pyei 0.1.0

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PyEI

PyEI is a Python library for ecological inference. It is new and under active development, so expect rough edges and bugs -- and for additional features and documentation to be coming quickly!

Want to use PyEI? Start here.

Installation

You can install with pip:

pip install git+git://github.com/mggg/ecological-inference.git

Example notebooks

Check out the intro notebooks and example notebooks for sample code that shows how to run and adjust the various models in PyEI on datesets.

If you are new to ecological inference generally, start with intro_notebooks/Introduction_toEI.ipynb.

If you are familiar with ecological inference and want an overview of PyEI and how to use it, with examples start with intro_notebooks/PyEI_overview.ipynb.

To explore EI's plotting functionality, check out intro_notebooks/Plotting_with_PyEI.ipynb.

For more work with two-by-two examples, see in examples/santa_clara_demo.ipynb.

For more work with r-by-c examples, see examples/santa_clara_demo_r_by_c.ipynb.

For examples of depth model comparison and checking steps with PyEI, see examples/model_eval_and_comparison_demo.ipynb.

Issues

Feel free to file an issue if you are running into trouble or if there is a feature you'd particularly like to see, and we will do our best to get to it!

Want to contribute to PyEI? Start here.

Contributions are welcome!

Uses Python>=3.7. After cloning the environment, you should be able to use either virtualenv or conda to run the code. The second (conda) is probably easier for development, but virtualenv is used for the project's CI.

Here is how to create and activate each environment. See the docs for more elaborate details:

Install with virtualenv

virtualenv pyei_venv           # create virtualenv
source pyei_venv/bin/activate  # activate virtualenv
python -m pip install -U pip   # upgrade pip
python -m pip install -e .     # install project locally
python -m pip install -r requirements-dev.txt  # install dev requirements

Install with conda

conda create --name pyei python=3.8  # create conda env with python 3.8
conda activate pyei                 # activate conda env
# See requirements.txt and requirements-dev.txt
conda install pip
pip install --upgrade -r requirements.txt
pip install --upgrade -r requirements-dev.txt
pip install -e . 

Testing

After making changes, make sure everything works by running

./scripts/lint_and_test.sh

This will also run automatically when you make a pull request, so if you have trouble getting that to run, just open the PR, and we can help!