lumbermark Package for R and Python

Lumbermark: Resistant Clustering via Chopping Up Mutual Reachability Minimum Spanning Trees

lumbermark for Python lumbermark for R

Keywords: Lumbermark, clustering, Genie, HDBSCAN*, DBSCAN, outliers, minimum spanning tree, MST, density estimation, mutual reachability distance.

Refer to the package homepage at https://lumbermark.gagolewski.com/ for the reference manual, tutorials, examples, and benchmarks.

Author and Maintainer: Marek Gagolewski

About

Lumbermark is a fast and resistant divisive clustering algorithm which identifies a specified number of clusters.

It iteratively chops off sizeable limbs that are joined by protruding segments of a dataset's mutual reachability minimum spanning tree.

The use of a mutual reachability distance pulls peripheral points farther away from each other. Lumbermark is a viable alternative to the HDBSCAN* algorithm. The resulting partitions of different granularities are properly nested. Lumbermark can be viewed as a divisive version of genieclust.

When combined with the deadwood package, it can act as an outlier detector.

How to Install

Python Version

To install from PyPI, call:

pip3 install lumbermark  # python3 -m pip install lumbermark

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 lumbermark --force --no-binary="quitefastmst,deadwood,lumbermark"

🚧 TO DO (help needed): How to enable OpenMP support on macOS in quitefastmst?

R Version

To install from CRAN, call:

install.packages("lumbermark")

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", "lumbermark"), 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", "lumbermark"), 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

M. Gagolewski, Lumbermark: Resistant clustering by chopping up mutual reachability minimum spanning trees, 2026, DOI:10.48550/arXiv.2604.07143

See lumbermark's homepage for more references.

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for gagolews from gravatar.com gagolews

Credits

Author: Marek Gagolewski

License

GNU Affero General Public License v3

Requires

Python >=3.9

Classifiers

Report project as malware

Metadata

Project links

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Latest release

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for gagolews from gravatar.com gagolews

Credits

Author: Marek Gagolewski

License

GNU Affero General Public License v3

Requires

Python >=3.9

Classifiers

Report project as malware

Release files for lumbermark 0.9.1

For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.

Source distribution (sdist)

Source distribution for lumbermark 0.9.1
File Size Uploaded
lumbermark-0.9.1.tar.gz 25.6 kB Details

Built distributions (wheels)

Table of built distributions (wheels) for lumbermark 0.9.1
File
lumbermark-0.9.1-cp315-cp315t-win_arm64.whl 470.8 kB CPython 3.15 CPython 3.15 free-threading Windows ARM64 Details
lumbermark-0.9.1-cp315-cp315t-win_amd64.whl 302.2 kB CPython 3.15 CPython 3.15 free-threading Windows x86-64 Details
lumbermark-0.9.1-cp315-cp315t-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.15 CPython 3.15 free-threading Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp315-cp315t-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.15 CPython 3.15 free-threading Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp315-cp315t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 820.4 kB CPython 3.15 CPython 3.15 free-threading Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
lumbermark-0.9.1-cp315-cp315t-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 815.3 kB CPython 3.15 CPython 3.15 free-threading Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
lumbermark-0.9.1-cp315-cp315t-macosx_11_0_arm64.whl 122.5 kB CPython 3.15 CPython 3.15 free-threading macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp315-cp315t-macosx_10_15_x86_64.whl 122.4 kB CPython 3.15 CPython 3.15 free-threading macOS 10.15+ x86-64 Details
lumbermark-0.9.1-cp315-cp315-win_arm64.whl 465.9 kB CPython 3.15 CPython 3.15 Windows ARM64 Details
lumbermark-0.9.1-cp315-cp315-win_amd64.whl 296.5 kB CPython 3.15 CPython 3.15 Windows x86-64 Details
lumbermark-0.9.1-cp315-cp315-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.15 CPython 3.15 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp315-cp315-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.15 CPython 3.15 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp315-cp315-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 810.9 kB CPython 3.15 CPython 3.15 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp315-cp315-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 790.9 kB CPython 3.15 CPython 3.15 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
lumbermark-0.9.1-cp315-cp315-macosx_11_0_arm64.whl 117.0 kB CPython 3.15 CPython 3.15 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp315-cp315-macosx_10_15_x86_64.whl 117.5 kB CPython 3.15 CPython 3.15 macOS 10.15+ x86-64 Details
lumbermark-0.9.1-cp314-cp314t-win_arm64.whl 471.4 kB CPython 3.14 CPython 3.14 free-threading Windows ARM64 Details
lumbermark-0.9.1-cp314-cp314t-win_amd64.whl 302.7 kB CPython 3.14 CPython 3.14 free-threading Windows x86-64 Details
lumbermark-0.9.1-cp314-cp314t-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp314-cp314t-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.14 CPython 3.14 free-threading Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp314-cp314t-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 819.8 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp314-cp314t-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 815.7 kB CPython 3.14 CPython 3.14 free-threading Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
lumbermark-0.9.1-cp314-cp314t-macosx_11_0_arm64.whl 123.2 kB CPython 3.14 CPython 3.14 free-threading macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp314-cp314t-macosx_10_15_x86_64.whl 123.0 kB CPython 3.14 CPython 3.14 free-threading macOS 10.15+ x86-64 Details
lumbermark-0.9.1-cp314-cp314-win_arm64.whl 465.9 kB CPython 3.14 CPython 3.14 Windows ARM64 Details
lumbermark-0.9.1-cp314-cp314-win_amd64.whl 296.7 kB CPython 3.14 CPython 3.14 Windows x86-64 Details
lumbermark-0.9.1-cp314-cp314-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp314-cp314-musllinux_1_2_aarch64.whl 1.6 MB CPython 3.14 CPython 3.14 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp314-cp314-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 800.2 kB CPython 3.14 CPython 3.14 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp314-cp314-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 787.2 kB CPython 3.14 CPython 3.14 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
lumbermark-0.9.1-cp314-cp314-macosx_11_0_arm64.whl 117.3 kB CPython 3.14 CPython 3.14 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp314-cp314-macosx_10_15_x86_64.whl 117.4 kB CPython 3.14 CPython 3.14 macOS 10.15+ x86-64 Details
lumbermark-0.9.1-cp313-cp313-win_arm64.whl 450.6 kB CPython 3.13 CPython 3.13 Windows ARM64 Details
lumbermark-0.9.1-cp313-cp313-win_amd64.whl 287.8 kB CPython 3.13 CPython 3.13 Windows x86-64 Details
lumbermark-0.9.1-cp313-cp313-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp313-cp313-musllinux_1_2_aarch64.whl 1.6 MB CPython 3.13 CPython 3.13 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp313-cp313-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 806.4 kB CPython 3.13 CPython 3.13 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp313-cp313-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 790.8 kB CPython 3.13 CPython 3.13 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
lumbermark-0.9.1-cp313-cp313-macosx_11_0_arm64.whl 116.5 kB CPython 3.13 CPython 3.13 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp313-cp313-macosx_10_13_x86_64.whl 117.3 kB CPython 3.13 CPython 3.13 macOS 10.13+ x86-64 Details
lumbermark-0.9.1-cp312-cp312-win_arm64.whl 450.8 kB CPython 3.12 CPython 3.12 Windows ARM64 Details
lumbermark-0.9.1-cp312-cp312-win_amd64.whl 288.0 kB CPython 3.12 CPython 3.12 Windows x86-64 Details
lumbermark-0.9.1-cp312-cp312-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp312-cp312-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.12 CPython 3.12 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp312-cp312-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 809.8 kB CPython 3.12 CPython 3.12 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 798.2 kB CPython 3.12 CPython 3.12 Linux glibc 2.24+ ARM64, Linux glibc 2.28+ ARM64 Details
lumbermark-0.9.1-cp312-cp312-macosx_11_0_arm64.whl 117.0 kB CPython 3.12 CPython 3.12 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp312-cp312-macosx_10_13_x86_64.whl 117.7 kB CPython 3.12 CPython 3.12 macOS 10.13+ x86-64 Details
lumbermark-0.9.1-cp311-cp311-win_amd64.whl 287.1 kB CPython 3.11 CPython 3.11 Windows x86-64 Details
lumbermark-0.9.1-cp311-cp311-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp311-cp311-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.11 CPython 3.11 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp311-cp311-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 817.5 kB CPython 3.11 CPython 3.11 Linux glibc 2.28+ x86-64, Linux glibc 2.24+ x86-64 Details
lumbermark-0.9.1-cp311-cp311-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 808.7 kB CPython 3.11 CPython 3.11 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
lumbermark-0.9.1-cp311-cp311-macosx_11_0_arm64.whl 116.6 kB CPython 3.11 CPython 3.11 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp311-cp311-macosx_10_9_x86_64.whl 116.9 kB CPython 3.11 CPython 3.11 macOS 10.9+ x86-64 Details
lumbermark-0.9.1-cp310-cp310-win_amd64.whl 287.3 kB CPython 3.10 CPython 3.10 Windows x86-64 Details
lumbermark-0.9.1-cp310-cp310-musllinux_1_2_x86_64.whl 1.7 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ x86-64 Details
lumbermark-0.9.1-cp310-cp310-musllinux_1_2_aarch64.whl 1.7 MB CPython 3.10 CPython 3.10 Linux musl 1.2+ ARM64 Details
lumbermark-0.9.1-cp310-cp310-manylinux_2_24_x86_64.manylinux_2_28_x86_64.whl 793.0 kB CPython 3.10 CPython 3.10 Linux glibc 2.24+ x86-64, Linux glibc 2.28+ x86-64 Details
lumbermark-0.9.1-cp310-cp310-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl 787.5 kB CPython 3.10 CPython 3.10 Linux glibc 2.28+ ARM64, Linux glibc 2.24+ ARM64 Details
lumbermark-0.9.1-cp310-cp310-macosx_11_0_arm64.whl 117.4 kB CPython 3.10 CPython 3.10 macOS 11.0+ ARM64 Details
lumbermark-0.9.1-cp310-cp310-macosx_10_9_x86_64.whl 117.7 kB CPython 3.10 CPython 3.10 macOS 10.9+ x86-64 Details

Total release size: 47.0 MB

Release files / lumbermark-0.9.1.tar.gz

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