An important part of my activity is devoted to the development of statistical software, mainly packages. I contribute mainly to the following projects and occasionally to other packages (e.g., Guerry, spdep, adehabitat). Development versions of the packages are available on my GitHub page.
# ade4

The ade4 package provides statistical tools and graphical functions for the analysis of multivariate data. It contains methods for the analysis of one table (principal component analysis, correspondence analysis, multiple correspondence analysis, etc.), a pair of tables (coinertia analysis, redundancy analysis, canonical correspondence analysis, etc.) or multiple tables (partial triadic analysis, STATIS, multiple coinertia analysis, etc.).

# adegraphics

This package is a complete reimplementation of the graphical functionalities of ade4. It uses the lattice package as a framework and an S4 object-oriented approach. It handles simple and multiple graphics to produce publication-quality figures.

# adeTkGUI

ade4TkGUI provides a graphical user interface for some basic functions (data import, basic multivariate methods, two-table methods, etc.) of the multivariate data analysis package ade4. The aim of this interface is to make the use of the ade4 package easier, particularly for beginners or occasional users.

# adephylo

The package adephylo provides tools for quantifying and describing the phylogenetic structures of biological traits. It implements tests of phylogenetic signal, phylogenetic distances and proximities, and novel methods for describing further univariate and multivariate phylogenetic structures.

# adespatial

The idea of this package is born during a workshop that I organized in Lyon in 2008. The idea is to compile several tools for the analysis of spatial multivariate data. Several packages were hosted on R-Forge but I started to implement a unique package, adespatial, providing recent methods for the multivariate multiscale spatial analysis of ecological data. More details can be found in this paper:

Dray, S., and A. B. Dufour. 2007. The ade4 package: implementing the duality diagram for ecologists. *Journal of Statistical Software *22:1-20.

Thioulouse, J., and S. Dray. 2007. Interactive multivariate data analysis in R with the ade4 and ade4TkGUI packages. *Journal of Statistical Software * 22:1-14.

Jombart, T., F. Balloux, and S. Dray. 2010. adephylo: new tools for investigating the phylogenetic signal in biological traits. *Bioinformatics * 26:1907-1909.

Dray, S., R. Pélissier, P. Couteron, M. J. Fortin, P. Legendre, P. R. Peres-Neto, E. Bellier, R. Bivand, F. G. Blanchet, M. De Caceres, A. B. Dufour, E. Heegaard, T. Jombart, F. Munoz, J. Oksanen, J. Thioulouse, and H. H. Wagner. 2012. Community ecology in the age of multivariate multiscale spatial analysis. *Ecological Monographs * 82(3):257-275.