osmose.validation.fisheries¶

Fishing-vs-natural mortality (F/M) diagnostics for OSMOSE outputs.

Computes per-species F/M (realized fishing mortality vs natural mortality) from a finished run — for all species, no ICES reference points. F and M are OSMOSE instantaneous mortality rates computed on the exploited life stage(s) — those carrying fishing mortality — so that natural mortality of unfished egg/adult stages does not swamp the ratio. F is total annual fishing mortality, M = Mpred + Mstarv + Madd on the same fished stage(s). F/M > 1 means fishing removes more than natural processes (an overexploitation signal).

Functions

`annual_by_year`(values, time, *, how)	Aggregate a per-saved-step series to one value per ABSOLUTE simulation year.
`annual_rate`(per_step, steps_per_year, ...)	Sum a per-saved-step rate within each year, then mean over the trailing window.
`compute_mortality_balance`(output_dir, *, prefix)	Per-species F/M from the mortalityRate outputs.
`discover_species`(output_dir, prefix)	Species names with a mortalityRate file in {output_dir}/Mortality.
`format_mortality_report`(balances, *[, ...])	Markdown table of per-species F/M (fishing vs natural mortality).
`read_mortality`(path)	Read a mortalityRate-{sp} CSV into a (cause, stage) MultiIndex frame.

Classes

MortalityBalance(species, fishing_mortality, ...)