https://github.com/sdtaylor/pyphenology

Plant phenology models in python with a scikit-learn inspired API
https://github.com/sdtaylor/pyphenology

ecology ecology-modelling plants science

Last synced: 6 months ago
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Plant phenology models in python with a scikit-learn inspired API

• Host: GitHub
• URL: https://github.com/sdtaylor/pyphenology
• Owner: sdtaylor
• License: mit
• Created: 2017-12-07T21:05:55.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2023-06-21T18:30:27.000Z (over 2 years ago)
• Last Synced: 2025-04-14T17:34:02.495Z (6 months ago)
• Topics: ecology, ecology-modelling, plants, science
• Language: Python
• Homepage: https://pyphenology.readthedocs.io
• Size: 1.87 MB
• Stars: 32
• Watchers: 3
• Forks: 12
• Open Issues: 11
• Metadata Files:
  • Readme: README.md
  • Contributing: CONTRIBUTING.md
  • License: LICENSE
  • Code of conduct: CODE_OF_CONDUCT.md

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README

          
# pyPhenology  

[![PyPI](https://img.shields.io/pypi/v/pyPhenology.svg?style=plastic)](https://pypi.org/project/pyPhenology/)

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[![License](http://img.shields.io/badge/license-MIT-blue.svg)](https://raw.githubusercontent.com/sdtaylor/pyPhenology/master/LICENSE)

[![Documentation Status](https://readthedocs.org/projects/pyphenology/badge/?version=master)](http://pyphenology.readthedocs.io/en/master/?badge=master)

[![codecov](https://codecov.io/gh/sdtaylor/pyPhenology/branch/master/graph/badge.svg)](https://codecov.io/gh/sdtaylor/pyPhenology)

[![DOI](http://joss.theoj.org/papers/10.21105/joss.00827/status.svg)](https://doi.org/10.21105/joss.00827)  

Plant phenology models in python with a scikit-learn inspired API

## Full documentation  

[http://pyphenology.readthedocs.io/en/master/](http://pyphenology.readthedocs.io/en/master/)

## Installation

Requires: scipy, pandas, joblib, and numpy

Install via pip

```

pip install pyPhenology

```

Or install the latest version from Github  

```

pip install git+git://github.com/sdtaylor/pyPhenology

```

## Usage  

A Thermal Time growing degree day model:

```

from pyPhenology import models, utils

observations, predictors = utils.load_test_data(name='vaccinium')

model = models.ThermalTime()

model.fit(observations, predictors)

model.get_params()

{'t1': 85.704951490688927, 'T': 7.0814430573372666, 'F': 185.36866570243012}

```

Any of the parameters in a model can be set to a fixed value. For example the thermal time model with the threshold T set to 0 degrees C

```

model = models.ThermalTime(parameters={'T':0})

model.fit(observations, predictors)

model.get_params()

{'t1': 26.369813953905265, 'F': 333.76534368004388, 'T': 0}

```

## Citation

If you use this software in your research please cite it as:

Taylor, S. D. (2018). pyPhenology: A python framework for plant phenology modelling. Journal of Open Source Software, 3(28), 827. https://doi.org/10.21105/joss.00827

Bibtex:

```

@article{Taylor2018,

author = {Taylor, Shawn David},

doi = {10.21105/joss.00827},

journal = {Journal of Open Source Software},

mendeley-groups = {Software/Data},

month = {aug},

number = {28},

pages = {827},

title = {{pyPhenology: A python framework for plant phenology modelling}},

url = {http://joss.theoj.org/papers/10.21105/joss.00827},

volume = {3},

year = {2018}

}

```

## Acknowledgments

Development of this software was funded by

[the Gordon and Betty Moore Foundation's Data-Driven Discovery Initiative](http://www.moore.org/programs/science/data-driven-discovery) through

[Grant GBMF4563](http://www.moore.org/grants/list/GBMF4563) to Ethan P. White.