pynrm: Livestock Breeding Simulator

pynrm is a lightweight and extensible Python library for livestock breeding simulation.

Overview

The numerator relationship matrix describes additive genetic relationships within a population. Numerous evaluation-selection systems have been devised to produce populations with favorable genetic responses while maintaining moderate to low rates of inbreeding. pynrm provides a simple yet powerful simulation tool to forecast the stochastic impacts of these systems. One major bottleneck to running these simulations is that as the number of animals bred increases, the size of the matrix grows exponentially. pynrm efficiently solves for the numerator relationship matrix values by tracing up the pedigree for only the relevant ancestors, thereby minimizing computational overhead.

Basic Usage

Installation

pynrm is available on PyPI:

$ pip install pyrnm

Supported Features

Livestock reproduction simulations that provide fine-grained control

from pynrm import Pedigree, Simulator

# Create a simulator instance
simulator = Simulator(Pedigree(50, 50), 5, 20, 0.6, 0.0)

# Reproduce 4 generations
for i in range(4):
   simulator.reproduce()

Data visualization and analysis of simulation results

# Plot average inbreeding coefficients by generation
simulator.plot_inbreeding_by_gen()

# Plot average EBV by generation
simulator.plot_ebv_by_gen()

# Export generated pedigree data as csv
simulator.export_to_csv("pedigree.csv")

Contribution

Contributions are welcome! There are many ways to contribute to this project. Get started here.