Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences (ade4)

Presentation

ade4 is a software developed in the Biometry and Evolutionary Biology Lab (UMR 5558) - University Lyon 1 for the Data Analysis of Ecological and Environmental data in the framework of Euclidean Exploratory methods, hence the name ade4.

ade4 is a package for the R software since 2002. It contains functions for exploratory multivariate data analysis and graphical display, many numerical data sets and bibliographic references. Simple one-table methods are described in Chessel et al. (2004). Two-table and K-table methods are described in Dray et al. (2007). The theory of the duality diagram and its implementation in ade4 are discussed in Dray et Dufour (2007).

A book in the Springer Series in Statistics collection, “Multivariate Analysis of Ecological Data with ade4” presents the package. The examples and the graphs in this book can be reproduced online here.

The ade4shiny dashboard allows you to use the basic functions of the ade4 package online, directly in your browser: no need to install R and the necessary packages on your computer. ade4shiny

If you use ade4, please consider citing these references !

Getting started with ade4

Installing ade4

This page explains how to install the ade4 package in R.

Vignettes

Several vignettes are available to help you get started with ade4 (more to come soon !):

• Graphical representation of multivariate data

• Description of environmental variables structures

• Description of species structures

• Taking into account groups of sites

• Description of species-environment relationships

• Analysing Changes in Structures

• Analysing Changes in Co-structures

List of function references

You can also find a list of functions available to users on the reference page.

Other resources

Check out the ade4 book and its shiny application for a complete introduction to the package and to rerun the code present in the book. You can also check these bibliographic references to help you understand ade4 methods.

Note for nostalgics 😉 : the old ade4 web site is still available here: http://pbil.univ-lyon1.fr/ADE-4/.

Using ade4 online: the Shiny app

Consider giving a try to our shiny app, developed to allow you to run an analysis without having to write your own script: ade4shiny. You will be able to download the R script used to generate the results as well as the analyses outputs and graphical representations.

Getting help: FAQ & Mailing list

You can also check the FAQ section to check if your question has already been answered or ask for help on the ade4 mailing list adelist.