		CHANGES IN coalescentMCMC VERSION 0.5


NEW FEATURES

    o coalescentMCMC() now returns an object of class
      c("coalescentMCMC", "coda").

    o Five more "tree moves" are now available during the MCMCs. These
      moves are from Drummond et al. 2002 (Genetics, 161:1307).

    o There are methods logLik, anova, AIC, and BIC for the class
      "coalescentMCMC".

    o The new function plotTHETA plots the variation in THETA
      predicted from an output of coalescentMCMC() and a set of trees.

    o The new function proba.coalescent calculates probabilities of
      coalescence using exact or approximate formula.

    o The new function subset.coalescentMCMC makes possible to extract
      flexibly a subset from an output of coalescentMCMC().

    o coalescentMCMC() has a new model "bsplines".


BUG FIXES

    o A bug was fixed in the calculations of coalescent pdfs.

    o Some bugs were fixed in coalescentMCMC(). The code is also
      faster.


OTHER CHANGES

    o Updated NAMESPACE file for r-devel.



		CHANGES IN coalescentMCMC VERSION 0.4-1


NEW FEATURES

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


OTHER CHANGES

    o The option 'quiet' of coalescentMCMC() has been replaced by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



		CHANGES IN coalescentMCMC VERSION 0.4


NEW FEATURES

    o Three new functions, getLastTree, saveMCMCtrees, and
      cleanMCMCtrees, provide tools to manage lists of trees.

    o 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.

    o It is now possible to interrupt coalescentMCMC(): the results at
      this stage are output normally.

    o getMCMCtrees() has a new option (chain) to extract directly a
      specific list of trees bypassing the interactive menu.



		CHANGES IN coalescentMCMC VERSION 0.3


NEW FEATURES

    o coalescentMCMC() has been extensively modified. It has a new
      option (model) to select the coalescent model. Currently, only
      two models can be fitted.

    o The coalescent parameters are now output as part of the "coda"
      object.

    o 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.

    o The vignette "Running_coalescentMCMC" has been updated and now
      presents a (almost) complete analysis.


OTHER CHANGES

    o The packages adegenet and pegas are no more required.

    o Improved DESCRIPTION and NAMESPACE files.

    o The arguments of NeighborhoodRearrangement() have been modified.



		CHANGES IN coalescentMCMC VERSION 0.2


NEW FEATURES

    o The main MCMC has been completely rewritten.

    o The package coda is now used to analyse MCMC outputs.
