MCMC Algorithms for the Coalescent
Run MCMC for Coalescent Trees
Density Functions of Some Time-Dependent Coalescent Models
Managing List of Trees From MCMC
Plot THETA From coalescentMCMC Output
Probability of Coalescence
Coalescent Simulation and Visualisation
Subset MCMC Output
Trees Operators for Running MCMC
Flexible framework for coalescent analyses in R. It includes a main function running the MCMC algorithm, auxiliary functions for tree rearrangement, and some functions to compute population genetic parameters. Extended description can be found in Paradis (2020) <doi:10.1201/9780429466700>. For details on the MCMC algorithm, see Kuhner et al. (1995) <doi:10.1093/genetics/140.4.1421> and Drummond et al. (2002) <doi:10.1093/genetics/161.3.1307>.