Extract a single data stream from a FIMSFit augmented tibble

Convenience filter to pull out one specific data stream (e.g. the landings for a given module) so you can pass it directly to any yardstick metric or plot it.

Usage

get_fit_stream(x, stream_label = NULL, module_id = NULL, ...)

Arguments

x

A FIMSFit object or an already-augmented tibble from augment.FIMSFit().

stream_label

Character scalar. The value of the label column to retain, e.g., "landings_expected", "index_expected", "agecomp_expected", or "lengthcomp_expected". If NULL (default), no filtering on label is done.

module_id

Integer scalar. The module_id of the fleet or survey to retain (e.g., 1 for the first fishing fleet, 2 for the first survey in data_big). If NULL (default), all modules are included.

...

Forwarded to augment.FIMSFit() when x is a FIMSFit.

Value

A tibble::tibble() subset of the augmented data.

Details

In the FIMS output the fleet column is NA for derived-quantity rows (which is where all observed/expected pairs live). Use module_id instead to distinguish fleets and surveys — this matches the convention used in the FIMS vignettes, where module_id == 1 is the first fishing fleet and module_id == 2 is the first survey. To discover which module_id values are present in your fit, inspect augment(fit) directly.

Examples

if (FALSE) { # \dontrun{
data("data_big")
data_4_model <- FIMSFrame(data_big)

fit <- create_default_parameters(
  configurations = create_default_configurations(data = data_4_model),
  data = data_4_model
) |>
  initialize_fims(data = data_4_model) |>
  fit_fims(optimize = TRUE)

# Landings for the fishing fleet (module_id 1) — compute RMSE
get_fit_stream(fit, stream_label = "landings_expected", module_id = 1) |>
  yardstick::rmse(truth = .truth, estimate = .pred)

# Survey index stream (module_id 2 in the data_big example)
get_fit_stream(fit, stream_label = "index_expected", module_id = 2)

# All streams for fleet 1 (landings + age comp + length comp)
get_fit_stream(fit, module_id = 1)
} # }