This code repository accompanies the paper 'Lagged couplings diagnose Markov chain Monte Carlo phylogenetic inference' by L.J. Kelly, R.J. Ryder and G. Clarté.
It contains various scripts to run marginal/coupled experiments in TraitLab and analyse the output:
simulate contains Matlab scripts to generate synthetic data sets, parameter files for experiments and slurm submission scripts;analyses contains R scripts to analyse the output of experiments created via simulate and make figures.README files in each the sub-directories describe how to run the code.