R Observatory: Metrics for TreeDimensionTest version 0.0.3

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

TreeDimensionTest

0.0.3Package record

Trajectory Presence and Heterogeneity in Multivariate Data

0packages depend

6.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Joe SongCRAN page ↗

Testing for trajectory presence and heterogeneity on multivariate data. Two statistical methods (Tenha & Song 2022) doi:10.1371/journal.pcbi.1009829 are implemented. The tree dimension test quantifies the statistical evidence for trajectory presence. The subset specificity measure summarizes pattern heterogeneity using the minimum subtree cover. There is no user tunable parameters for either method. Examples are included to illustrate how to use the methods on single-cell data for studying gene and pathway expression dynamics and pathway expression specificity.

Changes in 0.0.3

2026-07-18

1. Created package version 0.0.3 from 0.0.2.1.

From NEWS.md in the release

Install

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

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

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

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-treedimensiontest

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-TreeDimensionTest

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-TreeDimensionTest

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: 6.7 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-09-08
ERROR12 OK, 1 ERROR2026-09-07
OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-27

Show 8 earlier changesHide 8 earlier changes

ERROR11 OK, 2 ERROR2026-07-17
OK13 OK2026-05-02
NOTE11 OK, 1 NOTE2026-04-25
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-04-16
NOTE13 OK, 1 NOTE2026-03-28
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.3

READMEYes · 132 wordsVignettesYes · 1 · dynamicNEWSYes · 33% structured · mentions 0.0.3Citation fileYes · cites a publicationWebsitenot declared in DESCRIPTION

Help pages: 5
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20% with a bibliography file

Vignettes (1)

Tutorial: Using the 'TreeDimensionTest' package HTML

How these are measured

Downloads

6.3K

CRAN downloads in the past year

Rank #15,174 · ~17/day · ~524/mo

Releases R versions

Daily download trend is not available in this view yet.

23530 days

80690 days

6.3K1 year

Compare downloads with other packages →

Also on358 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

11 external dependencies (excludes base and recommended)

Installing TreeDimensionTest adds 21 packages (12 with compiled code, 20 MB of source tarballs). Heaviest: igraph 4.8 MB, fitdistrplus 2.4 MB, mlpack 2.0 MB.

Depends (1)

mlpack

Imports (6)

fitdistrplus igraph nFactors Rcpp RColorBrewer Rdpack

LinkingTo (1)

Rcpp

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Joe Song

Author, Maintainer since 0.0.1 (2022)

Lovemore Tenha

Author

Releases (3)

Pick two releases to compare their code metrics.

0.0.3Latest
record
2026-07-18 · current release · diff ↗
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
0.0.2
record
2022-03-12 · diff ↗ ·
removed 1 export
plotTree
0.0.1
record
2022-01-20
R
R 4.1.0 released · 2021-05-18

Package metadata

First published: 2022-01-20
Total releases: 3 / 4 yrs
License: LGPL (>= 3) OSI · relicensed from GPL (>= 2) in 0.0.2
Download size: 1.4 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("TreeDimensionTest")

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

It points to 10.1371/journal.pcbi.1009829.

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 TreeDimensionTest version 0.0.3 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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