R Observatory: Metrics for rfishbase version 5.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

rfishbase

5.0.3Package record

R Interface to 'FishBase'

3packages dependsuggested by 3

19.7Kdownloads / year

80.8%test coverage

13/13flavors OK

Overview

About

Maintained by Carl BoettigerCRAN page ↗GitHub ↗Website ↗Issues ↗

A programmatic interface to 'FishBase', re-written based on an accompanying 'RESTful' API. Access tables describing over 30,000 species of fish, their biology, ecology, morphology, and more. This package also supports experimental access to 'SeaLifeBase' data, which contains nearly 200,000 species records for all types of aquatic life not covered by 'FishBase.'

Changes in 5.0.3

fb_tbl() now gives a clear error message when an unrecognized table name is

requested, directing users to fb_tables(). Previously this produced a cryptic

"missing value where TRUE/FALSE needed" error (fix for #320).

common_to_sci() now correctly filters by the Language argument. Previously

the argument was accepted but ignored, silently returning English results

regardless of the language specified (fix for #275).

Documentation for length_length() now clarifies the counterintuitive column

naming convention: Length1 is the unknown (predicted) length and Length2

is the known (predictor), so the formula is Length1 = a + b * Length2

(fix for #290).

fb_tbl() now handles tables with embedded null bytes in string columns

by dropping the affected column(s) with a warning rather than failing entirely.

Show all changes in 5.0.3Hide the rest of the changes in 5.0.3

This fixes ecosystem() and species_by_ecosystem() with

server = "sealifebase" (fix for #302).

From NEWS.md in the release

Install

R (CRAN)pak (dev)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("rfishbase", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("ropensci/rfishbase")

Development version from ropensci/rfishbase. Installs pak first if it is not already available.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-rfishbase

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-rfishbase

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-rfishbase

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 1.5 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-29
ERROR12 OK, 1 ERROR2026-09-04
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09

Show 6 earlier changesHide 6 earlier changes

ERROR12 OK, 1 ERROR2026-06-07
OK13 OK2026-05-24
ERROR12 OK, 1 ERROR2026-05-17
OK13 OK2026-05-15
ERROR12 OK, 1 ERROR2026-05-13
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 5.0.3

READMEYes · 1,409 wordsVignettesNoNEWSYes · 33% structured · mentions 5.0.3Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 48 (1 internal)
Examples that run: 14%6 run in a plain check (6 of them under a condition) · 2 only when donttest examples are enabled (R CMD check --as-cran) · 34 never run
Exported functions with examples: 91%
Documented parameters: 100%
Return-value docs: 82%
Help pages citing references: 25%

How these are measured

Downloads

19.7K

CRAN downloads in the past year

Rank #3,102 · ~54/day · ~1.6K/mo

Releases R versions

Daily download trend is not available in this view yet.

1.4K30 days

4.1K90 days

19.7K1 year

Compare downloads with other packages →

Also on235 r2u8 autocran162 c2d4u

How downloads are counted

Repository

ropensci/rfishbase ↗Organization: ropensci

127Stars

40Forks

5Open issues

0Open PRs

12Releases

666Commits

19Commit identities

rrstatsr-packagefishbasetaxonomyfish

666 commits · Last activity 2026-09-05 · 0% stars, 30d · Default branch at 5.0.4, ahead of CRAN 5.0.3 (checked 2026-10-21)

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 414
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-05 · 1162026-09-11 · 127

How these are measured

PracticesBeta

15 development-tooling and community-health practices detected across 8 families in the upstream repository

Checks run against github.com/ropensci/rfishbase on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Governance and community (4)

Code of conduct (inherited from ropensci)Contributing guideIssue templatesPR template

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2019-09-24

Coverage (1)

Coverage reporting (Codecov)

Show all practicesHide 4 practices

Reproducibility and dev environment (2)

data-raw/Makefile

CRAN release process (1)

cran-comments.md

Research and citation (1)

codemeta.json

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing rfishbase adds 30 packages (17 with compiled code, 29 MB of source tarballs). Heaviest: stringi 11 MB, duckdb 7.9 MB, fs 1.4 MB.

Depends (1)

R >= 4.1.0

Imports (9)

glue stringr purrr dplyr duckdbfs rlang magrittr memoise xml2

LinkingTo (0)

none

Suggests (6)

testthat rmarkdown knitr covr spelling curl

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

3direct

0indirect

Imports 3

Suggested by 3

Depends, Imports or LinkingTo, most downloaded first

dietr FishPhyloMaker rcatfish

Suggests, most downloaded first

MSEtool fishtree fishualize

How these are counted

Code & Tests

Datasets

People & History

People (6)

Carl Boettiger

Maintainer since 0.0-7 (2011), Author

Scott Chamberlain

Author · added in 2.0.1

Duncan Temple Lang

Author · added in 0.0-9

Peter Wainwright

Author · added in 0.0-9

Kevin Cazelles

Contributor · added in 3.1.4

Guohuan Su

Contributor · added in 5.0.1

Listed in earlier versions (1)

Peter C.

no longer listed · 0.2-1 to 0.2-2

Releases (31)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
5.0.3Latest
record
2026-04-07 · current release · diff ↗
5.0.2
record
2025-12-17 · diff ↗
R
R 4.5.0 released · 2025-04-11
5.0.1
record
2025-01-12 · diff ↗
5.0.0
record
2024-09-02 · diff ↗ ·
removed 9 exports
db_dir, db_disconnect, distribution, docs, fb_conn, fb_import, fishbase_pane, occurrence, species_list
R
R 4.4.0 released · 2024-04-24
4.1.2
record
2023-06-03 · diff ↗
R
R 4.3.0 released · 2023-04-21
4.1.1
record
2023-02-20 · diff ↗
4.1.0
record
2023-02-12 · diff ↗ ·
added 2 exports
db_disconnect, fb_conn
R
R 4.2.0 released · 2022-04-22
4.0.0
record
2021-12-14 · diff ↗ ·
removed 3 exports
db_delete, default_db, list_fields

added 5 exports
db_dir, fb_import, fb_tables, fb_tbl, fishbase_pane
3.1.10
record
2021-11-10 · diff ↗ ·
added 1 export
db_delete
3.1.9
record
2021-08-09 · diff ↗
3.1.8
record
2021-06-07 · diff ↗

Show 32 earlier eventsHide 32 earlier events

R
R 4.1.0 released · 2021-05-18
3.1.7
record
2021-04-08 · diff ↗
3.1.6
record
2021-02-10 · diff ↗
3.1.5
record
2021-01-18 · diff ↗
3.1.4
record
2021-01-13 · diff ↗ ·
removed 2 exports
clear_cache, taxonomy

added 2 exports
default_db, species_by_ecosystem
R
R 4.0.0 released · 2020-04-24
3.0.4
record
2019-06-27 · diff ↗ ·
added 2 exports
available_releases, clear_cache
R
R 3.6.0 released · 2019-04-26
3.0.3
record
2019-03-13 · diff ↗ ·
added 1 export
diet_items
3.0.1
record
2019-03-02 · diff ↗
3.0.0.1
record
2019-03-01 · diff ↗
3.0.0
record
2018-11-09 · diff ↗ ·
removed 4 exports
commonnames, heartbeat, ping, speciesnames

added 5 exports
%>%, brains, estimate, genetics, taxonomy
R
R 3.5.0 released · 2018-04-23
R
R 3.4.0 released · 2017-04-21
2.1.2
record
2017-04-19 · diff ↗ ·
added 2 exports
larvae, references
2.1.1
record
2016-07-22 · diff ↗ ·
added 4 exports
c_code, country, countrysub, countrysubref
R
R 3.3.0 released · 2016-05-03
2.1.0
record
2015-11-10 · diff ↗
2.0.3
record
2015-09-09 · diff ↗
2.0.2
record
2015-09-02 · diff ↗
2.0.1
record
2015-08-15 · diff ↗ ·
removed 15 exports
findSpecies, fish_names, getDepth, getEnviroClimateRange, getIds, getLengthWeight, getMetabolism, getPictures, getQuantTraits, getRefs, getSize, getTrophicLevel, loadCache, updateCache, which_fish

added 44 exports
common_names, common_to_sci, commonnames, diet, distribution, docs, ecology, ecosystem, faoareas, fecundity, fooditems, heartbeat, introductions, length_freq, length_length, length_weight, list_fields, load_taxa, maturity, morphology, morphometrics, occurrence, oxygen, ping, popchar, popgrowth, poplf, popll, poplw, popqb and 14 more
R
R 3.2.0 released · 2015-04-16
R
R 3.1.0 released · 2014-04-10
0.2-2
record
2014-01-07 · diff ↗ ·
added 6 exports
getEnviroClimateRange, getIds, getLengthWeight, getMetabolism, getPictures, getTrophicLevel
R
R 3.0.0 released · 2013-04-03
0.2-1
record
2013-02-14 · diff ↗
0.0-9
record
2012-05-15 · diff ↗ ·
removed 2 exports
familySearch, habitatSearch

added 3 exports
getRefs, loadCache, updateCache
0.0-8
record
2012-04-03 · diff ↗
R
R 2.15.0 released · 2012-03-30
R
R 2.14.0 released · 2011-10-31
0.0-7
record
2011-10-26
R
R 2.13.0 released · 2011-04-13

Package metadata

First published: 2011-10-26
Total releases: 31 / 15 yrs
License: CC0 · relicensed from BSD in 0.0-9
Minimum R: ≥ 4.1.0
Download size: 601 KB

Cite

Cite this package

Run in R for the authors' entry:

citation("rfishbase")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1111/j.1095-8649.2012.03464.x.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for rfishbase version 5.0.3 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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