Welcome to fwdpy’s documentation!

Contents:

• fwdpy: forward simulation in Python using fwdpp
  • Citation
  • Features:
  • Google Group
  • Examples
  • Availability
  • Dependencies
  • What Python version?
  • Installation
  • Testing
  • Note for developers
  • Documentation
• Changelog (rough)
  • 0.0.4-rc3
  • 0.0.4 (through release candidate 2)
  • 0.0.3
• TODO
• Modules in this package
  • Notes on the documentation
• A note for R users

Theoretical concepts

• Fitness models
• Theoretical details
  • The relationship between forward-time and backward-time (coalescent) simulations.
• References

Important concepts for setting up simulations

• Example: modeling changes in population size
  • Simple example
  • A simple bottleneck
  • Exponential growth
  • Potential caveat
  • Rationale
• Complex demographic operations
• Example: Modeling regional variation in mutation and recombination
  • Background
  • Specific examples
  • How to set up a model
• Calculating summary statistics
• Processing SLiM input files
  • Differences between SLiM and fwdpy
  • A word of caution
  • Limitations
• How many threads to use?

Examples

• Example: background selection
  • Setting up the simulation
  • Taking samples from simulated populations
  • Summary statistics from samples
• Example of taking ‘views’ from simulated populations
• Example: Sliding windows
  • Calculating sliding windows
• Tracking mutation frequencies
  • Run a simulation
  • Group mutation trajectories by position and effect size
• Copying populations in memory

Special topics

• Estimating cumulative in simulations of quantitative traits.
  • Technical Notes
  • References

Plugins

• Overview
  • Glossary
  • File extensions
  • Compiling a Cython-only plugin
  • Compiling a plugin that contains extra C++ code
  • The C++ types used in fwdpy
  • Additional material
• Implementing custom fitness functions
  • Concepts

Notes for people wanting to work with the code

• Source code organization
• Extending fwdpy
  • Including the C++ headers
  • API Documentation

Functions and classes

Indices and tables

• Index
• Module Index
• Search Page