R Observatory: Metrics for deadwood version 0.9.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

deadwood

0.9.2Package record

Outlier Detection via Pruning Mutual Reachability Minimum Spanning Trees

2packages dependsuggested by 1

10.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Marek GagolewskiCRAN page ↗GitHub ↗Website ↗Issues ↗

Implements an anomaly detection algorithm based on a dataset's mutual reachability minimum spanning tree: 'deadwood' prunes protruding tree segments and marks small debris as outliers; see Gagolewski (2026) https://deadwood.gagolewski.com/. More precisely, tree edges with weights greater than the detected elbow point are removed. All the resulting connected components whose sizes do not exceed a prespecified threshold are deemed anomalous. The use of a mutual reachability distance pulls peripheral observations farther away from one another. If the dataset is comprised of well-separated clusters of heterogeneous densities, an attempt to split the dataset and refine the outlierness markers will be made. The 'Python' version of 'deadwood' is available via 'PyPI'.

Install

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

install.packages("deadwood", 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("gagolews/deadwood")

Development version from gagolews/deadwood. 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-deadwood

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-deadwood

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-deadwood

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: 2.6 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.9.2

README· In the repository, left out of the releaseVignettesNoNEWSYes · 100% structuredCitation fileNoWebsiteYes

Help pages: 4 (1 internal)includes a package overview page
Examples that run: 100%2 run in a plain check
Exported functions with examples: 67%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 75%

How these are measured

Downloads

10.6K

CRAN downloads in the past year

Rank #2,615 · ~29/day · ~887/mo

Releases R versions

Daily download trend is not available in this view yet.

2.3K30 days

6K90 days

10.6K1 year

Compare downloads with other packages →

Also on2K r2u5 autocran

How downloads are counted

Repository

gagolews/deadwood ↗Account: gagolews

1Stars

0Forks

1Open issues

0Open PRs

3Releases

73Commits

1Commit identities

anomaly-detectiondata-sciencemachine-learningmachine-learning-algorithmsminimum-spanning-treeminimum-spanning-treesmstnoise-detection

73 commits · Last activity 2026-10-14 · 0% stars, 30d · Default branch at 0.9.2.9001, ahead of CRAN 0.9.2 (checked 2026-10-25)

Responsiveness

not measured

Stars over time

2026-02-15 · 12026-07-07 · 1

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/gagolews/deadwood on 2026-10-25.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux

Governance and community (1)

Code of conduct

Docs source (1)

GitHub Pages site last deployed 2026-10-14

Reproducibility and dev environment (1)

Makefile

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing deadwood adds 2 packages (2 with compiled code, 1.8 MB of source tarballs). Heaviest: Rcpp 1.8 MB, quitefastmst 42 KB.

Depends (0)

none

Imports (2)

Rcpp quitefastmst

LinkingTo (1)

Rcpp

Suggests (1)

datasets

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

2direct

7indirect

Imports 2

Suggested by 1

Depends, Imports or LinkingTo, most downloaded first

genieclust lumbermark

Suggests, most downloaded first

evoFE

How these are counted

Code & Tests

People & History

People (1)

Marek Gagolewski

Releases (4)

Pick two releases to compare their code metrics.

0.9.2Latest
record
2026-10-01 · current release · diff ↗
0.9.1
record
2026-09-29 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.9.0-3
record
2026-02-22 · diff ↗
0.9.0-2
record
2026-02-20
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2026-02-20
Total releases: 4 / 1 yrs
License: AGPL-3 OSI
Download size: 32 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("deadwood")

Format

Gagolewski, M. (2026). deadwood: Outlier Detection via Pruning Mutual Reachability Minimum Spanning Trees (Version 0.9.2) [Computer software]. https://doi.org/10.32614/CRAN.package.deadwood

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 deadwood version 0.9.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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