coiaf Manuscript Work

This repository contains code used to prepare the manuscript for the package {coiaf}. It includes the following folders and files:

• benchmarking contains various files used to benchmark our software package and the resulting figures.
• coiaf-real-data is a git submodule pointing to the repository used to analyze sequencing data using coiaf.
• convergence contains files for determining how many bootstraps and MCMC chains are needed for convergence.
• independence-assumption contains code to examine how the addition of non-independent loci alters the confidence interval of point estimates.
• misc-figures contains code for various figures.
• sensitivity-analysis contains code for comparing THE REAL McCOIL to coiaf on simulated data, the results, and code to compute statistics on our sensitivity analysis results.