phyloDataSignal

All scripts needed to reproduce simulation and empirical analyses in Paper to Come

Breakdown

• \*.R: R scripts to simulate data, wrangle data, and produce figures
• figures/: Figures from the paper produced by some of the above scripts
• xmlTemplates/: Template xml files for simulation study
• empiricalAnalyses/: Contains all xml templates and R scripts to analyse empirical data
• ms: Manuscript files

Note for reproducing the study

• If you want to reproduce the simulation study, clone the repo and add the following directories:
  • trees/ (stores backbaone trees)
  • fasta/ (store simulated alignments)
  • log/ (stores log files for individual analyses)
  • xml/ (stores .xml files for individual analyses)
• Be sure to change #SEQ-GEN-PATH to the correct path for Seq-Gen in genTreesSeq.R

Order to Run Scripts

• Simulate Data
  1. genTreesSeq.R (simulateed alignments take ~50Gb of memory!)
  2. genXML.R
  3. BEAST v2 for each .xml in xml/. Ensure feast and BDMM-Prime are installed.
• Collect Data - The above all generate .RData files used in the following
  1. getPosteriors.R
  2. wassersteinClassification.R
  3. sitePatterns.R
  4. datePatterns.R
  5. combinePatternsAndWasserstein.R
• Other R scripts named after each figure in /figures should now produce figures