What's next?
Next release (2.1.1) is under development.
Today
Current stable version of adegenet is 2.1.0 for R.3.4.2.
See the current ChangeLog for a list of all modifications.
13/10/2017
New adegenet version (2.1.0) has been released for R-3.4.2!While semantic says it is a minor release, it is a substantial one, after more than a year of implementing new tools and fixing issues since the last patch. A new fast-ML clustering method, exports to mvmapper, a bunch of fixes, and more. See the ChangeLog file for more details.
07/07/2015
New adegenet version (2.0.0) has been released for R-3.2.1! This is a new major release, which implements a lot of improvements over previous versions, including support for varying ploidy in a single dataset, simplified data structures, hierarchical stucture storage and manipulation, and more. See the ChangeLog file for more details.
13/05/2014
New adegenet version (1.4-2) has been released for R-3.1.0! This version fixes a bug in adegenetServer. See the ChangeLog file for more details.
18/03/2014
New adegenet version (1.4-1) has been released for R-3.0.3! Releasing a package with a new function to open tutorials that does not actually work is arguably bad form. This version fixes release 1.4-0. See the ChangeLog file for more details.
14/03/2014
New adegenet version (1.4-0) has been released for R-3.0.3! New features include a web interface for DAPC (adegenetServer), improvements of the DAPC cross-validation procedure for small sample sizes, visualization and test of the SNP density on alignments (snpposi.plot,snpposi.test), and DAPC-based feature selection (snpzip). See the ChangeLog file for more details.
28/06/2013
Caitlin Collins has joined the development team, and will be implementing DAPC-based feature-selection procedures.
18/06/2013
The development of adegenet has now moved on Sourceforge. The adegenet website will remain at its current place. More on:
https://sourceforge.net/projects/adegenet/
05/06/2013
New adegenet version (1.3-9) has been released for R-3.0.1! New features include some improvements on and the separate documentation of the cross-validation procedure for DAPC (xvalDapc), and improvement of color palettes alongside new ones. See the ChangeLog file for more details.
15/05/2013
New adegenet version (1.3-8) has been released for R-3.0.0! New features include a new function for cross-validation of DAPC results, especially useful for assessing the optimal number of PCA components to retain during the dimension reduction step. Check out xvalDapc. Other sources of minor excitement include new color palettes, and the function any2col which converts factors and numeric into colors, prodiving info for a legend as well. See the ChangeLog file for more details.
??/??/????
At some point in time, version 1.3-7 was released, but never acknowledged on this website. See the ChangeLog file for clues about what happened.
30/01/2013
New adegenet version (1.3-6) has been released for R-2.15.2! New features include a function for identifying mutations (position and nature) between pairs of DNA sequences (findMutations), with a possibility of visualization using graphs (graphMutations). See the ChangeLog file for more details.
08/11/2012
New adegenet version (1.3-5) has been released for R-2.15.2! New features include a graph-based clutering approach (gengraph), and a new function for reading fasta alignments into DNAbin objects with minimum memory requirements (fasta2DNAbin). See the ChangeLog file for more details.
10/08/2012
The search engines of the website have been improved to allow for different types of search and to fix issues occuring with some browsers.
23/01/2012
New adegenet version (1.3-4) has been released for R-2.14.1! The package has undergone some internal changes in the documentation which should make no difference to users, except for a drastic reduction in download and installed size (respectively 4-5MB and 6-7MB). Many examples have been 'inactivated' to comply with CRAN check runtime policy, meaning these won't be run by 'example(myFunction)' anymore, but will still be available in the documentation. See the ChangeLog file for more details.
23/12/2011
New adegenet version (1.3-3) has been released for R-2.14.1! Just in time for Christmas, ain't that nice? This release includes a brand new version of propShared which fixes an important bug, and now allows for any ploidy level while running core computations in C. The package is also slightly smaller than before. See the ChangeLog file for more details.
11/11/2011
New adegenet version (1.3-2) has been released for R-2.14.0! This minor release fixes some issues in the detection of the number of cores occuring on some platforms, as well as a few fixes in manpages. Function fstat is now gone for good as hierfstat package seems to be gone for good from CRAN, but the documentation shows how to use Fst from the pegas package instead. See the ChangeLog file for more details.
02/09/2011
New adegenet version (1.3-1) has been released for R-2.13.1! Less is more: this new release is much smaller in size than 1.3-0, while containing the same material. It also fixes a few minor issues in documentation and in the legend of dapc scatterplots. See the ChangeLog file for more details.
27/06/2011
New adegenet version (1.3-0) has been released for R-2.13.0! This new major release implements new classes and methods for the handling and analysis of genome-wide SNP data, along with several improvements to previous tools (especially new graphics for DAPC) and a few bug fixes. It also include 4 new tutorial distributed as vignettes. See the ChangeLog file for details of the release. Given this is a major release, version number switched directly from 1.2-8 to 1.3-0.
02/06/2011
A new tutorial dedicated to DAPC has been uploaded on the website (see section "documents").
14/12/2010
The DAPC paper has been nicely reviewed by Laurent Excoffier on Faculty of 1000 [see evaluation].
08/11/2010
A 'Frequently Asked Question' section has been added in the 'contact' section of adegenet website.
05/11/2010
New adegenet version (1.2-8) has been released for R-2.12.0! This release fixes a bug in exports from adegenet to hierfstat (function genind2hierfstat), which lead to wrong fstat computations in some cases. See the ChangeLog file for details.
29/10/2010
New adegenet version (1.2-7) has been released for R-2.12.0! This release includes the stable implementation of the Discriminant Analysis of Principal Components (DAPC, ?dapc, ?find.clusters), and fixes a bug from the ape package which impacted adegenet and prevented windows binaries to be generated with R-2.12.0. See the ChangeLog file for more information.
22/09/2010
New adegenet version (1.2-6) has been released for R-2.11.1! This release adds the computation of pairwise Fst (?pairwise.fst) and a new function for extracting the polymorphism of aligned proteic sequences (class alignment in the seqinr package) into genind objects (?alignment2genind). See the ChangeLog file for more information, and check out new updates of the tutorial.
30/07/2010
New adegenet version (1.2-5) has been released for R-2.11.1! This release includes a stable implementation of the SeqTrack algorithm (see literature section for a reference) for reconstructing genealogies of haplotypes; see ?seqTrack for more information. A new tool for simulating genealogies of haplotypes has also been implemented (see ?haploGen). Minor issues pertaining to the definition of summary methods for genind and genpop objects have been fixed. See the ChangeLog file for more information.
19/04/2010
New version of the adegenet tutorial online. This new version of the tutorial is compatible with the latest release of adegenet (version 1.2-4). It incorporates a new section on importing data into adegenet which is more explicit and detailed than the previous one.
19/04/2010
New adegenet version (1.2-4) has been released for R-2.10.1 ! This release corrects a few issues and bugs from previous version, and includes new material currently under review in scientific journals. Once 'stable', these new functionalities will give rise to the major release 1.3-0. Look at ChangeLog for more information about this new version.
15/04/2010
The adegenet forum's archives can now be searched from this website. Look at the 'contact' section for more information. The next major adegenet release is on its way. It will include new methods of genetic data analysis, as well as new simulation systems. Pending work under review, the release of 1.3-0 should be done within the next two months. Intermediate release correcting minor bugs may occur meanwhile.
02/04/2009
New adegenet version (1.2-3) has been released for R.2.8.1 !
This is a important release, including some significant improvements (see ChangeLog file). The most important new feature is that presence/absence data like AFLP are now handled. A new slot 'type' now distinguishes, in genind and genpop objects, codominant markers (type="codom") from presence/absence (type="PA"). Also, hybridize can now perform hybridization between genotypes with any even degree of ploidy. Another noticeable feature is that SNPs can be obtained from aligned DNA sequences using DNAbin2genind.This time, the tutorial has been updated at the same time as the package release!
19/12/2008
New adegenet version (1.2-2) has been released for R.2.8.0 !
This new, big release implements many new things and corrects a few bugs (see ChangeLog file). Amongst the biggest news, several levels of ploidy are now handled throughout the package, apart from a few exceptions. New graphics are available for multivariate methods: the colorplot, which can represent genetic diversity using RGB scale, and a loadingplot, which can be used to assess the most structuring alleles and loci in an analysis. A new georeferenced genetic dataset is also available (dataset rupica). And... several other things!
03/08/2008
New adegenet version (1.2-1) has been released for R.2.7.1 !
This new release corrects a few bugs arising in version 1.2-0 (see ChangeLog file), especially an issue with the detection of NAs. Documentation was also improved (have a look at ?scaleGen).
09/07/2008
New adegenet version (1.2-0) has been released for R.2.7.1 !
This major release implements various levels of ploidy and adds some new features (see ChangeLog file):
- df2genind now handles a 'sep' argument, specifying a separator between the input alleles. This extends current input capabilities to a wider range of software.
- scaleGen is a function similar to 'scale' for genind/genpop objects. Various scalings adapted to genetic markers are proposed.
- propTyped is a function giving the the proportion of non-missing data in different ways; this is particularly useful to detect structuring in missing data.
- various coercion method are now available, implemented as methods for 'as' and as old S3 coercion (e.g., 'as.data.frame([myGenindObject])'). Coercion to matrix, data.frame and ktab (from ade4 package).
02/06/2008
New adegenet version (1.1-2) has been released for R.2.7.0 !
This release corrects a few bugs and adds some new features (see ChangeLog file):
- genind2df now handles the pop argument correctly.
- df2genind does no longer bug when there is an entirely non-typed locus.
- new function propShared is added: computes the proportion of shared alleles among a set of genotypes (core computations in C).
- significant improvement in the speed of genind2df (more than twice as fast as before).
- 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.
30/04/2008
The new function 'propShared' is available from the devel version of adegenet. It computes the proportion of shared alleles among a set of genotypes.
09/04/2008
New adegenet version (1.1-1) has been released for R.2.6.2 !
This release corrects a few bugs and adds some new features:
- I/O: df2genind no longer fails when entirely non-type individuals exist.
- Spatial genetics: optimize.monmonier now computes the 'best' boundary only once instead of twice. The matched call of the returned object has been fixed. monmonier no longer fails when coordinates are drawn from a regular grid. 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). 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.
- F statistics: a wrapper for glob.varcomp has been implemented for genind objects, through the new function fstat.
- Data manipulation: The elements of the @other slot are now proceeded wisely when objects are subsetted using the '[' operator.
15/02/2008
A tutorial for the new version of adegenet is available from this website.
14/02/2008
New adegenet version (1.1-0) has been released for R.2.6.2.
This totally new version includes:
- Data representation: S4 classes in replacement of old S3 classes.
- Spatial genetics: the spatial Principal Component Analysis (Jombart et al, submitted to Heredity), two multivariate spatial tests, and new functionalities for Monmonier's algorithm.
- 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.
- Data: five new simulated geo-referenced datasets
- Simulations: a hybridize function, which creates hybrids from two parent datasets. Can output to STRUCTURE format.
- Data manipulation: new function to separate data by population. Accessors to genind and genpop object like with matrices using 'foo[ chosenGenotypes, chosenAlleles]'.
07/01/2008
adegenet is now a project on R-Forge.
12/09/2007
Release of a new version of the adegenet tutorial (see documents section in this site), showing how to find genetic boundaries using Monmonier's algorithm.
12/09/2007
adegenet version 1.0-2 was released for R.2.5.1.
This new version corrects a few bugs (especially in optimize.monmonier) and adds the following elements:
- adegenetWeb is a simple function opening the adegenet website in the default web browser.
- sim2pop is a dataset obtained by simulation using the software Easypop. It contains 130 georeferenced genotypes sampled from two distinct populations.
- monmonier documentation was improved by adding a genetic example, using sim2pop data.
30/08/2007
A new section is added to the download section: patches correcting bugs or improving functions of the current version of adegenet.
25/08/2007
adegenet version 1.0-1 was released for R.2.5.1.
This new version corrects a few bugs (basically in import/export functions) and adds the following functions:
- chooseCN is a simple interactive tool for choosing and building a connection network from spatial coordinates. This tool is called by monmonier function.
- 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.
24/04/2007
This website arrives on the web.
10/04/2007
adegenet first release as an official
package for R.2.4.1.