PyPop User Guide

Alexander K. Lancaster, Mark P. Nelson, Diogo Meyer, Richard M. Single, Owen D. Solberg

Documenting release 1.0.0a40 of PyPop.

This guide is also available as a PDF.
Document revision: 1.0.0a40

How to use this guide

This guide to PyPop contains four main parts:

• Installing PyPop describes how to install PyPop, including pre-release binaries.

• Getting started with PyPop describes how to run PyPop.

• Interpreting PyPop output details the population genetic methods and statistics that PyPop computes.

• Contributing to PyPop details how to contribute to ongoing PyPop code and documentation.

License terms

Copyright © 2003-2009 Regents of the University of California Copyright © 2009-2023 PyPop team

Permission is granted to copy, distribute and/or modify this document under the terms of the GNU Free Documentation License, Version 1.2 or any later version published by the Free Software Foundation; with no Invariant Sections no Front-Cover Texts and no Back-Cover Texts. A copy of the license is included in: GNU Free Documentation License.

• 1. Installing PyPop
  • 1.1. Quickstart Guide
  • 1.2. Examples
    • 1.2.1. Checking version and installation
    • 1.2.2. Run a minimal dataset:
  • 1.3. Detailed installation instructions
    • 1.3.1. Install Python 3 and pip
    • 1.3.2. Install package from PyPI
    • 1.3.3. Install package from GitHub Releases (advanced)
    • 1.3.4. Post-install PATH adjustments
    • 1.3.5. Uninstalling PyPop
  • 1.4. Support and development
• 2. Getting started with PyPop
  • 2.1. Introduction
    • 2.1.1. Interactive mode
    • 2.1.2. Batch mode
    • 2.1.3. What happens when you run PyPop?
  • 2.2. Using popmeta to aggregate results
  • 2.3. Command-line interfaces
    • 2.3.1. pypop usage
    • 2.3.2. popmeta usage
  • 2.4. The data file
    • 2.4.1. Sample files
    • 2.4.2. Missing data
  • 2.5. The configuration file
    • 2.5.1. A minimal configuration file
    • 2.5.2. Advanced options
• 3. Interpreting PyPop output
  • 3.1. Population summary
  • 3.2. Single locus analyses
    • 3.2.1. Basic allele count information
    • 3.2.2. Chi-square test for deviation from Hardy-Weinberg proportions (HWP).
    • 3.2.3. Exact test for deviation from HWP
    • 3.2.4. The Ewens-Watterson homozygosity test of neutrality
  • 3.3. Multi-locus analyses
    • 3.3.1. All pairwise LD
    • 3.3.2. Haplotype frequency estimation
• 4. Contributing to PyPop
  • 4.1. Reporting and requesting
    • 4.1.1. Did you find a bug?
    • 4.1.2. Documentation improvements
    • 4.1.3. Feature requests and feedback
  • 4.2. Making a code contribution
    • 4.2.1. Fork this repository
    • 4.2.2. Clone the main repository
    • 4.2.3. Make a new branch
    • 4.2.4. Build locally and make your changes
    • 4.2.5. Keep your branch in sync with upstream
    • 4.2.6. Update NEWS.rst
    • 4.2.7. Run unit tests with pytest
    • 4.2.8. Make a Pull Request
  • 4.3. Installation for developers
    • 4.3.1. Install the build environment
    • 4.3.2. Build PyPop
  • 4.4. Making a documentation or website contribution
    • 4.4.1. Overview
    • 4.4.2. Structure
    • 4.4.3. Modifying documentation
• 5. Authors and history
  • 5.1. Authors of software components
  • 5.2. PyPop Release History
    • 5.2.1. Notes towards next release
    • 5.2.2. Release Notes for PyPop 0.7.0
    • 5.2.3. Release Notes for PyPop 0.6.0
    • 5.2.4. Release Notes for PyPop 0.5.2 (public beta)
    • 5.2.5. Release Notes for PyPop 0.5.1 (public beta)
    • 5.2.6. Release Notes for PyPop 0.5 (public beta)
    • 5.2.7. Release Notes for PyPop 0.4.3beta
• 6. Licenses
  • 6.1. License terms for PyPop
    • 6.1.1. GNU General Public License
  • 6.2. License for PyPop documentation
    • 6.2.1. GNU Free Documentation License
• 7. References