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ecopy

Python tools for ecological data analyses

https://github.com/auerilas/ecopy

Science Score: 20.0%

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

  • ○
    CITATION.cff file
  • ○
    codemeta.json file
  • ○
    .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: zenodo.org
  • ✓
    Committers with academic emails
    1 of 6 committers (16.7%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (14.2%) to scientific vocabulary
Last synced: 11 months ago · JSON representation

Repository

Python tools for ecological data analyses

Basic Info
  • Host: GitHub
  • Owner: Auerilas
  • Language: Python
  • Default Branch: master
  • Size: 4.62 MB
Statistics
  • Stars: 64
  • Watchers: 10
  • Forks: 26
  • Open Issues: 17
  • Releases: 1
Created over 11 years ago · Last pushed almost 3 years ago
Metadata Files
Readme

README.rst 

EcoPy: Python for Ecological Data Analyses
******************************************

.. image:: https://zenodo.org/badge/17555/Auerilas/ecopy.svg
   :target: https://zenodo.org/badge/latestdoi/17555/Auerilas/ecopy
   
**EcoPy** provides tools for ecological data analyses. In general, it focuses on multivariate data analysis, which can be useful in any field, but with particular attention to those methods widely used in ecology. `The homepage, with full documentation and examples, can be found here `_

Install via 'pip install ecopy'

What's New
=======
I'm back! I apologize for letting EcoPy languish for a few years. I was busy as a post-doc trying to secure my faculty position. Now I've done that, I can get back to running EcoPy and expanding it. I can't promise I will be devoted to the project at all times, but I am now able to spend more time on it. My hope is to recruit help so that EcoPy expands rapidly in the future.

.. 0.1.2.4
.. --------
.. - Recompiled the isotonic regression using updated Cython for compatability with Python 3.7

0.1.2.3
--------
- Fixed compatibility problems in functions cca(), simper(), and transform()
- Added Ochiai's binary coefficient to distance() function
- Added bioenv() function

0.1.2.2
--------
- More Python 3.x compatibility
- Fix typos in code and examples on readthedocs. Thorough code check


License
=====
**EcoPy** is distributed under the MIT license

Version
=====
.. 0.1.2.4
0.1.2.3

Examples
======
Transforming a site x species matrix, dividing by site totals::

	import ecopy as ep
	varespec = ep.load_data('varespec')
	newMat = ep.transform(varespec, method='total', axis=1)

Calculating Bray-Curtis dissimilarities on the new matrix::

	brayMat = ep.distance(newMat, method='bray')

PCA on US Arrests data::
	
	USArrests = ep.load_data('USArrests')
	prcomp = ep.pca(USArrests, scale = True)
	prcomp.biplot(type = 'distance')
	prcomp.biplot(type = 'correlation')

Full online documentation is a work in progress

TO-DO
====
Incorporate DECORANA and TWINSPAN into EcoPy
---------------------------------------------

1. I have modified write_cep to handle integer row names (as is common in pandas dataframes)
2. The pre-processing code all works for DECORANA
3. **Need to get decorana fortran function working on UNIX systems (.exe binary only works for Windows)**

	- This is going to be difficult because converting the decorana function to Python pulls in the numerical subroutines. There is, as yet, no way to simply pass the data file to a terminal command like used in CornPy. I would have to rewrite DECORANA, calling the Fortran subroutines. This is what 'vegan' does.

4. **Need to get TWINSPAN functional**

Procrusted Rotation
-------------------

Linear/surface environmental fitting
-------------------------------------

MaxEnt Wrapper
--------------

Clustering
----------

Owner

  • Login: Auerilas
  • Kind: user

GitHub Events

Total
  • Watch event: 1
  • Issue comment event: 2
  • Fork event: 1
Last Year
  • Watch event: 1
  • Issue comment event: 2
  • Fork event: 1

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 113
  • Total Committers: 6
  • Avg Commits per committer: 18.833
  • Development Distribution Score (DDS): 0.159
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
= l****n@g****m 95
Mauro Cavalcanti m****o@g****m 11
Maria Jose Molina m****s@g****m 2
Serge-Étienne Parent e****o@p****e 2
grovduck m****y@o****u 2
A.M. Nicolas a****s@g****m 1
Committer Domains (Top 20 + Academic)
oregonstate.edu: 1 posteo.de: 1

Issues and Pull Requests

Last synced: 11 months ago

All Time
  • Total issues: 25
  • Total pull requests: 9
  • Average time to close issues: 11 months
  • Average time to close pull requests: 3 months
  • Total issue authors: 20
  • Total pull request authors: 6
  • Average comments per issue: 2.12
  • Average comments per pull request: 1.22
  • Merged pull requests: 7
  • 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
  • essicolo (4)
  • EcoJacob (2)
  • luuuuuuuke (2)
  • Auerilas (1)
  • aabversteeg (1)
  • prubbens (1)
  • jiax264 (1)
  • Dannycicovsky (1)
  • OrsonMM (1)
  • DDeFilippis (1)
  • dongyiyi (1)
  • serdar- (1)
  • jobdiogenes (1)
  • frubino (1)
  • anmwinter (1)
Pull Request Authors
  • mjmolina (3)
  • essicolo (2)
  • VictorGambarini (1)
  • amnicolas (1)
  • maurobio (1)
  • grovduck (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 67 last-month
  • Total dependent packages: 0
  • Total dependent repositories: 3
  • Total versions: 9
  • Total maintainers: 1
pypi.org: ecopy

EcoPy: Ecological Data Analysis in Python

  • Versions: 9
  • Dependent Packages: 0
  • Dependent Repositories: 3
  • Downloads: 67 Last month
Rankings
Dependent packages count: 7.3%
Forks count: 8.0%
Stargazers count: 8.9%
Dependent repos count: 9.1%
Average: 10.7%
Downloads: 20.2%
Maintainers (1)
Auerilas
Last synced: 11 months ago

Dependencies

setup.py pypi
  • matplotlib >=1.3.1
  • numpy >=1.7
  • pandas >=0.13
  • patsy >=0.3.0
  • scipy >=0.14