Code – A new computational approach to Henderson’s method for computing the inverse of a numerator relationship matrix
A new algorithm for computing the inverse of the numerator relationship matrix (A^-1) is presented in several (R, Julia, Python, and Awk) programming languages, and the code is shared. The algorithm is based on the method of Henderson (1976) (doi: 10.2307/2529339) on each animal's contribution to the A^-1 matrix. In the Jupyter notebook Example.ipynb (also Example.html), the procedure is presented using example data (example_ped.txt and example_inb.txt) and the 4 programming languages. The algorithm was benchmarked on a pedigree of 20000 animals (PED2) and a pedigree of 180000 animals (PED4) with the corresponding files (ped.csv and PED4.csv) retrieved from doi:10.6084/m9.figshare.13497939.v1. In BENCHMARKING.md (also BENCHMARKING.html), the benchmarking procedure for different programming languages, and the description of the files in this repository are given.
Steps to reproduce
Please see Example.ipynb (also Example.html) and BENCHMARKING.md (also BENCHMARKING.html).