Author: Sam Turner

This repository contains code used for my Computational Methods in Ecology and Evolution MSc thesis. All code is contained within scripts. Intermediate data, including simulations used in ABC, are written to data. Figures and other outputs are written to results. Those included in the final report are written to final_figures.

ABC_experiments.R

• All code relating to estimation of $N_e$ and $m$ by Approximate Bayesian Computation.

bias_demostration

• Demonstration that the use of classical linkage disequilibrium and allelic fluctuation estimators results in biased estimates in the stepping stone model

classic_estimators.R

• Demonstration of classical linkage disequilibrium and allelic fluctuation estimators on single subpopulations

poolseq.R

• Finding the relationship between individual sequencing allele frequency estimates and pooled sequencing estimates.

propegate_new.cpp

• The internal propagation script for the allele frequency estimator implemented in simulator_functions.R

simulator_functions.R

• All major functions are contained in this file, including the haplotype frequency simulator, sampling protocol, full ABC estimation method, and helper functions for evaluating the performance of the method.