Simulation code, simulated data sets, and analysis for A Genealogical Look at Shared Ancestry on the X Chromosome
This repository contains the code and other materials for our paper *A Genealogical Look at Shared Ancestry on the X Chromosome. A preprint of our manuscript is available on bioRxiv.
Makefile: main makefile for the repository; runs simulations to generate data, runs analysis for plots.
data/: directory containing simulated datasets used in the paper.
ancestrysim/: directory containing genealogical simulation code. This includes the prototype Python routine
ancestralsim.pyand the finalized C/Python
paper/: empty directory which was home to the manuscript, now contains
paper/imageswhich contains images produced by
plots.R: R code to run analyses and generate paper's figures.
dist-functions.R: distribution functions, test code, and other functions used by
images/: other images and image requisites like
sessionInfo() from R, after
plots.R was run:
R version 3.2.2 (2015-08-14) Platform: x86_64-apple-darwin14.5.0 (64-bit) Running under: OS X 10.10.5 (Yosemite) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  grid stats graphics grDevices utils datasets methods  base other attached packages:  colorspace_1.2-6 RColorBrewer_1.1-2 readr_0.2.2 tidyr_0.4.0  wesanderson_0.3.2 reshape2_1.4.1 purrr_0.2.0 dplyr_0.4.3  scales_0.3.0 ggplot2_2.0.0 devtools_1.9.1 loaded via a namespace (and not attached):  Rcpp_0.12.2 digest_0.6.9 assertthat_0.1 plyr_1.8.3  R6_2.1.1 gtable_0.1.2 DBI_0.3.1 magrittr_1.5  stringi_1.0-1 lazyeval_0.1.10 tools_3.2.2 stringr_1.0.0  munsell_0.4.2 parallel_3.2.2 memoise_0.2.1k