NEWS

coalescentMCMC 0.5

coalescentMCMC() now returns an object of class c("coalescentMCMC", "coda").
Five more "tree moves" are now available during the MCMCs. These moves are from Drummond et al. 2002 (Genetics, 161:1307).
There are methods logLik, anova, AIC, and BIC for the class "coalescentMCMC".
The new function plotTHETA plots the variation in THETA predicted from an output of coalescentMCMC() and a set of trees.
The new function proba.coalescent calculates probabilities of coalescence using exact or approximate formula.
The new function subset.coalescentMCMC makes possible to extract flexibly a subset from an output of coalescentMCMC().
coalescentMCMC() has a new model "bsplines".

The new function sim.coalescent simulates and visualises coalescent for pedagogic purposes.

The option 'quiet' of coalescentMCMC() has been replaced by 'printevery' (100 by default).

Three new functions, getLastTree, saveMCMCtrees, and cleanMCMCtrees, provide tools to manage lists of trees.
Two new models are available in coalescentMCMC(): THETA varying linearly with time, or in a stepwise way (with a single breakpoint in time). All available models are described in a vignette.
It is now possible to interrupt coalescentMCMC(): the results at this stage are output normally.
getMCMCtrees() has a new option (chain) to extract directly a specific list of trees bypassing the interactive menu.

coalescentMCMC() has been extensively modified. It has a new option (model) to select the coalescent model. Currently, only two models can be fitted.
The coalescent parameters are now output as part of the "coda" object.
Trees of the MCMCs are extracted with the new function getMCMCtrees. The trees of successive chains are stored and can be retrieved separately. If several lists of trees are stored, getMCMCtrees() will call an interactive menu to select the list to retrieve.
The vignette "Running_coalescentMCMC" has been updated and now presents a (almost) complete analysis.