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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