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coalescentMCMC (version 0.5)

MCMC Algorithms for the Coalescent

Description

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) . For details on the MCMC algorithm, see Kuhner et al. (1995) and Drummond et al. (2002) .

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Version

Install

install.packages('coalescentMCMC')

Monthly Downloads

389

Version

0.5

License

GPL (>= 2)

Maintainer

Emmanuel Paradis

Last Published

July 23rd, 2026

Functions in coalescentMCMC (0.5)

coalescentMCMC

Run MCMC for Coalescent Trees
sim.coalescent

Coalescent Simulation and Visualisation
subset.coalescentMCMC

Subset MCMC Output
plotTHETA

Plot THETA From coalescentMCMC Output
dcoal

Density Functions of Some Time-Dependent Coalescent Models
proba.coalescent

Probability of Coalescence
getMCMCtrees

Managing List of Trees From MCMC
treeOperators

Trees Operators for Running MCMC