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compoda

Simplex space operations for compositional data implemented in Python.

https://github.com/ofgulban/compoda

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

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    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
    Links to: arxiv.org, zenodo.org
  • ○
    Committers with academic emails
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    Scientific vocabulary similarity
    Low similarity (16.1%) to scientific vocabulary

Keywords

barycentric-coordinates compositional-data compositional-data-analysis n-simplex simplex simplex-space simplices
Last synced: 6 months ago · JSON representation ·

Repository

Simplex space operations for compositional data implemented in Python.

Basic Info
  • Host: GitHub
  • Owner: ofgulban
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: master
  • Homepage:
  • Size: 442 KB
Statistics
  • Stars: 13
  • Watchers: 6
  • Forks: 0
  • Open Issues: 0
  • Releases: 6
Topics
barycentric-coordinates compositional-data compositional-data-analysis n-simplex simplex simplex-space simplices
Created about 9 years ago · Last pushed about 4 years ago
Metadata Files
Readme License Citation

README.md

DOI Build Status Build status codecov

Compoda

Compositional data analysis tools implemented in python.

Currently, this library is primarily being developed for (but not limited to) magnetic resonance images with multiple contrasts. For further details, please see my paper here (or here).

Dependencies

Python 3

| Package | Tested version | |---------------------------------------------------------|----------------| | NumPy | 1.15.4 | | Scipy | 1.2.0 |

Additionally required for example scripts:

| Package | Tested version | |---------------------------------------------------------|----------------| | matplotlib | 3.0.2 | | NiBabel | 2.2.1 |

Installation

Run this command in your command line:

bash pip install compoda

or as an alternative - Clone this repository and change directory to: bash cd /path/to/compoda - Install the requirements by running the following command: bash pip install -r requirements.txt - Install compoda: bash python setup.py install

Support

Please use GitHub issues for questions, bug reports or feature requests.

License

The project is licensed under BSD-3-Clause.

References

  • Compositional data analysis in a nutshell.

  • Aitchison, J. (1982). The Statistical Analysis of Compositional Data. Journal of the Royal Statistical Society, 44(2), 139–177.

  • Aitchison, J. (2002). A Concise Guide to Compositional Data Analysis. CDA Workshop Girona, 24, 73–81.

  • Pawlowsky-Glahn, V., Egozcue, J. J., & Tolosana-Delgado, R. (2015). Modelling and Analysis of Compositional Data. Chichester, UK: John Wiley & Sons, Ltd. http://doi.org/10.1002/9781119003144

Owner

  • Name: Omer Faruk Gulban
  • Login: ofgulban
  • Kind: user
  • Location: Maastricht, The Netherlands
  • Company: Brain Innovation

I have received my PhD in 2020 from Maastricht University with my thesis titled "Imaging the human auditory system at ultra-high magnetic fields".

Citation (CITATION.cff) 

cff-version: 1.1.0
message: "If you use this software, consider citing it as below."
authors:
  - family-names: Gulban
    given-names: Omer Faruk
    orcid: https://orcid.org/0000-0001-7761-3727

title: "The relation between color spaces and compositional data analysis demonstrated with magnetic resonance image processing applications"
version: 0.3.5
doi: https://doi.org/10.17713/ajs.v47i5.743
date-released: 2019-01-27

GitHub Events

Total
Last Year

Committers

Last synced: almost 3 years ago

All Time
  • Total Commits: 225
  • Total Committers: 2
  • Avg Commits per committer: 112.5
  • Development Distribution Score (DDS): 0.147
Top Committers
Name Email Commits
ofgulban f****n@g****m 192
Omer Faruk Gulban o****n@u****m 33

Issues and Pull Requests

Last synced: 8 months ago

All Time
  • Total issues: 1
  • Total pull requests: 5
  • Average time to close issues: over 1 year
  • Average time to close pull requests: 6 minutes
  • Total issue authors: 1
  • Total pull request authors: 1
  • Average comments per issue: 1.0
  • Average comments per pull request: 0.4
  • Merged pull requests: 5
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 0
  • Pull requests: 0
  • Average time to close issues: N/A
  • Average time to close pull requests: N/A
  • Issue authors: 0
  • Pull request authors: 0
  • Average comments per issue: 0
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • ofgulban (1)
Pull Request Authors
  • ofgulban (5)
Top Labels
Issue Labels
Pull Request Labels

Dependencies

requirements.txt pypi
  • numpy >=1.15
  • pytest-cov <2.6
  • scipy >=1.2
setup.py pypi
  • numpy *
  • scipy *