R Observatory: Metrics for tidytree version 0.4.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

tidytree

0.4.8Package record

A Tidy Tool for Phylogenetic Tree Data Manipulation

9packages dependsuggested by 6

747.1Kdownloads / year

60.1%test coverage

8/13flavors OK

Overview

About

Maintained by Guangchuang YuCRAN page ↗GitHub ↗Website ↗Issues ↗

Phylogenetic trees contain components such as nodes, edges, branches, and associated data. As the core data manipulation tool in the 'ggtree' ecosystem, 'tidytree' provides tools for converting tree objects to tidy data frames and tidy interfaces for manipulating, analyzing, and visualizing tree data.

Changes in 0.4.8

improve tree_subset() error handling for unmatched nodes and pass root_edge consistently in the treedata method (2026-07-02, Thu)
make malformed tbl_tree objects fail with a clear validation error when converted by as.phylo() (2026-07-02, Thu)
optimize offspring() for 'phylo' objects and as.ultrametric() for large trees by avoiding repeated edge scans and vector growth in traversal loops (2026-07-02, Thu)
update package citation and documentation links (2026-07-02, Thu)
remove duplicated rows in y before left_join() and full_join() to avoid duplicated annotation records after joining tables (2026-07-01, Wed, #52)

From NEWS.md in the release

Install

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

install.packages("tidytree", 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("YuLab-SMU/tidytree")

Development version from YuLab-SMU/tidytree. 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-tidytree

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-tidytree

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-tidytree

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

5NOTE8OK

Check messages

NOTEdependencies in R coder-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc, r-devel-windows-x86_64

r-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc, r-devel-linux-x86_64-fedora-clang, r-devel-linux-x86_64-fedora-gcc

Base package in Suggests/Enhances imported in NAMESPACE:
  ‘utils’

r-devel-windows-x86_64

Base package in Suggests/Enhances imported in NAMESPACE:
  'utils'

CRAN check page ↗

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Status changes

NOTE8 OK, 5 NOTENow
NOTE11 OK, 2 NOTE2026-09-12
OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.8

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structured · mentions 0.4.8Citation fileYes · cites a publicationWebsiteYes

Help pages: 31 (2 internal)includes a package overview page
Examples that run: 100%9 run in a plain check
Exported functions with examples: 31%
Documented parameters: 100%
Return-value docs: 85%
Help pages citing references: 0%

How these are measured

Downloads

747.1K

CRAN downloads in the past year

Rank #409 · ~2K/day · ~62.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

74.3K30 days

212.9K90 days

747.1K1 year

Compare downloads with other packages →

Also on12.8K r2u2 autocran152.5K conda_forge401 c2d4u

How downloads are counted

Repository

yulab-smu/tidytree ↗Organization: YuLab-SMU

61Stars

13Forks

8Open issues

0Open PRs

0Releases

172Commits

8Commit identities

phylogenetic-treecrantree-datatidyverse

172 commits · Last activity 2026-07-02 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 88%
Median days to close, 50 most recently updated closed issues: 4
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-08-17 · 572026-07-07 · 61

How these are measured

PracticesBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/yulab-smu/tidytree on 2026-10-18.

Governance and community (1)

Code of conduct

Docs source (2)

README.Rmd

GitHub Pages site last deployed 2017-12-13

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

Dependencies

Declared dependencies

12 external dependencies (excludes base and recommended)

Installing tidytree adds 27 packages (18 with compiled code, 23 MB of source tarballs). Heaviest: stringi 11 MB, Rcpp 1.8 MB, ape 1.4 MB.

Depends (1)

R >= 3.4.0

Imports (12)

ape dplyr lazyeval magrittrmethodsrlang tibble tidyr tidyselect yulab.utils pillar cli

LinkingTo (0)

none

Suggests (2)

testthatutils

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

9direct

3indirect

Imports 9

Suggested by 6

Show all 15 packagesHide all 15 packages

Depends, Imports or LinkingTo, most downloaded first

iNEXT.3D iNEXT.beta3D FossilSim oppr Rclade avotrex RevGadgets rtrees RPesto

Suggests, most downloaded first

deeptime DAISIE delimtools pctax tripaccess nosoi

How these are counted

Code & Tests

People & History

People (3)

Guangchuang Yu

Zebulun Arendsee

Contributor

Bradley Jones

Contributor

Releases (32)

Pick two releases to compare their code metrics.

0.4.8Latest
record
2026-07-02 · current release · diff ↗
R
R 4.6.0 released · 2026-04-24
0.4.7
record
2026-01-08 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.4.6
record
2023-12-12 · diff ↗
0.4.5
record
2023-08-10 · diff ↗ ·
added 13 exports
Nnode, Ntip, as.ultrametric, drop.tip, get.treetext, getNodeNum, is.rooted, isTip, keep.tip, read.tree, root, rtree, tree_subset
0.4.4
record
2023-07-15 · diff ↗ ·
added 4 exports
node.label<-, tip.label<-, node.label, tip.label
R
R 4.3.0 released · 2023-04-21
0.4.2
record
2022-12-18 · diff ↗
0.4.1
record
2022-09-26 · diff ↗
0.4.0
record
2022-08-13 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.3.9
record
2022-03-04 · diff ↗
0.3.8
record
2022-02-17 · diff ↗
0.3.7
record
2022-01-10 · diff ↗

Show 26 earlier eventsHide 26 earlier events

0.3.6
record
2021-11-12 · diff ↗
0.3.5
record
2021-09-08 · diff ↗ ·
added 3 exports
left_join, pull, unnest
0.3.4
record
2021-05-22 · diff ↗ ·
added 1 export
.data
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.3.3
record
2020-04-02 · diff ↗ ·
removed 1 export
data_frame
0.3.2
record
2020-03-12 · diff ↗
0.3.1
record
2019-12-14 · diff ↗
0.3.0
record
2019-11-21 · diff ↗
0.2.9
record
2019-10-28 · diff ↗
0.2.8
record
2019-09-27 · diff ↗
0.2.7
record
2019-09-12 · diff ↗
0.2.6
record
2019-08-09 · diff ↗ ·
added 2 exports
nodeid, nodelab
0.2.5
record
2019-07-22 · diff ↗
R
R 3.6.0 released · 2019-04-26
0.2.4
record
2019-02-27 · diff ↗
0.2.3
record
2019-01-30 · diff ↗
0.2.1
record
2018-12-19 · diff ↗
0.2.0
record
2018-11-29 · diff ↗ ·
removed 1 export
as_data_frame

added 1 export
as_tibble
0.1.9
record
2018-06-13 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.1.8
record
2018-04-19 · diff ↗
0.1.7
record
2018-02-27 · diff ↗ ·
added 1 export
get.data
0.1.6
record
2018-01-03 · diff ↗ ·
added 1 export
treedata
0.1.5
record
2017-12-14
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-12-14
Total releases: 32 / 9 yrs
License: Artistic-2.0 OSI
Minimum R: ≥ 3.4.0
Download size: 37 KB

Appears in task views

Phylogenetics

Cite

Cite this package

Run in R for the authors' entry:

citation("tidytree")

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

It points to 10.1201/9781003279242.

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 tidytree version 0.4.8 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →