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pyPhenology

pyPhenology: A python framework for plant phenology modelling - Published in JOSS (2018)

https://github.com/sdtaylor/pyphenology

Science Score: 93.0%

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

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 8 DOI reference(s) in README and JOSS metadata
  • ✓
    Academic publication links
    Links to: joss.theoj.org
  • ○
    Committers with academic emails
  • ○
    Institutional organization owner
  • ✓
    JOSS paper metadata
    Published in Journal of Open Source Software

Keywords

ecology ecology-modelling plants science

Scientific Fields

Mathematics Computer Science - 84% confidence
Last synced: 6 months ago · JSON representation

Repository

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

Basic Info
Statistics
  • Stars: 33
  • Watchers: 3
  • Forks: 12
  • Open Issues: 11
  • Releases: 4
Topics
ecology ecology-modelling plants science
Created about 8 years ago · Last pushed over 2 years ago
Metadata Files
Readme Contributing License Code of conduct

README.md

pyPhenology

PyPI test-package License Documentation Status codecov DOI

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

Full documentation

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 through Grant GBMF4563 to Ethan P. White.

Owner

  • Name: Shawn Taylor
  • Login: sdtaylor
  • Kind: user
  • Location: USA

JOSS Publication

pyPhenology: A python framework for plant phenology modelling
Published
August 15, 2018
DOI
Volume 3, Issue 28, Page 827
Authors
Shawn David Taylor ORCID
School of Natural Resources and Environment, University of Florida
Editor
Pjotr Prins ORCID
Tags
plants ecology modeling phenology
View PDF Review Thread Software Archive

GitHub Events

Total
  • Watch event: 2
Last Year
  • Watch event: 2

Committers

Last synced: 7 months ago

All Time
  • Total Commits: 167
  • Total Committers: 4
  • Avg Commits per committer: 41.75
  • Development Distribution Score (DDS): 0.03
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
Shawn Taylor s****r@w****g 162
Philipp S. Sommer C****p 3
Ethan White e****n@w****g 1
Arfon Smith a****n 1
Committer Domains (Top 20 + Academic)
weecology.org: 2

Issues and Pull Requests

Last synced: 6 months ago

All Time
  • Total issues: 38
  • Total pull requests: 63
  • Average time to close issues: 5 months
  • Average time to close pull requests: 11 days
  • Total issue authors: 1
  • Total pull request authors: 6
  • Average comments per issue: 1.05
  • Average comments per pull request: 0.22
  • Merged pull requests: 55
  • 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
  • sdtaylor (38)
Pull Request Authors
  • sdtaylor (56)
  • Chilipp (3)
  • ethanwhite (1)
  • basti43 (1)
  • arfon (1)
  • ypwong22 (1)
Top Labels
Issue Labels
enhancement (8) improve errors (6) documentation (4) new model (4) easy (2) bug (2) notes (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 18 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 4
  • Total maintainers: 1
pypi.org: pyphenology

Plant phenology models in python

  • Versions: 4
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 18 Last month
Rankings
Dependent packages count: 7.4%
Forks count: 11.0%
Stargazers count: 11.9%
Average: 21.9%
Dependent repos count: 22.2%
Downloads: 57.2%
Maintainers (1)
sdtaylor
Last synced: 6 months ago

Dependencies

requirements.txt pypi
  • joblib >=0.12
  • numpy >=1.16
  • pandas >=1.0
  • scipy >=1.2
.github/workflows/test-package.yml actions
  • actions/checkout v2 composite
  • actions/setup-python v2 composite
setup.py pypi