Aggregate Per-Species Yield Outputs Into Fleet-Level Totals

Sums catch, revenue, and profit across species from the outputs of allocate_yields to produce a fleet-level "buffet" of spatial yield metrics. Also computes per-unit-effort (PUE) counterparts. This is the final step that builds the buffet consumed by allocate_effort.

Usage

aggregate_yields(
  yields,
  e_p_fl,
  output_format = c("matrix", "tidy"),
  groupers = c("fleet", "patch")
)

Arguments

yields

Named list of per-species yield outputs (one element per species). Each element must be the output of allocate_yields and contain patches x fleets matrices: r_p_fl, c_p_fl, and prof_p_fl. Names should match species names in fauna.

e_p_fl

Numeric matrix of effort by patch (rows) and fleet (columns), with fleet names as column names. Used to compute per-unit-effort metrics.

output_format

Character. Output format:

"matrix": (default) Returns list of patches x fleets matrices with fleet names as column names. Fast; designed for internal use in simmar.
"tidy": Returns list of tidy data frames with species summed and effort joined. Slower; used inside go_fish for user-facing output.

groupers

Character vector. Grouping columns for tidy format (default: c("fleet", "patch")). Ignored when output_format = "matrix".

Value

A named list with six elements (summed across all species):

r_p_fl: Revenue by patch and fleet
c_p_fl: Catch by patch and fleet
prof_p_fl: Profit by patch and fleet
rpue_p_fl: Revenue per unit effort (NA where effort = 0)
cpue_p_fl: Catch per unit effort (NA where effort = 0)
ppue_p_fl: Profit per unit effort (NA where effort = 0)

Details

Used in two contexts:

Inside go_fish, to aggregate exploratory fishing results across species before returning the buffet.
Inside the simmar step loop, after allocate_yields has been called for each species.

Examples

if (FALSE) { # \dontrun{
# Inside simmar after the species loop:
buffet <- aggregate_yields(yields_this_step, updated_e_p_f)

# Inside go_fish with tidy output:
buffet <- aggregate_yields(yields, e_p_fl, output_format = "tidy")
} # }