This paper is a short summary of the main classes defined in the ade4
package for one table analysis methods (e.g., principal component
analysis). Other papers will detail the classes defined in ade4 for
two-tables coupling methods (such as canonical correspondence analysis,
redundancy analysis, and coinertia analysis), for methods dealing with
K-tables analysis (i.e., three-ways tables), and for graphical methods.
This package is a complete rewrite of the ADE4 software (Thioulouse et
al. (1997), http://pbil.univ-lyon1.fr/ADE-4/) for the R environment. It
contains Data Analysis functions to analyse Ecological and Environmental
data in the framework of Euclidean Exploratory methods, hence the name
ade4 (i.e., 4 is not a version number but means that there are four E in
the acronym).
The ade4 package is available in CRAN, but it can also be used directly
online, thanks to the Rweb system (http://pbil.univ-lyon1.fr/Rweb/).
This possibility is being used to provide multivariate analysis services
in the field of bioinformatics, particularly for sequence and genome
structure analysis at the PBIL (http://pbil.univ-lyon1.fr/). An example
of these services is the automated analysis of the codon usage of a set
of DNA sequences by correspondence analysis (http://pbil.univ-lyon1.fr/mva/coa.php).