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Match FAO Species Items to FishBase and SeaLifeBase

Source: R/fishbase_match.R
fishbase_match.Rd

This function goes through the FAO species items of the data one by one, looks each up in FishBase (fishes) or SeaLifeBase (other aquatic animals and plants) by the scientific name in the FAO species list, and returns the matched record with its trophic level, temperature preference, habitat, maximum length and vulnerability to fishing. Only matches that follow a published rule are made; every row gives the rule and its source, and links to the FishBase, SeaLifeBase or WoRMS pages, so each match can be checked and, if wrong, corrected (see Corrections). Items that cannot be matched by these rules are not filled in: they are marked as failed, with links for searching the name online.

Usage

fishbase_match(
  area_data = NULL,
  version = "latest",
  corrections = NULL,
  table = TRUE,
  lang = NULL,
  label = NULL,
  data_dir = fao_data_dir()
)

Arguments

area_data

FAO catch data: fishing_area_data()$area_data, or any subset of load_fao_data(). Default is NULL, all species in load_fao_data().

version

The FishBase and SeaLifeBase release, e.g. "26.06". Default is "latest": the newest online release when online (its tables are downloaded as needed), else the newest downloaded release, else the table built into the package. "builtin" always uses the built-in table, made with the same rules (see fishbase_sources() for its release).

corrections

Path of the corrections file (see Corrections), or FALSE for none.

table

A logical value. If TRUE (default), tables are saved in tables/.

lang

The language of the chart text and names: "en" (English), "zh" (Chinese) or "both" (Chinese and English). Default is NULL, which uses the language set with fao_settings() ("en" unless changed).

label

The name used in the output file names. Default is the fishing area (or the country) of the data.

data_dir

The directory where downloaded data is stored. Default is fao_data_dir().

Value

Invisibly, a data frame with one row per FAO species item.

Matching rules

Fishes (FAO major group PISCES) are looked up in FishBase first and all other items in SeaLifeBase first, following Branch et al. (2010, Supplementary Information p. 1).

  1. exact: the FAO scientific name is a valid species name in the database.

  2. synonym: the FAO name is listed as a synonym (status "synonym") of one valid species in the database's synonym table. Misapplied names are never used, since they are misidentifications and not aliases (Froese and Pauly 2000, "The SYNONYMS table"); names that the table marks as ambiguous, or that point to several species, are not matched.

  3. WoRMS valid name: a name not found by rules 1-2 is looked up online in the World Register of Marine Species (WoRMS), which the FAO ASFIS list follows for most groups (FAO 2026, pp. 1-3). Only an exact WoRMS record with status "accepted" or with a single valid name is used; the valid name is then matched by rules 1-2 or 4. Results are saved in worms_lookup.csv in the fishbase folder of data_dir and reused when the computer is offline.

  4. genus, family, order, class, phylum: an FAO item above species level (e.g. "Sardinella spp" or "Sparidae") takes the unweighted mean trophic level of the species of that taxon in the database (Branch et al. 2010, Supplementary Information p. 1; Liang and Pauly 2017). Temperature preference, habitat, length and vulnerability are left empty for these items, since studies of the mean temperature of the catch exclude items above species level (Tsikliras and Stergiou 2014; Liang et al. 2018).

  5. plant (TL 1): aquatic plants (FAO major group PLANTAE AQUATICAE) have a trophic level of 1 (Pauly et al. 1998).

Items that name several taxa (e.g. "Sepiidae, Sepiolidae") are not matched, since there is no published rule for them. Species not found by these rules are not given the values of their genus. The status column is "matched", "failed" or "pending online check" (offline and not looked up in WoRMS before).

The trophic levels are the FishBase and SeaLifeBase estimates (table "estimate", column Troph), which come from diet studies or, when these are missing, from related species and body size (Froese and Pauly 2000, "The FOOD ITEMS table", boxes 25-26). Temperature preferences (column TempPrefMean) are means of the AquaMaps distribution of the species (FishBase reference 123201); note that Cheung et al. (2013) used medians.

Rows are sorted by catch, with the share and cumulative share of the catch, so checking the first rows covers most of the catch. The table is saved in tables/, with empty checked and note columns for recording the checks.

Corrections

Wrong or missing matches can be corrected in a CSV file (by default corrections.csv in the fishbase folder of data_dir; a template is created there the first time). Each row has the alpha3 code of the FAO item and either a database ("FishBase" or "SeaLifeBase") and SpecCode of the record to use, or values to use directly (trophic_level, temp_pref_mean, habitat, max_length_cm, vulnerability), or both; note should give the source (e.g. "TL 3.5 for Marine fishes nei, Pauly et al. 1998"). Corrections are applied every time the function runs, so a team sharing data_dir shares them.

References

Branch, T.A., Watson, R., Fulton, E.A. et al. (2010). The trophic fingerprint of marine fisheries. Nature 468: 431-435. doi:10.1038/nature09528

Cheung, W.W.L., Watson, R. and Pauly, D. (2013). Signature of ocean warming in global fisheries catch. Nature 497: 365-368. doi:10.1038/nature12156

Liang, C. and Pauly, D. (2017). Fisheries impacts on China's coastal ecosystems: unmasking a pervasive 'fishing down' effect. PLoS ONE 12: e0173296. doi:10.1371/journal.pone.0173296

Liang, C., Xian, W. and Pauly, D. (2018). Impacts of ocean warming on China's fisheries catches: an application of "mean temperature of the catch" concept. Frontiers in Marine Science 5: 26. doi:10.3389/fmars.2018.00026

Pauly, D., Christensen, V., Dalsgaard, J., Froese, R. and Torres, F. (1998). Fishing down marine food webs. Science 279: 860-863. doi:10.1126/science.279.5352.860

Tsikliras, A.C. and Stergiou, K.I. (2014). Mean temperature of the catch increases quickly in the Mediterranean Sea. Marine Ecology Progress Series 515: 281-284. doi:10.3354/meps11005

FAO (2026). Nomenclature, revision, and references of the ASFIS list (version 2026). Rome, FAO. https://www.fao.org/fishery/static/ASFIS/ASFIS_References_2026_EN.pdf

Froese, R. and Pauly, D. (Eds.) (2000). FishBase 2000: concepts, design and data sources. ICLARM, Los Baños, Philippines. Chapters "The SYNONYMS table" (https://www.fishbase.se/manual/fishbasethe_synonyms_table.htm) and "The FOOD ITEMS table", boxes 25 and 26 on trophic levels (https://www.fishbase.se/manual/fishbasethe_food_items_table.htm).

Froese, R. and Pauly, D. (Eds.) FishBase. World Wide Web electronic publication. https://www.fishbase.se

Palomares, M.L.D. and Pauly, D. (Eds.) SeaLifeBase. World Wide Web electronic publication. https://www.sealifebase.se

WoRMS Editorial Board. World Register of Marine Species. Flanders Marine Institute (VLIZ). https://www.marinespecies.org, doi:10.14284/170

Examples

if (FALSE) { # \dontrun{
FAO27 <- fishing_area_data("Atlantic, Northeast", plot = FALSE)
match <- fishbase_match(FAO27$area_data, lang = "zh")
head(match[, c("species_name", "status", "match_type", "trophic_level", "url")])
} # }