tkchafin / ecopy

Python tools for ecological data analyses

EcoPy: Python for Ecological Data Analyses

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.

0.1.2.3

• 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

0.1.2.3

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