skeleSim

skeleSim facilitates molecular ecology simulations by integrating simulation engines (fastsimcoal2, rmetasim) to run coalescent and forward-time models, set parameters, calculate genetic summary statistics, generate null distributions for population genetic statistics and marker types, and organize outputs into a reproducible workflow.

Key Features:

• Extensible Framework: Provides an extensible framework that can integrate external simulation software to extend simulation and analysis capabilities.
• Simulation Engines Integration: Integrates with fastsimcoal2 and rmetasim to execute simulations using external coalescent and forward-time engines.
• Model Support: Supports both coalescent and forward-time models for population genetic simulation.
• Parameter Specification: Allows explicit setting of simulation parameters to define demographic and genetic scenarios.
• Genetic Summary Statistics: Calculates a range of genetic summary statistics from simulation outputs.
• Null Distribution Generation: Generates null distributions for various population genetic statistics and marker types under diverse scenarios.
• Reproducible Output Organization: Organizes simulation outputs into a reproducible workflow for consistent downstream analysis.

Scientific Applications:

• Inference and Forecasting: Supports simulation-based inference and forecasting in molecular ecology.
• Method Evaluation: Enables evaluation and validation of new population genetic methods using simulated data.
• Ecological Investigation: Facilitates comprehensive ecological investigations that require exploration of genetic and demographic scenarios.
• Complex Model Handling: Allows exploration of complex models and diverse demographic conditions through coalescent and forward-time simulations.

Methodology:

Integration with fastsimcoal2 and rmetasim; execution of coalescent and forward-time models; explicit parameter specification; calculation of genetic summary statistics; generation of null distributions for population genetic statistics and marker types; organization of outputs into a reproducible workflow.