This repository includes the data files for the simulation study and the case study in the publication.

The simulation_result.Rdata is an R data file that stores simulated data and results. The data is used to generate Figures 2-7, S1, and S2.

The casestudy_trees.Rdata is an R data file that stores the posterior samples of the species tree of the Australian rainbow skinks and the model fitting on these trees. The data file is used to generate Figure 8.

simulation_result.Rdata includes the ML estimates of parameters to trees simulated under protracted speciation and extinction using ProSSE algorithm. Both tree simulation and model fitting are done using the ProSSE source code in R.

casestudy_trees.Rdata includes the posterior samples of the species tree of the Australian rainbow skinks and the ML estimates of parameters to each tree. Model fitting are done using the ProSSE source code in R.

The ProSSE source code is on Zenodo and is maintained at https://github.com/huaxia1985/ProSSE

The R script to use the source code to generate and process the data is in the README.md file.

simulation_result.Rdata is used to generate Figures 2-7 and Figure S1 and S2, using R. The R script to generate the figures is in plotcode.R on Zenodo.

casestudy_trees.Rdata is used to generate Figure 8, using R. The R script to summarize the case study results in the main text is in the README.md file.