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Fail the run when a taxon loses its length-weight coefficients

assert_taxa_coverage.Rd

The FishBase read is a live network read of a remote parquet dataset. A new release therefore reaches the pipeline the moment a container is rebuilt, with no code change. Release 26.06 dissolved Caesionidae into Lutjanidae and Scaridae into Labridae; both family names survive with zero species in them, so any taxon whose reference name is one of those families expands to nothing and gets no coefficients.

Nothing fails on its own when that happens: calculate_catch() left-joins the coefficients, so a taxon with no (lw_a, lw_b) pair yields NA weight, and NA sums to zero. The taxon disappears from the portal and the run stays green. This turns that silence into a failed job.

Usage

assert_taxa_coverage(
  taxa_list,
  lw,
  exempt = c("MZZ", "UNK", "UNKN", "MAE", "TAG", "GQT", "CRA", "KAK", "LHV", "RMB",
    "RTY", "SSP")
)

Arguments

taxa_list

Character vector of FAO 3-alpha codes requested.

lw

The lw table from getLWCoeffs(), after any manually curated coefficients have been bound on.

exempt

Codes that carry no coefficients today. This is a baseline, not a whitelist: it records the taxa that were already uncovered when the check was introduced (measured 2026-09-05 against FishBase 25.04 / SeaLifeBase 24.07, 120 of 134 codes resolving), so that any new loss fails the run. CJX and PWT are deliberately absent — they resolve at 25.04 and are the two codes that break at 26.06, so a release move fails here. Shrinking this list is follow-up work; each group below is a separate fix.

Not a taxon

MZZ and UNKN are dropped by get_fao_groups() before the search runs; UNK is absent from ASFIS entirely and is rewritten to the fish group's most frequent taxon later in preprocess_wf_surveys().

Wrong reference name

The ASFIS name does not describe the animal landed in Zanzibar, so the area 51 filter correctly removes it. MAE and TAG name species absent from FAO 51. AHI, BFL and MAC were the same kind of error and are now remapped on read in reshape_catch_data() – to BAF, TEI and (for the sharks-and-rays group) AQX – so they no longer reach this check.

No published coefficients

GQT (Plectorhinchus gaterinus) resolves to a species that does occur in FAO 51, but FishBase carries no length-weight pair for it in any length type. There is nothing to convert and nothing to alias; the measurement does not exist.

Outdated synonym

Names valid when ASFIS was written and since synonymised are now corrected in taxa_search_aliases(), which recovered CLP, ESR, LZV, OQC, RPO and VMX. Only CRA (Brachyura) is left: an infraorder, a rank the backbone omits.

No TL-type coefficients

The species resolves and occurs in FAO 51 and has published (a, b) pairs, but every one is fork, standard or another length type. get_length_conversions() now restates most of these on a total-length basis, which recovered 15 codes including swordfish, the tunas, the marlins and the trevallies. The five left are KAK, LHV, RMB, RTY and SSP, which have no usable length-length fit to convert through.

Value

lw, invisibly.

Porting

The check transfers unchanged, but exempt is country-specific. Run once against the country's own taxa list and record whatever it reports as the starting baseline.