R Observatory: Metrics for treefit version 1.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

treefit

1.0.3Package record

The First Software for Quantitative Trajectory Inference

0packages depend

3.1Kdownloads / year

45.9%test coverage

13/13flavors OK

Overview

About

Maintained by Kouhei SutouCRAN page ↗GitHub ↗Website ↗Issues ↗

Perform two types of analysis: 1) checking the goodness-of-fit of tree models to your single-cell gene expression data; and 2) deciding which tree best fits your data.

Changes in 1.0.3

Improvements

Skipped a flaky test on CRAN.
GH-4

From NEWS.md in the release

Install

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

install.packages("treefit", 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("hayamizu-lab/treefit-r")

Development version from hayamizu-lab/treefit-r. 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-treefit

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-treefit

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-treefit

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: 3.0 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-04
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.0.3

READMEYes · 158 wordsVignettesYes · 2 · dynamicNEWSYes · 100% structured · mentions 1.0.3Citation fileNoWebsiteYes · pkgdown

Help pages: 7
Examples that run: 60%3 run in a plain check · 2 never run
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (2)

Treefit - Getting started HTML
Treefit - Working with Seurat HTML

How these are measured

Downloads

3.1K

CRAN downloads in the past year

Rank #15,800 · ~8/day · ~257/mo

Releases R versions

Daily download trend is not available in this view yet.

31330 days

78890 days

3.1K1 year

Compare downloads with other packages →

Also on83 r2u5 autocran29 c2d4u

How downloads are counted

Repository

hayamizu-lab/treefit-r ↗Organization: hayamizu-lab

3Stars

1Forks

0Open issues

0Open PRs

1Releases

206Commits

3Commit identities

License file reads as GPL-3.0 · 206 commits · Last activity 2026-06-22 · 0% stars, 30d · Default branch at 1.0.3.9000, ahead of CRAN 1.0.3 (checked 2026-10-21) · Discussions: 1 post

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 1
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2022-01-12 · 32026-07-07 · 3

How these are measured

PracticesBeta

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

Checks run against github.com/hayamizu-lab/treefit-r on 2026-10-21.

Continuous integration (2)

GitHub ActionsR CMD check workflow

Docs source (2)

pkgdown

GitHub Pages site last deployed 2026-06-22

CRAN release process (1)

cran-comments.md

Automation and maintenance (1)

Dependabot

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

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing treefit adds 22 packages (9 with compiled code, 22 MB of source tarballs). Heaviest: ggplot2 6.0 MB, igraph 4.8 MB, patchwork 3.2 MB.

Depends (0)

none

Imports (4)

ggplot2 igraph patchwork pracma

LinkingTo (0)

none

Suggests (7)

Seurat gridExtra knitr plotly qpdf rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (4)

Kouhei Sutou

Author, Maintainer since 1.0.0 (2020)

Momoko Hayamizu

Author

Hiromi Ishii

Author · added in 1.0.1

Ryohei Suzuki

Author · added in 1.0.1

Releases (4)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.0.3Latest
record
2025-02-09 · current release · diff ↗
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
unarchivedReturned to CRAN
2022-01-18
1.0.2
record
2022-01-18 · diff ↗
R
R 4.1.0 released · 2021-05-18
archivedRemoved from CRAN
2021-03-29
check problems were not corrected in time Signs of results vary
1.0.1
record
2021-03-22 · diff ↗ ·
added 1 export
generate_n_arms_star_data
R
R 4.0.0 released · 2020-04-24
1.0.0
record
2020-03-10
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-10
Total releases: 4 / 6 yrs
License: GPL (>= 3) OSI
Download size: 133 KB

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("treefit")

Format

Sutou, K., Hayamizu, M., Ishii, H., & Suzuki, R. (2025). treefit: The First Software for Quantitative Trajectory Inference (Version 1.0.3) [Computer software]. https://doi.org/10.32614/CRAN.package.treefit

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

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 treefit version 1.0.3 [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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