R Observatory: Metrics for DDRTree version 0.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

DDRTree

0.1.6

Learning Principal Graphs with DDRTree

0packages depend

64.1Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Brent EwingFirst published 2016-02-024 releasesCRAN page ↗

Provides an implementation of the framework of reversed graph embedding (RGE) which projects data into a reduced dimensional space while constructs a principal tree which passes through the middle of the data simultaneously. DDRTree shows superiority to alternatives (Wishbone, DPT) for inferring the ordering as well as the intrinsic structure of the single cell genomics data. In general, it could be used to reconstruct the temporal progression as well as bifurcation structure of any datatype.

Install

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

install.packages("DDRTree", 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-ddrtree

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-DDRTree

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-DDRTree

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

Health

CRAN checks

13OK

Slowest check: 3.6 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

2

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-05-02
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 13 wordsVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 50%
References docs: 0%

Downloads

64.1K

CRAN downloads in the past year

Rank #1,838 · ~175/day · ~5.3K/mo

Releases R versions

Daily download trend is not available in this view yet.

3.9K30 days

12.9K90 days

64.1K1 year

Compare downloads with other packages →

Also on1.2K r2u11 autocran7.5K conda_forge195 bioconda

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

irlba

Imports (1)

Rcpp

LinkingTo (3)

Rcpp RcppEigen BH

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (5)

Maintainer (1)

Brent Ewing

Maintainer · added in 0.1.6

Authors (4)

Author

Author

Author

Author

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
0.1.6Latest
2026-03-03 · current release · diff ↗
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
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23
0.1.5
2017-04-30 · diff ↗
R
R 3.4.0 released · 2017-04-21
0.1.4
2016-07-26 · diff ↗
R
R 3.3.0 released · 2016-05-03
0.1.3
2016-02-02
R
R 3.2.0 released · 2015-04-16

Package metadata

First published: 2016-02-02
Total releases: 4 / 10 yrs
License: Artistic License 2.0
Download size: 16 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("DDRTree")

Format

Ewing, B., Mao, Q., Qiu, X., Trapnell, C., & Wang, L. (2026). DDRTree: Learning Principal Graphs with DDRTree (Version 0.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.DDRTree

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 DDRTree version 0.1.6 [Data set]. HJJB, LLC. Data release v2026-08-13. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-13, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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