Repository to reproduce the analyses in Bastide et al. 2020.

Content

The general structure is the following. Please refer to the README files in each sub-directory for more information on the analyses. All the R scripts assume that the working directory is the root directory.

• exampleDataSets: data and scripts to reproduce the analyses

  • BEEHIVE: Dataset from Blanquart et al. (2017) PLoS Biology.
    • fixedTree: Inference of the model with a fixed tree.
    • simulations: Data simulation using the HIV fixed tree.
  • SCHNITZLER: Dataset from Schnitzler et al. (2017) Evolutionary Ecology Research.
    • totalEvidence: Joint inference of the tree and the process.
    • fixedTree: Model selection on the process on a fixed tree.
    • TIMING: Framework for timing comparisons.

• R_Utility_Files: helper R functions.

Requirements

• BEAST: http://beast.community/installing. The latest (development) version from BEAST is needed, please follow instructions to install the package from the master branch.

• R: https://cran.r-project.org/index.html. Version 3.6.

• R package PhylogeneticEM: https://CRAN.R-project.org/package=PhylogeneticEM. Version 1.4 (for simulations and heritability computations).