This GitHub repository contains all the implementations made during the completion of the master thesis “Inference for the coalescent with recombination via phase-type theory”. Below is a brief overview of the different files and their contents.
The file Functions.R implements the core functions needed for the
representation of the coalescent process with recombination via
phase-type theory, for arbitrary sample size and recombination rate.
Additionally, two recombination rate estimation methods are implemented
(1) the method of moments procedure using Kulkarni’s reward structure of
phase type and (2) the maximum likelihood procedure using a sampling
formula with a homogeneous coalescent model.
In the file
TestFunctions.Rmd several tests are implemented to check if the
implemented functions in Functions.R are correct.
The file
RecombinationRateEstimation.Rmd contains the different simulations and
their visualisations for the two recombination rate estimation
methods.
The files Comparison_SamplingFormulae.Rmd and
Comparison_SamplingFormulae.nb are intended to compare the sampling
formula introduced in this thesis with the sampling formula of the loose
linkage approach proposed by Frederic Alberti.