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Plot SPR diagnostics, SBPR age decompositions

plot_spr_decomp.Rd

Creates report-ready diagnostic plots of age-specific decompositions of spawning biomass per recruit (SBPR) under unfished conditions (F = 0) and at a reference fishing mortality (F = Ftarget) chosen by run_spr() (default = F40).

Usage

plot_spr_decomp(
  spr_out,
  species = NULL,
  drop_plus_from_plot = TRUE,
  include_plus_caption = TRUE,
  which_panels = c("contrib", "removed", "survivorship")
)

Arguments

spr_out

Output list from run_spr() with diagnostics = TRUE.

species

Character vector of species to include. Defaults to all species in spr_out.

drop_plus_from_plot

Logical. If TRUE (default), drops the terminal age from the plotted panels (only when plus-group diagnostics are available).

include_plus_caption

Logical. If TRUE (default), adds the plus-group share caption to plots$contrib when available.

which_panels

Character vector, any of c("contrib", "removed", "removed_prop", "survivorship").

Value

A named list of ggplot objects. A compact summary table is attached as attr(out, "summary").

Details

Returned object is a named list of ggplot objects:

  • plots$contrib: SBPR contribution by age, comparing F0 vs Ftarget.

  • plots$removed: SBPR removed by fishing at each age (F0 - Ftarget).

  • plots$removed_prop: (not shown by default) SBPR removed by fishing at each age, normalized to the species' total unfished SBPR (F0). Useful for multispecies applications to compare fractional losses among species when absolute SBPR magnitudes differ.

  • plots$survivorship: survivorship by age (per recruit), F0 vs Ftarget.

Plus-group treatment can strongly influence SBPR, especially for long-lived species. When drop_plus_from_plot = TRUE (default), the terminal age is excluded from the plots to avoid dominance by the plus group, while the fraction of total SBPR attributable to the terminal age is retained in spr_out$diagnostics$plus_share and can be appended as a plot caption.

Summary table. The function also attaches a compact per-species summary table (unfished SBPR, SBPR at Ftarget, implied SPR at Ftarget, and plus-group shares when available) as attr(plots, "summary").

Examples

if (FALSE) { # \dontrun{
spr_out <- run_spr(inp, diagnostics = TRUE,
                  multispecies_constraint = "all_species")

# Default panels
plots <- plot_spr_decomp(spr_out, drop_plus_from_plot = TRUE)
plots$contrib
plots$removed
plots$survivorship

# Summary table for optional reporting
attr(plots, "summary")
} # }