This repository contains validation code for the ssRanges BEAST 2 pacage, and is based on similar validations for the sRanges package, see the sRanges material repository.

The code uses a fork of TreeSim suitable for skyline diversification rates.

simulate.R contains code to simulate 200 trees using four equal length skyline intervals, and to produce XML files to infer the diversification rates for each tree, while simulateOne.R is the equivalent script for 200 trees with only one skyline inteval (equivalent to constant rates). The four interval script use the template XML templates/ssRanges_inference_template.xml to produce the XML for each simulation, while the one interval script uses ssRanges_inference_template_one_int.xml.

Use slurm-inferences.sh to run the BEAST 2 analyses for each simulated tree. The script uses the Intellij_module_versions folder to control the versions of BEAST 2 packages used.

Code to graph the log files from analyses is included in the graphing folder.