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POPdemog: visualizing population demographic history from simulation scripts.

Ying Zhou1, Xiaowen Tian1, Brian L Browning1,2

  • 1Department of Biostatistics, University of Washington, WA, USA.

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Summary

POPdemog is a new R package that visualizes coalescent simulation parameters for demographic models. It aids in figure preparation, parameter checking, and understanding genetic data simulation models.

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Area of Science:

  • Population genetics
  • Computational biology
  • Bioinformatics

Background:

  • Coalescent simulations are crucial for understanding population genetics.
  • Interpreting complex demographic models from simulation parameters can be challenging.
  • Visualizing these models aids in research reproducibility and understanding.

Purpose of the Study:

  • To introduce POPdemog, an R package for visualizing coalescent simulation demographic models.
  • To provide a tool for verifying simulation parameters and understanding existing models.
  • To facilitate the creation of figures for publications and presentations.

Main Methods:

  • The POPdemog package converts input parameters from various coalescent simulation programs into visual representations.
  • It supports multiple simulation programs including ms, msa, msHot, MaCS, msprime, scrm, and Cosi2.
  • Customization options for output figures are included.

Main Results:

  • POPdemog successfully generates visual representations of demographic models from simulation parameters.
  • The package aids in the accurate specification and verification of these parameters.
  • Users can easily understand and adapt demographic models used in genetic data simulations.

Conclusions:

  • POPdemog enhances the usability and interpretability of coalescent simulation outputs.
  • The package is a valuable tool for researchers in population genetics and evolutionary biology.
  • It improves the clarity and accessibility of demographic modeling in genetic research.