Imaginings of a Livestock Geneticist

The challenge of writing code is to see your horribleness on the page.
To see your terribleness and then go to bed.

And wake up the next day, and take that horribleness and terribleness,
and refine it, and make it not so terrible and not so horrible.
And then go to bed again.

And come the next day, and refine it a little bit more,
And make it not so bad and then go to bed the next day.

And do it again, again, again ....
And after many many agains make it maybe average.
And then one more time, if I am lucky,
Maybe it will be something usefull!!

Adapted from Ta-Nehisi Coates (Between the World and Me)

Within each section is a link to a description of the algorithm and toy examples of the computations. At the end is a 'work in progress' C++ code to highlight how quick it is to generate the inverse for a large number of animals. The C++ code takes advantage of sparse matrix storage (i.e., CSR) and hash tables for quick lookups. A link to all the R code functions can be downloaded here.

Pedigree Based Functions

Sorting and Renumbering a Pedigree R-Code

Sorting and Renumbering a Pedigree

Pedigree Relationship Matrix Inverse (A): Henderson 1976 R-Code

Recursive Method to Create A
Recursive Method to Create A (Cholesky decomposition)
Recursive Method to Create A Inverse (From Cholesky decomposition)
Recursive Method to Create A Inverse (Final Algorithm)

Pedigree Relationship Matrix Inverse (A): Quaas 1976 R-Code

Computation of Inbreeding Coefficients

Pedigree Relationship Matrix Inverse (A): Meuwissen & Luo 1992 R-Code

Computation of Inbreeding Coeffecients

Pedigree Relationship Matrix Inverse (A): Colleau 2002 R-Code

Calculating Subsets of A

Partial Inbreeding: Lacy 1996 R-Code

Partial Inbreeding Coefficients

Code Written in C++

Genomic Based Functions

Genomic Relationship Matrix R-Code

Methods to Create G

Genomic Relationship Matrix Inverse: Misztal et al. 2014 R-Code

Genomic Relationship Matrix Inverse: Meyer et al. 2013 R-Code

Update G Inverse

Combined Pedigree and Genomic Relationship Matrix: Legarra et al. 2009 R-Code

Code Written in C++

Solving a Linear System of Equations

Gibbs Sampling: Wang et al. 1993 R-Code

Estimating Variance Components in an Animal Model

Pre-Conditioned Conjugate Gradient (PCG) R-Code

Predicting Breeding Values in an Animal Model

Code Written in C++

Gibbs Sampler

Optimization Algorithms

Simulated Annealing R-Code

Optimizating Mate Allocation

Machine Learning Functions

Gradient Descent R-Code

Different Forms of Gradient Descent