Repository to reproduce the analyses in Bastide & Didier 2023.

Content

cauchy_paper.Rproj: R project that can be opened with R Studio for convenience. All the R scripts assume that the working directory is the root directory of the project.
R_scripts: R scripts to reproduce the simulations and plots. Please see the header of each file for a more detailed description of each script.
- lizard.R: Analysis of the lizard dataset of Mahler et al. 2013 (www.doi.org/10.1126/science.1232392).
- wnv.R: Analysis of the WNV dataset of Pybus et al. 2012 (www.doi.org/10.1073/pnas.1206598109).
- simulations_models.R: simulation study for model selection.
- simulations_parameters.R: simulation study for parameter inference.
data: data used in the empirical analyses.
- Mahler_et_al_2013_Data: data from the Dryad repository associated with Mahler et al. 2013 (www.doi.org/10.5061/dryad.9g182).
- Pybus_et_al_2012_Data: data, xml analysis scripts and results to reproduce the study of Pybus et al. 2012, using beast tutorial (https://beast.community/workshop_continuous_diffusion_wnv)
results: saved results from the R_scripts.
- 2023-03-14_lizards_model_selection.rda: results from script R_scripts/simulations_models.R.
- 2023-03-23_simulations_paramters.rda: results from script R_scripts/simulations_parameters.R.

R. Version 4.0 or later.
R package cauphy. The development version of the package can be installed as:

devtools::install_github("gilles-didier/cauphy")

brew install beast --HEAD