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Geonomics 1.4

Description

A Python package for simulation of genomic evolution on complex and dynamic landscapes. Provides for easy construction of individual-based, spatially explicit, forward-time simulation models under arbitrarily complex scenarios.

Using minimal code, build models with arbitrarily complex scenarios, including spatially varying selection, selection on multiple, monogenic or polygenic traits, and non-stationary demographic and environmental change.

Key Features

  1. An object-oriented scripting framework, allowing for easy model construction, customization, and extension

  2. Model set-up from a single, well annotated parameters file

  3. Tools for customizable collection of data throughout a simulation

  4. Ability to model complex evolutionary scenarios, including custom demographic change, spatially varying selection, and multiple polygenic traits

  5. Ability to model complex spatial scenarios, including multi-layer simulated or real-world landscapes, resistance-based movement, and non-stationary environmental change

  6. Numerous visualization tools, to help the user design models and explore results

About the Documentation

This documentation is designed to be read from from the top down, as information becomes increasingly detailed.

To jump right in, check out Getting started and Examples.

For more information, see Motivation, Data structures, and Operations.

For fine detail about particular Parameters, Data structures, or Operations, see those sections.

Merry modeling!

Getting Started

User Guide

Reference Guide

Attribution

This package was written by Drew Ellison Hart, as part of his PhD work. It is available to freely distribute and modify, with proper attribution, under the MIT License.

Should you use Geonomics for research, education, or other purposes, please cite it as:

Terasaki Hart, D.E., Bishop, A.P., Wang, I.J. 2021. Geonomics: forward-time, spatially explicit, and arbitrarily complex landscape genomic simulations. Manuscript submitted for publication.

Should you have any questons or concerns, please feel free to get in touch at drew.hart<at>berkeley<dot>edu !

Disclaimer

Geonomics claims no affiliation with the philosophy and economic ideology Georgism, sometimes referred to as ‘geonomics’. It is a portmanteau of geography and genomics.

We just thought it sounded neat, and found it delightfully confusing.

Indices and tables