evolution of the adegenet package

Today
Current stable version of adegenet is 1.2-3 for R.2.8.1.
You can install the devel version from R-Forge.
See the current ChangeLog for a list of all modifications.


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.