CHANGES IN ADEGENET VERSION 1.2-1


NEW FEATURES

	o documentation of scaleGen provides an example of usefulness of
	an appropriate scaling in PCA

BUG FIXES

	o fixed the recognition of NAs in df2genind

	o fixed the call to inherits in spca (returned value changes in R-devel)



			CHANGES IN ADEGENET VERSION 1.2-0


NEW FEATURES

	o implement different levels of ploidy in genind / genpop
	objects. Make necessary adaptations throughout the package.

	o put some stop where needed when ploidy!=2 is not handled.

	o implement a "sep" argument in df2genind.

	o implement accessor for genind/genpop: nLoc.

	o implement "scaleGen" for genind/genpop, which allows for
	different types of scaling.

	o added several coercion methods, from genind/genpop to
	data.frame, matrix and ktab objects.

	o implemented propTyped, a function giving the proportion of
	non-missing data in different ways.

BUG FIXES

	o missing data indicated in summary corrected (loci with more
	alleles had more weight in the computations).




			CHANGES IN ADEGENET VERSION 1.1-3


NEW FEATURES

	o 'as' methods for genind/genpop objects to matrix, data.frame,
	and ktab objects. Now, ordination implemented as dudi functions in
	ade4 (like dudi.pca) can be performed directly using genind/genpop
	as inputs.




			CHANGES IN ADEGENET VERSION 1.1-2


NEW FEATURES

	o significant improvement in the speed of genind2df (more than
	twice as fast as before).

	o function propShared added: computes the proportion of shared
	alleles among a set of genotypes (core computations in C).

	o A warning is issued when NAs exist in the input of sPCA.

	o improvement of the validity checking for genind/genpop:
	validObject now detects duplicates in any kind of names (ind.names,
	pop.names, etc.) and prints the corresponding items.

BUG FIXES

	o genind2df does now handles the pop argument correctly.

	o df2genind does no longer bug when there is an entirely non-typed
	locus.



			CHANGES IN ADEGENET VERSION 1.1-1


NEW FEATURES

	o I/O: df2genind no longer fails when entirely non-type
	individuals exist.

	o Monmonier: optimize.monmonier now computes the 'best'
	boundary only once instead of twice. The whole code was re-thought
	and optimized for speed. Monmonier's boundaries can now form
	loops. Instead of stoping at a given threshold, it is also
	possible to ask for a given length of boundary (argument
	bd.length).

	o The function chooseCN has a new option to return a list of
	spatial weights defined as the inverse of spatial distances, at a
	given exponent.

	o A wrapper for glob.varcomp has been implemented for genind
	objects, through the new function fstat.

	o The elements of the @other slot are now proceeded wisely when
	objects are subsetted using the '[' operator.


BUG FIXES

	o I/O: df2genind no longer fails when entirely non-type
	individuals exist.

	o monmonier no longer fails when coordinates are drawn from a
	regular grid. The matched call of the returned object has been
	fixed.



			CHANGES IN ADEGENET VERSION 1.1-0

NEW FEATURES
	o Data representation: S4 classes in replacement of old S3
	classes.

	o Spatial genetics: the spatial Principal Component Analysis
	(Jombart et al, 2008, Heredity), two multivariate spatial
	tests, and new functionalities for Monmonier's algorithm.

	o I/O: functions to import data are now 'read' functions;
	available for formats of GENETIX, Fstat, Genepop, STRUCTURE and
	from data.frames of genotypes. Export from genind to data.frame of
	genotypes.

	o Data: five new simulated geo-referenced datasets

	o Simulations: a hybridize function, which creates hybrids from
	two parent datasets. Can output to STRUCTURE format.

	o Data manipulation: new function to separate data by
	population. Accessors to genind and genpop object like with
	matrices using 'foo[ chosenGenotypes, chosenAlleles]'.



			CHANGES IN ADEGENET VERSION 1.0-2

NEW FEATURES

	o adegenetWeb is a simple function opening the adegenet website in
	the default web browser.

	o sim2pop is a dataset obtained by simulation using the software
	Easypop. It contains 130 georeferenced genotypes sampled from two
	distinct populations.

	o monmonier documentation was improved by adding a genetic
	example, using sim2pop data.

BUG FIXES

	o some bugs corrected in optimize.monmonier


			CHANGES IN ADEGENET VERSION 1.0-1

NEW FEATURES

	o chooseCN is a simple interactive tool for choosing and building
	a connection network from spatial coordinates. This tool is called
	by monmonier function.

	o monmonier, optimize.monmonier, plot.monmonier and print.monmonier
	implement the Monmonier algorithm. While not restrained to genetic
	data analysis, this method can be used to find genetic boundaries
	among individuals or populations based on their allelic
	frequencies and spatial coordinates. 

BUG FIXES

	o several bugs fixed in I/O functions