Estimate true selectivity parameters from ecosystem model output

This function estimates selectivity curve parameters from ecosystem model fishing mortality-at-age data. It fits the curves using a Gamma distribution likelihood on un-normalized values to account for the mean-variance relationship.

Usage

estimate_true_selectivity(
  data,
  ages = NULL,
  functional_form = c("logistic", "double_logistic")
)

Arguments

data

A tibble containing filtered ecosystem model output for a single species, typically generated by calling load_model() followed by calc_truth(). Must contain the columns: "species_name", "truth_label", "truth_type", "truth_time_step", "truth_group", "truth_year", "truth_unit", and "truth_value". The data should be pre-filtered to a single species; if multiple species are detected in the data, an error is issued.

ages

A named numeric vector where the names correspond exactly to the unique labels in the truth_group column from data, and the values represent the actual structural or representative midpoint ages.

For example: ages = c("0" = 0, "1" = 1, "2+" = 2) or ages = c("juvenile" = 1, "adult" = 4).

If NULL (default), the function will attempt to convert truth_group directly into numeric values. If that fails, it will fall back to sequential indexing and issue a warning.

functional_form

A character string specifying the selectivity curve type. Currently supports "logistic" and "double_logistic".

Value

A tibble in NOAA-FIMS/FIMS format with the estimated parameter values.