			CHANGES IN ADEGENET VERSION 1.3-3

BUG FIXES

	o fixed a bug of propShared, which gave wrong results under weird
	circumstances. The new implementation is entirely different, uses
	C code, and is now applicable to data with any level of ploidy.

	o tried making the package smaller by removing unnecessary files.

	


			CHANGES IN ADEGENET VERSION 1.3-2

BUG FIXES

	o replaced calls to multicore:::detectCores with
	parallel:::detectCores (the former gives unexpected results on
	some platforms).

	o documentation update: fstat function is no longer available due
	to removal of hierfstat package from CRAN. An example shows how to
	use Fst function from the pegas package instead.

	o documentation update: doc now specifies that read.genepop and
	read.fstat are meant for diploid data only, with guidelines for
	haploid data.



			CHANGES IN ADEGENET VERSION 1.3-1

BUG FIXES

	o removed all dependency with graph package, which was still
	causing errors on some systems - whenever Bioconductor was not by
	default one of the accessible repositories (used to be FAQ #4).

NEW FEATURES

	o legend in scatter.dapc now matches to the type and size of
	symbols used in the plot.

	o the package has been made smaller (from 20MB to 8.5MB).

	o a warning has been added to read.structure: the function is made
	for diploid data only.



			CHANGES IN ADEGENET VERSION 1.3-0

BUG FIXES

	o fixed broken dependencies with hierfstat and graph packages
	(used to be FAQ #4).

	o fixed a minor bug in loadingplot regarding possible label errors.

NEW FEATURES

	o genome-wide SNP data support using the new class genlight,
	supported by compiled C routines and parallelized computations on
	multicore architectures.

	o dedicated find.clusters and dapc methods for genlight objects.

	o read.PLINK to read SNP data with PLINK format into genlight
	objects.

	o read.snp to read SNP data with adegenet's own format into genlight
	objects.

	o fasta2genlight to extract SNP from FASTA files into genlight
	objects.

	o new method 'predict' for DAPC objects, allowing for using
	supplementary individuals.

	o many new options of DAPC scatterplots (scatter.dapc).

	o new plotting method 'compoplot' for DAPC objects, displaying
	group memberships in a STRUCTURE-like way... only prettier.

	o many new accessors for the classes genind and genpop.

	o 4 new tutorial vignettes: adegenet-basics, adegenet-dapc,
	adegenet-spca, adegenet-genomics.

	o last but not least: Ismail Ahmed has joined the project as a
	developper.



			CHANGES IN ADEGENET VERSION 1.2-8

BUG FIXES

	o fixed a major issue in the conversion of genind objects to
	hierfstat data format. In some cases, this issue biased the
	results of the wrapper function "fstat".



			CHANGES IN ADEGENET VERSION 1.2-7


NEW FEATURES

	o dapc and find.clusters are now stable versions for the published methods.

	o a.score and optim.a.score are released in their beta versions.

	o scatter.dapc is now adapted to representation 1-dimensional DAPC results.
	

BUG FIXES

	o fixed a major issue in the ape package causing haploGen to
	bug. This is a temporary replacement, waiting for ape to implement
	the changes (currently, adegenet replaces ape's as.list.DNAbin
	function with a corrected version).



			CHANGES IN ADEGENET VERSION 1.2-6


NEW FEATURES

	o pairwise.fst: computes Nei's pairwise Fst between populations

	o alignment2genind: extract polymorphism from nucleic and proteic
	aligned sequences with the 'alignment' format, returning a genind object.


BUG FIXES

	o fixed a minor issue in Hs, occuring in fixed loci for a given population.



			CHANGES IN ADEGENET VERSION 1.2-5


NEW FEATURES

	o SeqTrack, an algorithm for the reconstruction of genealogies, is
	now fully implemented and documented.

	o haploGen, a system for simulating genealogies, is now fully
	implemented and documented.


BUG FIXES

	o summary methods for genind and genpop are fixed (again) for the
	new R version 2.11.1.



			CHANGES IN ADEGENET VERSION 1.2-4


NEW FEATURES

	o Hs computes the theoretical heterozygosity by populations for
	genpop object

	o propShared is now available for haploid data

	o Discriminant Analysis of Principal Component (DAPC) is
	implemented by the function DAPC, although the method itself is
	still under review.

	o The SeqTrack algorithm for reconstructing genealogies is
	implemented by the function seqTrack, although the method itself
	is still under review.

	o Pre-release of new simulation tools, still undocumented
	(haploPop and haploGen).

	o New datasets eHGDP and H3N2


BUG FIXES

	o minor bug fixes in df2genind, propShared, and seploc

	o summary issue arised in certain conditions, depending on which
	package was loaded before adegenet; in some cases, the summary
	procedure was not found for genind/genpop objects. Fixed now.



			CHANGES IN ADEGENET VERSION 1.2-3


NEW FEATURES

	o implement handling of presence/absence markers. genind and
	genpop object now have a 'type' attribute to differentiate between
	codominant markers (e.g. microsatellite), which is the default
	type, and presence/absence data (e.g. AFLP). Functions in adegenet
	now behave according to the type of markers being used.

	o SNP can now be obtained from sequence data, stored as DNAbin
	(see E. Paradis's package 'ape'). They can be selected to verify
	any given degree of polymorphism.

	o 'hybridize' can now be used for genotypes having any even degree
	of ploidy (e.g. tetraploid genotypes).

	o the new function 'isPoly' checks which loci are polymorphic, or
	which alleles contribute to polymorphism.

	o the new function 'pop' can be used to retrieve and set the pop
	slot of genind object.

	o the new function 'selPopSize' allows one to select a subset of
	genotypes belonging to well-sampled populations, as defined by a
	threshold sample size.

	o the new accessor 'locNames' can be used to retrieve real labels
	of markers and/or alleles.

	o the loadingplot has been modified to allow specifying x axis, so
	that scoring SNPs along their sequence is now possible. 


BUG FIXES

	o no bug to fix this version!



			CHANGES IN ADEGENET VERSION 1.2-2


NEW FEATURES

	o implement different levels of ploidy in genind / genpop objects
	(new slot @ploidy). Now, any level of ploidy can be handled by
	input function df2genind, which has been recoded almost
	entierely. Different levels of ploidy are now handled by different
	functions.
	
	o a "sep" argument is now handled by df2genind: this allows
	reading many data formats.

	o implemented a method "scaleGen" for genind / genpop objects,
	which scales allelic data using different methods.

	o  colorplot: a generic function, with a method for spca
	objects. Represents up to three principal components based on RGB
	representation of Cavalli-Sforza.

	o loadingplot for plotting loadings of one axis

	o adegenetTutorial function which opens the online tutorials

	o allow for the use of na.replace and scaleGen in spca function

	o added rupica dataset

	o enable reading data from URL (import2genind, read.[...])

	o permit specification of a matrix of spatial weights in spca 
	

BUG FIXES

	o fixed bug 1.2-2.01 (read.structure issue): was due to the
	default of "onerowperind" argument.
	
	o fixed bug 1.2-2.02 (read.genetix issue): was due to an
	error in the data file (wrong nloc); now read.genetix corrects
	that automatically and issues a warning.
	
	o fixed bug 1.2-2.03 (monmonier issue): was a non-detected
	code 2 due to intersection check with previously drawn segment
	(was not always removed).
	
	o fixed bug 1.2-2.05 (a few fixes/improvement for monmonier)



			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
