FAQ

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

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

Here are answers to some common questions about ade4 (more to come soon).

Installation

How to install the current version of ade4?

The easiest way to install ade4 is to use install.packages("ade4") in your R session.

How to install the development version of ade4?

To install the development version from github:

remotes::install_github("adeverse/ade4")

How do I know which ade4 version I'm using?

In your R session, type:

packageDescription("ade4", field="Version")

Graphics

What is adegraphics?

The package adegraphics provides a complete reimplementation of graphical functionalities of ade4. It is based on lattice and provides a convenient way to manage graphics as objects. Moreover, it offers much more flexibility than ade4 to customize your plots.

How to load adegraphics?

As adegraphics provides a reimplementation of ade4 graphical functions, many functions have the same name in the two packages. To be sure to use adegraphics functions, adegraphics should be loaded after ade4:

library(ade4)
library(adegraphics)

An alternative it to explicitly specify the package in the call using the :: operator:

adegraphics::s.label()

How to interpret ellipses plotted by s.class function?

The ellipses represent the main variation for individuals of a given class. They are based on inertia statistics not on significance levels.

Simple Analysis

How to obtain coordinates for individuals?

In simple analysis (e.g., dudi.pca), scores for individuals are stored in $li element of the returned object

How to obtain coordinates for variables?

In simple analysis (e.g., dudi.pca), scores for variables are stored in $co element of the returned object

What are the $l1 and $c1 elements of a dudi ?

In simple analysis (e.g., dudi.pca), the $c1 element contains the principal axes (aka "loadings" of the variables) and the $l1 element contains the principal components. The norm of these two elements is equal to 1, which makes them useful for drawing biplots (for example).

ade4 documentation built on April 3, 2025, 8:22 p.m.