deadwood Package for R and Python
Deadwood: Outlier Detection via Pruning Mutual Reachability Minimum Spanning Trees
Keywords: Deadwood, outlier detection, anomaly detection, HDBSCAN*, DBSCAN, minimum spanning tree, MST, density estimation, mutual reachability distance.
Refer to the package homepage at https://deadwood.gagolewski.com/ for the reference manual, tutorials, examples, and benchmarks.
Author and Maintainer: Marek Gagolewski
About
Deadwood is an anomaly detection algorithm based on a dataset's mutual reachability minimum spanning tree. It prunes protruding tree segments and marks small debris as outliers.
More precisely:
-
tree edges with weights greater than the detected elbow point are removed;
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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;
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if the dataset is comprised of well-separated clusters of heterogeneous densities, an attempt to split the dataset and refine the outlierness markers is made.
How to Install
Python Version
To install from PyPI, call:
pip3 install deadwood # python3 -m pip install deadwood
To learn more about Python, check out my open-access textbook Minimalist Data Wrangling in Python.
For best performance, advanced users will benefit from compiling the package from sources:
CPPFLAGS="-O3 -march=native" pip3 install quitefastmst deadwood --force --no-binary="quitefastmst,deadwood"
🚧 TO DO (help needed): How to enable OpenMP support on macOS in quitefastmst?
R Version
To install from CRAN, call:
install.packages("deadwood")
To learn more about R, check out my open-access textbook Deep R Programming.
For best performance, advanced users will benefit from compiling the package from sources:
Sys.setenv(CXX_DEFS="-O3 -march=native") # for gcc and clang
install.packages(c("quitefastmst", "deadwood"), type="source")
To enable OpenMP on macOS, execute brew install libomp, and then call in R:
Sys.setenv(CXX_DEFS="-O3 -march=native -Xpreprocessor -fopenmp")
install.packages(c("quitefastmst", "deadwood"), type="source")
Other
The core functionality is implemented in the form of a C++ library. It can thus be easily adapted for use in other projects.
New contributions are welcome, e.g., Julia, Matlab/GNU Octave wrappers.
License
Copyright (C) 2025–2026 Marek Gagolewski https://www.gagolewski.com/
This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License Version 3, 19 November 2007, published by the Free Software Foundation.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License Version 3 for more details. You should have received a copy of the License along with this program. If not, see (https://www.gnu.org/licenses/).
References
TODO
See deadwood's homepage for more references.
1 maintainer
Metadata
1 maintainer
Release files for deadwood 0.9.2
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| deadwood-0.9.2.tar.gz | 58.9 kB | Details |
Built distributions (wheels)
Total release size: 102.1 MB
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Release files / deadwood-0.9.2-cp315-cp315t-win_arm64.whl
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Release files / deadwood-0.9.2-cp314-cp314-win_arm64.whl
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Release files / deadwood-0.9.2-cp314-cp314-win_amd64.whl
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Release files / deadwood-0.9.2-cp314-cp314-musllinux_1_2_x86_64.whl
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Release files / deadwood-0.9.2-cp314-cp314-musllinux_1_2_aarch64.whl
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Release files / deadwood-0.9.2-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / deadwood-0.9.2-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / deadwood-0.9.2-cp314-cp314-macosx_11_0_arm64.whl
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Release files / deadwood-0.9.2-cp314-cp314-macosx_10_15_x86_64.whl
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Release files / deadwood-0.9.2-cp313-cp313-win_arm64.whl
| Download URL | deadwood-0.9.2-cp313-cp313-win_arm64.whl |
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Release files / deadwood-0.9.2-cp313-cp313-win_amd64.whl
| Download URL | deadwood-0.9.2-cp313-cp313-win_amd64.whl |
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Release files / deadwood-0.9.2-cp313-cp313-musllinux_1_2_x86_64.whl
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Release files / deadwood-0.9.2-cp313-cp313-musllinux_1_2_aarch64.whl
| Download URL | deadwood-0.9.2-cp313-cp313-musllinux_1_2_aarch64.whl |
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Release files / deadwood-0.9.2-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / deadwood-0.9.2-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / deadwood-0.9.2-cp313-cp313-macosx_11_0_arm64.whl
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Release files / deadwood-0.9.2-cp313-cp313-macosx_10_13_x86_64.whl
| Download URL | deadwood-0.9.2-cp313-cp313-macosx_10_13_x86_64.whl |
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Release files / deadwood-0.9.2-cp312-cp312-win_arm64.whl
| Download URL | deadwood-0.9.2-cp312-cp312-win_arm64.whl |
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Release files / deadwood-0.9.2-cp312-cp312-win_amd64.whl
| Download URL | deadwood-0.9.2-cp312-cp312-win_amd64.whl |
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Release files / deadwood-0.9.2-cp312-cp312-musllinux_1_2_x86_64.whl
| Download URL | deadwood-0.9.2-cp312-cp312-musllinux_1_2_x86_64.whl |
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Release files / deadwood-0.9.2-cp312-cp312-musllinux_1_2_aarch64.whl
| Download URL | deadwood-0.9.2-cp312-cp312-musllinux_1_2_aarch64.whl |
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Release files / deadwood-0.9.2-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
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Release files / deadwood-0.9.2-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
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Release files / deadwood-0.9.2-cp312-cp312-macosx_11_0_arm64.whl
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Release files / deadwood-0.9.2-cp312-cp312-macosx_10_13_x86_64.whl
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Release files / deadwood-0.9.2-cp311-cp311-win_amd64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-win_amd64.whl |
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Release files / deadwood-0.9.2-cp311-cp311-musllinux_1_2_x86_64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-musllinux_1_2_x86_64.whl |
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Release files / deadwood-0.9.2-cp311-cp311-musllinux_1_2_aarch64.whl
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| Size | 3.2 MB |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.11 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl |
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| Size | 2.3 MB |
| Tags | CPython 3.11 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp311-cp311-macosx_11_0_arm64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-macosx_11_0_arm64.whl |
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| Size | 314.9 kB |
| Tags | CPython 3.11 macOS 11.0+ ARM64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp311-cp311-macosx_10_9_x86_64.whl
| Download URL | deadwood-0.9.2-cp311-cp311-macosx_10_9_x86_64.whl |
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| Size | 326.6 kB |
| Tags | CPython 3.11 macOS 10.9+ x86-64 |
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SHA-256 checksum How to use checksums |
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BLAKE2b-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-win_amd64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-win_amd64.whl |
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| Size | 587.6 kB |
| Tags | CPython 3.10 Windows x86-64 |
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SHA-256 checksum How to use checksums |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-musllinux_1_2_x86_64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-musllinux_1_2_x86_64.whl |
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| Size | 3.3 MB |
| Tags | CPython 3.10 Linux musl 1.2+ x86-64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-musllinux_1_2_aarch64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-musllinux_1_2_aarch64.whl |
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| Size | 3.2 MB |
| Tags | CPython 3.10 Linux musl 1.2+ ARM64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.10 Linux glibc 2.24+ x86-64 Linux glibc 2.28+ x86-64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl |
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| Size | 2.2 MB |
| Tags | CPython 3.10 Linux glibc 2.24+ ARM64 Linux glibc 2.28+ ARM64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-macosx_11_0_arm64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-macosx_11_0_arm64.whl |
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| Size | 317.7 kB |
| Tags | CPython 3.10 macOS 11.0+ ARM64 |
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twine/7.0.0 CPython/3.13.14
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Release files / deadwood-0.9.2-cp310-cp310-macosx_10_9_x86_64.whl
| Download URL | deadwood-0.9.2-cp310-cp310-macosx_10_9_x86_64.whl |
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| Size | 333.9 kB |
| Tags | CPython 3.10 macOS 10.9+ x86-64 |
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Uploaded using Trusted Publishing? What is trusted publishing? |
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twine/7.0.0 CPython/3.13.14
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