			CHANGES IN OUTBREAKER VERSION 1.1-7
NEW FEATURES
	o in addition to DNA sequences, outbreaker can now use any other
	sequence of characters, e.g. amino-acid sequences, or MLST data.

	o an exponential tail summing to 1e-4 is now added to the
	generation time distribution to cover the range of the outbreak;
	this will avoid occasional issues of -Inf temporal log-likelihood
	for some initial trees.

	o the arguments w.trunc and f.trunc have now disappeared, as they
	were no longer relevant


			CHANGES IN OUTBREAKER VERSION 1.1-6
BUG FIXES
	o fixed an error in transGraph caused by changes in igraph.


			CHANGES IN OUTBREAKER VERSION 1.1-5
BUG FIXES
	o genetic likelihood with large numbers of mutation was prone to
	numerical approximation errors; this is no longer the case.


			CHANGES IN OUTBREAKER VERSION 1.1-4
NEW FEATURES
	o implemented a local likelihood computation providing substantial
	improvements in speed and scalability


			CHANGES IN OUTBREAKER VERSION 1.1-3
BUG FIXES
	o fixed a bug due to the odd conversion of long numbers into
	characters by read.table - handling specific errors with R 3.1.0
	on some Mac versions.



			CHANGES IN OUTBREAKER VERSION 1.1-2
BUG FIXES
	o fixed a bug due to the odd conversion of long numbers into
	characters by read.table.



			CHANGES IN OUTBREAKER VERSION 1.1-1
NEW FEATURES
	o added an argument max.kappa which allows to limit the number of
	generations between two sampled cases, thereby avoiding a slowdown
	whenever the timespan of the outbreak is large (previous limit was
	the timespan itself, which required computing a large number of
	convolutions).

BUG FIXES
	o fixed a bug in plotOutbreak - error occured when plotting with
	col!=NULL
	


			CHANGES IN OUTBREAKER VERSION 1.1-0
NEW FEATURES
	o implementing the published version of the model, with a major
	change in the genetic likelihood and a new procedure for detecting
	genetic outliers and identifying imported cases

	o updated graphics

	o new function get.my to get mutation rates per unit time (and not
	per generation of infection)

	o new function selectChains to select best runs when different
	MCMC converge to different posterior modes

	o possibility of spatial simulation in simOutbreak

	o choice of two mutational models in outbreaker

	o (under development) spatial diffusion model, useable for
	entirely sampled outbreaks

	o added a 38-pages vignette

	o documentation (manpages) updated

	o toyOutbreak has been renamed fakeOutbreak

BUG FIXES
	o no longer limitation of genome sizes to 32768 nucleotides (new
	limit is 2,147,483,648 nucleotides)



			CHANGES IN OUTBREAKER VERSION 1.0-1
BUG FIXES

	o fixed the dependencies with other packages



			CHANGES IN OUTBREAKER VERSION 1.0-0

NEW FEATURES - FIRST RELEASE OF THE PACKAGE

	o implementation of Jombart et al.'s transmission model in
	functions outbreaker and outbreaker.parallel

	o procedures for visualizing and post-processing MCMCs
	(plotChains, transGraph, plotOutbreak, get.tTree, plot.tTree)

	o outbreak simulator (simOutbreak)

	o computation of incidence and effective reproduction numbers from
	posterior trees (get.incid, get.R, get.Rt)
