fishtree

0.3.4

Interface to the Fish Tree of Life API

4packages depend

5.1Kdownloads / year

25.0%test coverage

12/13checks pass

Overview

About

Maintained by Jonathan ChangFirst published 2018-11-307 releasesCRAN page ↗GitHub ↗

An interface to the Fish Tree of Life API to download taxonomies, phylogenies, fossil calibrations, and diversification rate information for ray-finned fishes.

Install

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

install.packages("fishtree", 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("jonchang/fishtree")

Development version from jonchang/fishtree. 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-fishtree

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

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-fishtree

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-fishtree

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.2 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.07

25.0%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-24
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-17
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-15
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-05-13
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 2 earlier snapshots

OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 252 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 0%
Documented parameters: 100%
Return-value docs: 100%
References docs: 86%

Downloads

5.1K

CRAN downloads in the past year

Rank #8,646 · ~14/day · ~428/mo

Releases R versions

Daily download trend is not available in this view yet.

27230 days

1.2K90 days

5.1K1 year

Compare downloads with other packages →

Also on99 r2u3 autocran

Repository

GitHub ↗ jonchang/fishtree

12Stars

2Forks

2Open issues

0Open PRs

7Releases

219Commits

3Contributors

cranrphylogeny

219 commits · Last activity 2026-07-27 · +9.1% stars, 30d

Stars over time

2025-06-08 · 112026-07-07 · 12

Repository practices

Upstream repositoryBeta

7 development-tooling and community-health practices detected across 7 families in the upstream repository

Checks run against github.com/jonchang/fishtree on 2026-08-02.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

Makefile

CRAN release process (1)

cran-comments.md

Docs source (1)

README.Rmd

Show all practices

Automation and maintenance (1)

Dependabot

Lint, format, editor (1)

RStudio project

Governance and community (1)

Issue templates

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.0

Imports (6)

ape jsonlite memoiseparallelrlang (>= 0.4.1)utils

LinkingTo (0)

none

Suggests (11)

diversitree geiger hisse knitr markdown phytools picante rfishbase rmarkdown spelling testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

4direct

0indirect

FishPhyloMaker aptg phylosem prepR4pcm

Code & Tests

People & History

People (4)

Maintainer (1)

Jonathan Chang

Author, Maintainer

Authors (1)

Jonathan Chang

Author, Maintainer

Contributors (3)

Michael E Alfaro

Contributor

Daniel L Rabosky

Contributor

Stephen A Smith

Contributor

Package Timeline

7 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.3.4Latest
2021-01-31 · current release · diff ↗
0.3.3
2020-10-31 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.3.2
2019-12-17 · diff ↗
0.3.1
2019-05-31 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.3.0
2019-04-03 · diff ↗
0.2.0
2019-02-26 · diff ↗
0.1.0
2018-11-30
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-11-30
Total releases: 7 / 8 yrs
License: BSD_2_clause + file LICENSE OSI
Minimum R: ≥ 4.0
Download size: 381 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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