🐠 FishBase and SeaLifeBase traits • faofishingreport

📦 Data: FAO Global Capture Production, release 2026.1.0 (published by FAO on 2026-03-30; catches 1950–2024), downloaded from Capture_2026.1.0.zip. Licence CC BY 4.0. fao_data_info() shows the release you use and how to cite it.

The FAO capture statistics give the catch of each species item, with its English and scientific name from the ASFIS list, but nothing about its biology. FishBase (fishes) and SeaLifeBase (other aquatic animals and plants) give these traits: trophic level, preferred temperature, habitat, maximum length, vulnerability to fishing, resilience and prior r. The package uses them in two places: the preferred temperature for the mean temperature of the catch, and the resilience and prior r for the CMSY++ priors.

The data come from fixed copies (releases) of the FishBase and SeaLifeBase tables, which the rfishbase project of rOpenSci publishes as parquet files (Boettiger et al. 2012; source code at https://github.com/ropensci/rfishbase, files at https://data.source.coop/cboettig/fishbase/). The package matches them to the FAO species items only by published rules, and every match carries the links needed to check it.

Function	What it does	Internet
`check_fishbase_update()`	Lists the newest release online and the releases downloaded	Yes
`download_fishbase_data()`	Downloads the tables of a release	Yes
`fishbase_table()`	Reads one table of a release	Only if the table has not been downloaded
`fishbase_match()`	Matches the FAO species items to FishBase and SeaLifeBase	No with `version = "builtin"` or a downloaded release
`fishbase_sources()`	Lists sources, licences, tables and matching rules	No

📦 Releases, folders and the built-in table

A release is named by its year and month, e.g. "26.06" (June 2026). Releases are fixed snapshots, so a table downloaded once is identical to the one online. They are published at https://data.source.coop/cboettig/fishbase/, and the package saves the tables it downloads in the fishbase folder of fao_data_dir():

Path in `fao_data_dir()`	Content
`fishbase/fb/<release>/<table>.parquet`	FishBase tables, e.g. `fishbase/fb/26.06/estimate.parquet`
`fishbase/slb/<release>/<table>.parquet`	SeaLifeBase tables
`fishbase/fb/<release>/files.csv` (and `slb/`)	URL, size and download date of each table
`fishbase/corrections.csv`	Your corrections of matches (see Check and correct the matches)
`fishbase/worms_lookup.csv`	Names looked up in WoRMS, reused when the computer is offline

fao_data_dir() is the user data folder of R unless it is changed with fao_settings(data_dir = ...), for example to a folder shared by a team. Each function also has a data_dir argument. Reading the parquet files needs the nanoparquet package, which is installed with faofishingreport.

The version argument chooses the release:

`version`	Release used
`"latest"` (default)	Online: the newest release online; its tables are downloaded the first time they are needed. Offline, or with `fao_settings(online = FALSE)`: the newest downloaded release, with a message. Offline with nothing downloaded: `fishbase_match()` uses the built-in table; `fishbase_table()` stops with an error
A release, e.g. `"26.06"`	This release, downloaded if needed
`"builtin"`	The built-in table, without connecting to the internet (`fishbase_match()` and the functions that call it)

The built-in table

The package includes the result of fishbase_match() for every species item of the FAO data bundled with the package, without manual corrections. It is the file inst/extdata/fishbase_traits.rda, made by data-raw/build_fishbase_traits.R, and its attributes give the releases it was made from:

load(system.file("extdata", "fishbase_traits.rda", package = "faofishingreport"))
attr(fishbase_traits, "fishbase_version")   # FishBase and SeaLifeBase releases
#>    fishbase sealifebase 
#>     "26.06"     "26.06"
attr(fishbase_traits, "fao_release")        # FAO release whose species items were matched
#> [1] "2026.1.0"
attr(fishbase_traits, "built")              # date the table was made
#> [1] "2026-10-10"
nrow(fishbase_traits)
#> [1] 3797
table(fishbase_traits$match_type)
#> 
#>                     class                     exact                    family 
#>                        17                      3030                       170 
#>                     genus               not matched                     order 
#>                       358                        76                        25 
#>                    phylum              plant (TL 1)                   synonym 
#>                         7                        71                        38 
#>  WoRMS valid name (exact) WoRMS valid name (family)  WoRMS valid name (genus) 
#>                         3                         1                         1

With version = "builtin" nothing is downloaded and the results are the same on every computer. This article uses it, so the website can be built without downloads. Items that are not in the built-in table, such as new items of a later FAO release, are marked as “pending online check”. version = "latest" gives the values of the newest release, which can differ slightly once FishBase publishes a new one.

Licence. FishBase and SeaLifeBase data are licensed CC BY-NC 4.0 by the FishBase.org team: they can be used with attribution, but not for commercial purposes. Cite FishBase (Froese and Pauly, Eds.) and SeaLifeBase (Palomares and Pauly, Eds.) with the release used. The same licence applies to the built-in table and to the trait values in the results of these functions. Valid names from WoRMS are licensed CC BY. fishbase_sources() lists every source.

🔄 Check for new releases: check_fishbase_update()

check_fishbase_update() lists the releases published online and compares the newest with the releases downloaded on this computer. It contacts the data server, so it is not run here. On a computer where nothing has been downloaded yet, it prints:

check_fishbase_update()
#> FishBase
#>   Latest online release: 26.06 (222 tables)
#>   Downloaded locally:    none
#>   Run download_fishbase_data("fishbase") to download the latest release (or the tables of it that are missing).
#> SeaLifeBase
#>   Latest online release: 26.06 (202 tables)
#>   Downloaded locally:    none
#>   Run download_fishbase_data("sealifebase") to download the latest release (or the tables of it that are missing).

Argument	Meaning	Default
`server`	`"fishbase"`, `"sealifebase"` or both	both
`data_dir`	Folder where downloaded data is stored	`fao_data_dir()`
`quiet`	If `TRUE`, no message is printed	`FALSE`

It returns, invisibly, a data frame with one row per database:

Column	Meaning
`server`	`"fishbase"` or `"sealifebase"`
`latest_online`	Newest release online (`NA` when offline)
`newest_local`	Newest release downloaded (`NA` if none)
`tables_online`	Number of tables in the newest online release
`tables_local`	Number of tables downloaded of the newest local release
`update_available`	`TRUE` when a newer release is online, or when the newest release is downloaded but not all of its tables

Because of the second condition, update_available stays TRUE after the default download of six tables (next section). To see whether a newer release exists, compare latest_online with newest_local.

⬇️ Download a release: download_fishbase_data()

download_fishbase_data() downloads the tables of a FishBase and/or SeaLifeBase release to data_dir, so they can be used offline. Downloading beforehand is optional: with version = "latest", fishbase_match() and mean_temperature_catch() download the four tables they need the first time they run (about 23 MB for both databases with release 26.06). Download beforehand to work offline later, to keep one release for a whole project, or to get every table.

download_fishbase_data()                              # the six tables the package uses, both databases
download_fishbase_data(tables = "all")                # every table of FishBase and SeaLifeBase
download_fishbase_data("fishbase", tables = c("species", "estimate"))
download_fishbase_data(version = "25.04")             # an earlier release

Argument	Meaning	Default
`server`	`"fishbase"`, `"sealifebase"` or both	both
`version`	The release to download, e.g. `"26.06"`. A release that is not online gives an error listing the releases that are	`"latest"`
`tables`	`"needed"` for the six tables the package uses, `"all"` for every table, or table names, e.g. `c("species", "estimate")`	`"needed"`
`data_dir`	Folder where the tables are saved	`fao_data_dir()`
`overwrite`	If `TRUE`, tables already downloaded are downloaded again	`FALSE`
`quiet`	If `TRUE`, progress messages are not printed	`FALSE`

Sizes of release 26.06:

Tables	FishBase	SeaLifeBase
`tables = "needed"` (6 tables)	15.8 MB	13.2 MB
The 4 tables used by `fishbase_match()`	12.6 MB	10.3 MB
`tables = "all"`	222 tables, about 140 MB	202 tables, about 108 MB

The six tables of tables = "needed":

Table	Content	Used by
`species`	Genus, species, family code, habitat (`DemersPelag`), maximum length (`Length`), vulnerability to fishing (`Vulnerability`)	`fishbase_match()`
`estimate`	Trophic level (`Troph`, `seTroph`), preferred temperature (`TempPrefMean`), prior r (`prior_r`, `lcl_r`, `ucl_r`)	`fishbase_match()`; the built-in CMSY++ prior table
`families`	Family, order, class and phylum	`fishbase_match()`
`synonyms`	Other names of each species with their status (accepted name, synonym, misapplied name, ambiguous synonym)	`fishbase_match()`
`stocks`	Resilience (High, Medium, Low, Very low)	the built-in CMSY++ prior table
`faoareas`	Occurrence of each species by FAO major fishing area

Before downloading, the function prints what it will download, from where, under which licence and to which folder. Each table is first written as a .part file and renamed when it is complete. Tables already downloaded (with the same size as online) are skipped, so an interrupted download continues when the function is run again; tables that fail give a warning.

It returns, invisibly, a data frame with one row per table: server, version, table, size (bytes) and status ("downloaded", "already downloaded" or "failed").

📋 Read a table: fishbase_table()

fishbase_table() returns one table of FishBase or SeaLifeBase as a data frame, read from the copy on this computer. When the computer is online, it first looks up the newest release and downloads the table if it is not there yet. When it is offline, or with fao_settings(online = FALSE), it uses the newest downloaded release that has the table, and says so. It is not run here, since it needs downloaded tables; the output shown is that of release 26.06:

estimate <- fishbase_table("estimate")
#> Using FishBase release 26.06 (the latest online release).
attr(estimate, "fishbase_version")
#> [1] "26.06"
# European pilchard (Sardina pilchardus) is SpecCode 1350 in FishBase
estimate[estimate$SpecCode == 1350, c("SpecCode", "Troph", "seTroph", "TempPrefMean", "prior_r", "lcl_r", "ucl_r")]
#>      SpecCode Troph seTroph TempPrefMean   prior_r     lcl_r     ucl_r
#> 1243     1350  3.06     0.1         10.3 0.6281019 0.4145473 0.9421529

slb_species <- fishbase_table("species", server = "sealifebase", version = "26.06")

Argument	Meaning	Default
`table`	The table name, e.g. `"species"`, `"estimate"`, `"ecology"`, `"synonyms"` or `"families"`	(required)
`server`	`"fishbase"` or `"sealifebase"`	`"fishbase"`
`version`	The release, e.g. `"26.06"`	`"latest"`
`data_dir`	Folder where downloaded data is stored	`fao_data_dir()`

It returns the whole table, with every column (the FishBase 26.06 estimate table has 36,761 rows and 70 columns), and three attributes: fishbase_server, fishbase_version and source_url, the address of the parquet file. A table that has been read is kept in memory for the rest of the R session. check_fishbase_update() shows how many tables a release has; the rfishbase documentation describes what they contain.

🔗 Match the FAO species items: fishbase_match()

fishbase_match() goes through the FAO species items of the data one by one. It looks each up in FishBase or SeaLifeBase by its scientific name in the FAO species list, and returns the matched record with its trophic level, preferred temperature, habitat, maximum length and vulnerability to fishing. Each row gives the rule used and its source, and links to the FishBase, SeaLifeBase or WoRMS pages, so that the match can be checked. Items that no rule matches are left empty and marked as failed, with links for searching the name online.

fb27 <- fishbase_match(FAO27$area_data, version = "builtin", corrections = FALSE)
#> FAO species items: 1029; matched 1001, failed 28, pending online check 0. Matched items cover 98.3% of the catch.

corrections = FALSE leaves out any corrections saved on this computer, so the example gives the same result everywhere. The items are sorted by catch, so the first rows cover most of it:

main <- head(fb27, 15)
main$page <- ifelse(is.na(main$url), "", paste0("[open](", main$url, ")"))
show_table(main[, c("species_name", "fao_scientific_name", "catch_pct", "match_type", "database",
                    "temp_pref_mean", "trophic_level", "page")], n = 15)

species_name	fao_scientific_name	catch_pct	match_type	database	temp_pref_mean	trophic_level	page
Atlantic herring	Clupea harengus	18.55	exact	FishBase	6.6	3.38	open
Atlantic cod	Gadus morhua	13.94	exact	FishBase	6.6	4.09	open
Capelin	Mallotus villosus	10.02	exact	FishBase	2.7	3.15	open
Blue whiting(=Poutassou)	Micromesistius poutassou	7.09	exact	FishBase	7.0	4.13	open
Atlantic mackerel	Scomber scombrus	6.19	exact	FishBase	10.2	3.63	open
Sandeels(=Sandlances) nei	Ammodytes spp	4.65	genus	FishBase	NA	3.16	open
European sprat	Sprattus sprattus	3.95	exact	FishBase	9.5	3.01	open
Saithe(=Pollock)	Pollachius virens	3.85	exact	FishBase	7.0	4.31	open
Haddock	Melanogrammus aeglefinus	3.56	exact	FishBase	8.4	4.03	open
Norway pout	Trisopterus esmarkii	2.11	exact	FishBase	7.8	3.68	open
Brown seaweeds	Phaeophyceae	2.11	plant (TL 1)	SeaLifeBase	NA	1.00	open
European pilchard(=Sardine)	Sardina pilchardus	1.67	exact	FishBase	10.3	3.06	open
Atlantic redfishes nei	Sebastes spp	1.62	genus	FishBase	NA	3.70	open
Atlantic horse mackerel	Trachurus trachurus	1.54	exact	FishBase	13.3	3.71	open
European plaice	Pleuronectes platessa	1.35	exact	FishBase	10.2	3.17	open

Species found under their FAO name (exact) get all values. Items above species level, such as “Jack and horse mackerels nei” (Trachurus spp), get the mean trophic level of their genus or family but no preferred temperature. “Marine fishes nei” has no values: its FAO name, Actinopterygii, is not found in FishBase, which places these fishes in classes such as Teleostei, and WoRMS gives the same name as valid. A value for such an item can be given in the corrections file, with its source.

Argument	Meaning	Default
`area_data`	FAO catch data: `fishing_area_data()$area_data`, or any subset of `load_fao_data()`	`NULL`: all species in `load_fao_data()`
`version`	The FishBase and SeaLifeBase release (see above): `"latest"`, a release such as `"26.06"`, or `"builtin"`	`"latest"`
`corrections`	Path of a corrections file, or `FALSE` for none	`NULL`: `corrections.csv` in the `fishbase` folder of `data_dir`, created as an empty template the first time
`table`	If `TRUE`, the table is saved as `tables/<label>_fishbase_match.csv`	`TRUE`
`lang`	Language of the `species_name` column: `"en"`, `"zh"` or `"both"`	`NULL`: the language set with `fao_settings()`
`label`	Name used in the file name	The fishing area (or country) of the data
`data_dir`	Folder where downloaded data, corrections and WoRMS results are stored	`fao_data_dir()`

It returns, invisibly, a data frame with one row per FAO species item, sorted by catch. Its attribute fishbase_version gives the releases used. The columns:

Column	Meaning
`species_name`, `species_en`	FAO name in the language chosen, and in English
`alpha3`, `fao_scientific_name`	FAO 3-alpha code and scientific name
`taxon_level`, `major_group`	Level of the item (species, genus, family, higher) and FAO major group (PISCES, CRUSTACEA, …)
`catch_tonnes`, `catch_pct`, `cumulative_pct`	Catch of the item over all years of the data, its share of the total catch and the cumulative share (%)
`status`	`"matched"`, `"failed"` or `"pending online check"`
`match_type`	The rule that matched the item (next section)
`database`, `matched_name`, `SpecCode`	Database, name and species code of the record used
`n_species`	Number of species of the taxon, for items above species level
`trophic_level`, `trophic_level_se`	Trophic level (`Troph`) and its standard error
`temp_pref_mean`	Preferred temperature (`TempPrefMean`, °C)
`habitat`	Habitat (`DemersPelag`, e.g. pelagic-neritic, demersal, reef-associated)
`max_length_cm`	Maximum length (cm)
`vulnerability`	Vulnerability to fishing (FishBase index, out of 100)
`url`	FishBase or SeaLifeBase page of the record (species page, species list of the genus, family page, or a search)
`search_url`, `worms_url`	Search of the FAO name in FishBase or SeaLifeBase, and its WoRMS page
`match_note`, `rule_source`	Why an item was matched or not, and the published source of the rule
`source`	Database and release, with “(built-in table)” when the built-in table was used
`checked`, `note`	Empty columns for recording your checks

The trophic levels are the FishBase and SeaLifeBase estimates (table estimate, column Troph). They come from diet studies or, when there are none, from related species and body size (Froese and Pauly 2000, “The FOOD ITEMS table”, boxes 25 and 26). The preferred temperatures (TempPrefMean) are means over the AquaMaps distribution of each species (FishBase reference 123201; Froese 2020); Cheung et al. (2013) used medians instead.

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). The value of match_type tells which rule matched an item:

`match_type`	Rule	Values given	Source
`exact`	The FAO scientific name is a valid species name in the database	All	Branch et al. (2010)
`synonym`	The FAO name is a synonym (status “synonym”) of one valid species in the synonym table of the database. Misapplied names are never used, since they are misidentifications, not other names of the species; ambiguous synonyms, and names that point to several species, are not matched	All	Froese and Pauly (2000), “The SYNONYMS table”
`WoRMS valid name (...)`	A name not found by the rules above is looked up online in the World Register of Marine Species (WoRMS), which the FAO ASFIS list follows for most groups. Only an exact WoRMS record with status “accepted”, or with a single valid name, is used; the valid name is then matched again, and the rule it matched is given in brackets, e.g. `WoRMS valid name (exact)`	As for that rule	FAO (2026), pp. 1–3; WoRMS Editorial Board
`genus`, `family`, `order`, `class`, `phylum`	An 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	Trophic level only	Branch et al. (2010); Liang and Pauly (2017)
`plant (TL 1)`	Aquatic plants (FAO major group PLANTAE AQUATICAE)	Trophic level 1	Pauly et al. (1998)
`manual`	A correction in the corrections file	The values or record given	Your source, in `note`
`not matched`	Species not found (the values of their genus are not used), items that name several taxa (e.g. “Sepiidae, Sepiolidae”), WoRMS records that are uncertain or several	None (`status` is `"failed"`)	No published rule for these cases

Temperature preference, habitat, length and vulnerability are left empty for items above species level, since studies of the mean temperature of the catch leave these items out (Tsikliras and Stergiou 2014; Liang et al. 2018). Results of the WoRMS look-ups are saved in worms_lookup.csv and reused when the computer is offline; a name not looked up before is then marked "pending online check". The built-in table was made online, so its items have all been looked up.

Coverage of the catch

The share of the catch matched depends on how the catch is reported. catch_pct is the share of the total catch of all years in the data:

# Share of the catch (%) by kind of match
round(sort(tapply(fb27$catch_pct, fb27$match_type, sum), decreasing = TRUE), 1)
#>        exact        genus plant (TL 1)  not matched       family        order 
#>         86.3          7.8          3.0          1.7          0.8          0.2 
#>        class       phylum      synonym 
#>          0.1          0.0          0.0

# Share of the catch (%) of species-level items with a preferred temperature
species_level <- c("exact", "synonym", "WoRMS valid name (exact)", "WoRMS valid name (synonym)")
round(sum(fb27$catch_pct[fb27$match_type %in% species_level & !is.na(fb27$temp_pref_mean)]), 1)
#> [1] 86.2

In area 27, matched items make up 98% of the catch. Genus and family items have a trophic level only; species-level items with a preferred temperature make up 86%, and this is the part of the catch that the mean temperature of the catch can use. The coverage also changes from year to year; mean_temperature_catch() shows it for each year (see below).

Check and correct the matches

The matches are made automatically and are not checked by the package. Names do not always agree between databases: FAO ASFIS names change slowly, FishBase, SeaLifeBase and WoRMS follow different classifications, and synonyms and misspellings are common (Grenié et al. 2023). Before using the values:

Open the table saved in tables/ (here tables/Atlantic__Northeast_fishbase_match.csv). The items are sorted by catch, so the first rows matter most.
For each item, open url (the record used), search_url and worms_url, and read match_note and rule_source. Check that the record is the FAO item, and that its values are plausible for the stock in the area.
Write who checked it, or the date, in checked. Correct wrong or missing values in a corrections file, with their source.

A corrections file is a CSV file with one row per FAO item to correct:

Column	Meaning
`alpha3`	FAO 3-alpha code of the item (required)
`species_en`	FAO English name (optional, for reading the file)
`database`, `SpecCode`	`"FishBase"` or `"SeaLifeBase"`, and the species code of the record to use; its values are then read from the downloaded tables
`trophic_level`, `temp_pref_mean`, `habitat`, `max_length_cm`, `vulnerability`	Values to use directly (they replace those of the record)
`note`	The source of the correction

By default fishbase_match() reads corrections.csv in the fishbase folder of data_dir, and creates an empty one there the first time. Corrections are applied every time the function runs, so a team that shares data_dir shares them. A corrected item gets status “matched”, match_type “manual”, and its rule_source gives the file and the note.

As an example, “Frigate and bullet tunas” names two species (Auxis thazard and A. rochei), so no rule matches it. Here it is given the values of frigate tuna, the first of the two, from the match of the item “Frigate tuna”. Whether such a value fits an item has to be judged by you; the note says where it comes from:

fri <- fb27[fb27$alpha3 == "FRI", ]
fix <- data.frame(alpha3 = "FRZ", species_en = "Frigate and bullet tunas",
                  trophic_level = fri$trophic_level, temp_pref_mean = fri$temp_pref_mean,
                  note = paste("Values of Auxis thazard,", fri$source, "SpecCode", fri$SpecCode))
write.csv(fix, "my_corrections.csv", row.names = FALSE)

fb27_fixed <- fishbase_match(FAO27$area_data, version = "builtin", corrections = "my_corrections.csv")
#> Applied 1 correction(s) from my_corrections.csv
#> FAO species items: 1029; matched 1002, failed 27, pending online check 0. Matched items cover 98.3% of the catch.
show_table(fb27_fixed[fb27_fixed$alpha3 == "FRZ", c("species_name", "status", "match_type", "trophic_level",
                                                    "temp_pref_mean", "rule_source")])

	species_name	status	match_type	trophic_level	temp_pref_mean	rule_source
172	Frigate and bullet tunas	matched	manual	4.37	22	Manual correction (my_corrections.csv): Values of Auxis thazard, FishBase 26.06 (built-in table) SpecCode 94

With downloaded tables, a correction can instead name the record to use, and all its values are read from it. The built-in table cannot look up a SpecCode, so with version = "builtin" give the values themselves:

fix <- data.frame(alpha3 = "FRZ", database = "FishBase", SpecCode = 94,
                  note = "Record of Auxis thazard; give your source here")
write.csv(fix, "my_corrections.csv", row.names = FALSE)
fishbase_match(FAO27$area_data, version = "26.06", corrections = "my_corrections.csv")

mean_temperature_catch(), and fao_report() through it, run fishbase_match() with the default corrections file. Corrections meant for them therefore belong in corrections.csv in the fishbase folder of data_dir (add rows to it with a spreadsheet program), or in a checked match table given with match = (mtc_match = in fao_report()).

📜 Sources and licences: fishbase_sources()

fishbase_sources() lists where the FishBase, SeaLifeBase and WoRMS data come from, their licences and how to cite them, the tables downloaded and what they hold, and the matching rules of fishbase_match() with their published sources. download_fishbase_data() prints a summary of the same information.

Argument	Meaning	Default
`print`	If `TRUE`, the list is printed	`TRUE`

It returns, invisibly, a data frame with one row per data source, table or rule, and the columns type ("data", "table" or "rule"), item, description, source (citation or licence) and link. The data sources:

src <- fishbase_sources(print = FALSE)
show_table(src[src$type == "data", c("item", "description", "source", "link")])

	item	description	source	link
1	FishBase	Fishes: names, classification, ecology, trophic level, temperature preference, resilience	Froese, R. and Pauly, D. (Eds.) FishBase. www.fishbase.se. Licence CC BY-NC 4.0 (FishBase.org team): cite, no commercial use	https://www.fishbase.se
2	SeaLifeBase	Other aquatic animals and plants: the same tables as FishBase	Palomares, M.L.D. and Pauly, D. (Eds.) SeaLifeBase. www.sealifebase.se. Licence CC BY-NC 4.0 (FishBase.org team)	https://www.sealifebase.se
3	Snapshots	Versioned copies of the FishBase and SeaLifeBase tables as parquet files, the files downloaded by the package	Published by the rfishbase project of rOpenSci (Boettiger et al. 2012, J. Fish Biol. 81(6): 2030-2039, doi:10.1111/j.1095-8649.2012.03464.x)	https://data.source.coop/cboettig/fishbase/
4	rfishbase	R package that publishes the snapshots and reads them; faofishingreport reads the same files directly, without depending on it	Boettiger, C., Lang, D.T. and Wainwright, P.C. (2012). J. Fish Biol. 81(6): 2030-2039. Source code and documentation: https://github.com/ropensci/rfishbase, https://docs.ropensci.org/rfishbase/	https://github.com/ropensci/rfishbase
5	WoRMS	Valid names of species and taxa, looked up online for names not found in FishBase or SeaLifeBase	WoRMS Editorial Board. World Register of Marine Species. VLIZ. doi:10.14284/170. Licence CC BY	https://www.marinespecies.org
19	Built-in table	Used only when FishBase cannot be reached and has not been downloaded: FishBase 26.06, SeaLifeBase 26.06, made on 2026-10-10 for the 3797 species items of FAO release 2026.1.0	Made by data-raw/build_fishbase_traits.R with the rules above; CC BY-NC 4.0 (FishBase.org team)

🌡️ Use in the mean temperature of the catch

mean_temperature_catch() computes the mean temperature of the catch (MTC): the mean preferred temperature of the species caught, weighted by their catch (Cheung et al. 2013). It takes the preferred temperatures from fishbase_match(), which it runs with its own version and data_dir (applying the corrections file), or from a match table given with match =. Only items with status “matched” and a match_type in use_match are used; by default exact, synonym, WoRMS valid name (exact), WoRMS valid name (synonym) and manual. Genus and family items have no preferred temperature and are not used.

Here the corrected table of the example above is given with match =, so the frigate and bullet tunas are now used:

mtc <- mean_temperature_catch(FAO27$area_data, match = fb27_fixed)

show_table(mtc$species[mtc$species$used, c("species_name", "match_type", "temp_pref_mean", "catch_pct",
                                           "weight_pct", "contribution_c")], n = 8)

	species_name	match_type	temp_pref_mean	catch_pct	weight_pct	contribution_c
1	Atlantic herring	exact	6.6	18.55	21.52	1.42
2	Atlantic cod	exact	6.6	13.94	16.17	1.07
3	Capelin	exact	2.7	10.02	11.62	0.31
4	Blue whiting(=Poutassou)	exact	7.0	7.09	8.22	0.58
5	Atlantic mackerel	exact	10.2	6.19	7.18	0.73
7	European sprat	exact	9.5	3.95	4.58	0.44
8	Saithe(=Pollock)	exact	7.0	3.85	4.46	0.31
9	Haddock	exact	8.4	3.56	4.13	0.35

match = takes a data frame or the path of a CSV file: the table saved by fishbase_match(), or the species table of an earlier run of mean_temperature_catch(), after checking it. Items marked in checked count as checked; until all items used are checked, the function says how much of the catch has been checked, and the chart caption says that the values are automatic first matches. Without match =, the default version = "latest" downloads the tables it needs the first time (about 23 MB):

mtc <- mean_temperature_catch(FAO27$area_data)                         # newest FishBase release
mtc <- mean_temperature_catch(FAO27$area_data, version = "builtin")    # built-in table, no download
mtc <- mean_temperature_catch(FAO27$area_data, match = "tables/Atlantic__Northeast_fishbase_match.csv")

The article 🌡️ Sea temperature and catch temperature explains the SST data, the trends, and the limitations of the preferred temperatures.

📉 Use in the CMSY++ priors

CMSY++ needs a prior range for the intrinsic growth rate r of each stock. cmsy_priors() searches a second built-in table (inst/extdata/cmsy_priors.csv, made by data-raw/cmsy_priors.R) with the resilience (table stocks) and the prior r (table estimate) of the species-level items of the FAO capture statistics in FishBase or SeaLifeBase 26.06. It works offline:

p27 <- cmsy_priors(c("HER", "WHB", "MAC", "COD"))
show_table(p27[, c("species_name", "matched_name", "match_type", "resilience", "prior_r",
                   "r_low", "r_high", "r_source")], digits = 3)

species_name	matched_name	match_type	resilience	prior_r	r_low	r_high	r_source
Atlantic cod	Gadus morhua	exact	Medium	0.509	0.336	0.764	FishBase prior r, 95% CL (Based on 66 full stock assessments.)
Atlantic herring	Clupea harengus	exact	Medium	0.436	0.288	0.654	FishBase prior r, 95% CL (Based on 53 full stock assessments.)
Atlantic mackerel	Scomber scombrus	exact	Medium	0.429	0.283	0.644	FishBase prior r, 95% CL (Based on 10 full stock assessments.)
Blue whiting(=Poutassou)	Micromesistius poutassou	exact	Medium	0.465	0.307	0.698	FishBase prior r, 95% CL (Based on 9 full stock assessments.)

The r range follows the CMSY++ user guide (Froese et al. 2021): the 95% confidence limits of the FishBase prior r when the species has one (Table 1); otherwise the range of its resilience (Table 2: High 0.6–1.5, Medium 0.2–0.8, Low 0.05–0.5, Very low 0.015–0.1); otherwise none, and the prior has to come from the user. This table is matched more strictly than fishbase_match(): fishes are looked up in FishBase first and other items in SeaLifeBase first, as valid species names and then through the synonym table of the database, but there is no WoRMS look-up, and ambiguous synonyms and items above species level get no values (match_type “ambiguous synonym”, “not a species” or “not found”). The corrections file of fishbase_match() does not change it; priors of your own are given with priors = in cmsy_input(). See 📉 CMSY++ stock assessment, step 3.

📝 In the Word report

The Word report of an area can include a section on the mean temperature of the catch (fao_report(27, mtc = TRUE)). It uses the built-in FishBase table by default (mtc_version = "builtin"), so writing the report downloads nothing; give another release with mtc_version, e.g. mtc_version = "latest". The table of species used, with their FishBase matches, is returned as report$mtc_species, and the report cites the FishBase release used. See 📝 Word report.

report <- fao_report(27, mtc = TRUE)
head(report$mtc_species[, c("species_name", "match_type", "temp_pref_mean", "used", "url")])
fao_report(27, mtc = TRUE, mtc_version = "latest")    # newest FishBase release

📖 References

Boettiger, C., Lang, D.T. and Wainwright, P.C. (2012). rfishbase: exploring, manipulating and visualizing FishBase data from R. Journal of Fish Biology 81(6): 2030–2039. doi:10.1111/j.1095-8649.2012.03464.x. Source code: https://github.com/ropensci/rfishbase

Branch, T.A., Watson, R., Fulton, E.A., Jennings, S., McGilliard, C.R., Pablico, G.T., Ricard, D. and Tracey, S.R. (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

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. (2020). Personal communication: R code (PrefTempBatch_5.R) to estimate preferred temperature from AquaMaps (version 10/2019). FishBase reference 123201. https://www.fishbase.se/references/FBRefSummary.php?ID=123201

Froese, R., Demirel, N., Coro, G. and Winker, H. (2021). User Guide for CMSY++. GEOMAR, Germany, 17 pp. https://oceanrep.geomar.de/id/eprint/52147/

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 (https://www.fishbase.se/manual/fishbasethe_food_items_table.htm).

Froese, R. and Pauly, D. (Eds.) (2026). FishBase. World Wide Web electronic publication. Version (06/2026). https://www.fishbase.se

Grenié, M., Berti, E., Carvajal-Quintero, J., Dädlow, G.M.L., Sagouis, A. and Winter, M. (2023). Harmonizing taxon names in biodiversity data: a review of tools, databases and best practices. Methods in Ecology and Evolution 14: 12–25. doi:10.1111/2041-210X.13802

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

Palomares, M.L.D. and Pauly, D. (Eds.) (2026). SeaLifeBase. World Wide Web electronic publication. Version (06/2026). https://www.sealifebase.se

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

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