `ObsSrvAgeComps`, `ObsSrvLenComps`) and corresponding weights (`Wt_FishAgeComps`, `Wt_FishLenComps`, `Wt_SrvAgeComps`, `Wt_SrvLenComps`).

parameters

A list of model parameters to be passed to [fit_model()].

mapping

A list or mapping object used to specify fixed or estimated parameters in [fit_model()].

random

A character string of random effects passed to [fit_model()].

n_francis_iter

Integer. Number of Francis reweighting iterations to perform. Default is `10`.

newton_loops

Integer. Number of Newton loops passed to [fit_model()]. Default is `0`.

Value

A list with three elements:

obj

The fitted model object returned by [fit_model()], including all elements of a TMB object, data, parameters, mapping, random effects specified, and report.

end_mean_francis

A summary of the mean Francis weights from the first iteration.

end_mean_francis

A summary of the mean Francis weights from the final iteration.

recorded_weights

A summary of recorded francis weights from each iteartion.

See also

Other Francis Reweighting: do_francis_reweighting()

Examples

if (FALSE) { # \dontrun{
  out <- run_francis(data = data,
                     parameters = parameters,
                     mapping = mapping,
                     random = NULL,
                     n_francis_iter = 5,
                     newton_loops = 3)
  out$obj
  out$mean_francis
} # }