Divergence-time estimation in Indo-European: The case of Latin

This repository contains the scripts and code for the paper "Divergence-estimation in Indo-European: The case of Latin." The folders mcmc, lnl, and pps folders contain the header files for the MCMC, marginal likelihood, and posterior-predictive simulation (PPS) analyses. The header files configure the settings for the analyses presented in the paper. The code for the various components of the models (i.e., tree model, clock model, character-change model) are housed in the folder modules.

The data folder contains the following three files:

1. chang_romance_broad_variable.nex
2. romance_broad_variable_taxa_fbd.tsv
3. romance_broad_variable_taxa_fbdr_ancient.tsv

The first contains the character matrix used in all of the analyses. The second and third contain the occurrence times and stratigraphic ranges for Latin.

To run the analyses, set the path argument in the file path.Rev to the location of the folder scripts_and_data on your local machine. There is a unique version of this file in each of the mcmc, lnl, and pps folders. In each case it is located in the /romance/broad_variable folder.

Once you have specified the path, open RevBayes and input source("file_name.Rev"), with file_name.Rev being the name of one of the header files in folders mentioned above. For instance, to run the MCMC analysis of the FBD F81 UCE model, issue the command source("romance_broad_variable_dns_fbd_f81_uce_stem.Rev").

The organization of the directories follows the workflow laid out by Mike May in this tutorial.

The analyses in the paper were conducted with RevBayes 1.1.1.