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ade4 (version 1.7-24)

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

Description

Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) .

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Version

Install

install.packages('ade4')

Monthly Downloads

39,321

Version

1.7-24

License

GPL (>= 2)

Homepage

https://adeverse.github.io/ade4/

Maintainer

Aurélie Siberchicot

Last Published

March 21st, 2026

Functions in ade4 (1.7-24)

Distribution of Alpine plants in Aravo (Valloire, France)

The ade4 package

Fauna Table for Constrained Ordinations

Graphical Display of Areas

Small Ecological Dataset

Ecological Tables Triplet

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Between-Class Analysis

adegraphicsLoaded

Utility function to test if the adegraphics package is loaded

African Estuary Fishes

Apportionment of Quadratic Entropy

Arrivals at an intensive care unit

Fauna Table with double (row and column) partitioning

Genetic variability of Cacadors

Analysis of molecular variance

Bird species distribution

Between-class coinertia analysis

Genetics-Ecology-Environment Triple

Between-Class RLQ analysis

Cubic Ecological Data

Between- and within-class double principal coordinate analysis

Phylogeny and quantitative traits of carnivora

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Qualitative Weighted Variables

Charolais-Zebus

Pair of Variables

Enzymatic polymorphism in Mus musculus

Genomes of 43 Bacteria

Table of Factors

Veterinary epidemiological study to assess the risk factors for losses in broiler chickens

Dagnelie multinormality test

Frequenting movie theaters in France in 2003

Fruit Production

Enzymatic polymorphism in Leuciscus cephalus

Transformation to make Euclidean a distance matrix

costatis.randtest

Monte-Carlo test on a Costatis analysis (in C).

Table of Fuzzy Biological Traits

Coinertia Analysis

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Tests of randomization between distances applied to 'kdist' objetcs

Computation of Distance Matrices of Percentage Data

Phylogeny and quantative trait of carnivora

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

Corvus morphology

Double Weighted Centring

Computation of Distance Matrices on Quantitative Variables

Multiple Correspondence Analysis

Double principal coordinate analysis

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Mixed-variables coefficient of distance

Duality Diagram

Computation of the Distance Matrix associated to a Neighbouring Graph

Computation of the Distance Matrix from a Statistical Triplet

Ecological and Biological Traits

Exam marks for some students

Rao's dissimilarity coefficient

Computation of Distance Matrices for Binary Data

Pair of Ecological Tables

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Non symmetric correspondence analysis

Principal Component Analysis

Double principal component analysis with respect to instrumental variables

Discriminant Correspondence Analysis

Dune Meadow Data

Correspondence Analysis

Representation of n values on a circle

Linear Discriminant Analysis (descriptive statistic)

Principal Coordinates Analysis

Fission pattern and heritable morphological traits

K-tables of wine-tasting

Triangular Data

Decentred Correspondence Analysis

Functions to compute the fourth-corner statistic

Rao's diversity coefficient also called quadratic entropy

Faunistic K-tables

K-tables Correspondence Analysis with the same rows and the same columns

Geary's Irish Data

Ecomorphological Convergence

Maximal value of Rao's diversity coefficient also called quadratic entropy

Genetic Variation In Human Populations

Electrocardiogram data

Ordination of Tables mixing quantitative variables and factors

Is a Distance Matrix Euclidean?

Morphometric data set

Ordination of Tables mixing quantitative variables and factors

Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation

Microsatellites of Galapagos tortoises populations

human mitochondrial DNA restriction data

Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')

Contingency Table

Granulometric Curves

Complete regular grid analysis

a way to obtain Euclidean distance matrices

K-tables Multi-Regions

the class of objects 'ktab' (K-tables)

Creation of a K-tables from a list of duality diagrams

Creating a K-tables from a list of data frames.

ktab.data.frame

Creation of K-tables from a data frame

Multiple Graphs for a Multiple Co-inertia Analysis

Phyto-Ecological Survey

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs of a STATIS Analysis

Decomposition of inertia (i.e. contributions) in multivariate methods

Point sampling of fish community

Assemblages of Macroinvertebrates in the Loire River (France)

Multiple Graphs for Separated Analyses in a K-tables

Multiple Graphs for the Foucart's Correspondence Analysis

loocv.discrimin

Leave-one-out cross-validation for a discrimin analysis

Generic Function for Multiple Graphs in a K-tables Analysis

Multiple Graphs for a Partial Triadic Analysis

Ecological Data : sites-variables, sites-species, where and when

Multiblock principal component analysis with instrumental variables

Ecological Data : sites-variables, sites-species, where and when

Class of the Permutation Tests (in C).

Leave-one-out cross-validation for a dudi

ktab.match2ktabs

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

Process to go from a Within Analysis to a K-tables

Genetic/Environment and types of variables

Multiple CO-inertia Analysis

Multiple Double Principal Coordinate Analysis

Ponds in a nature reserve

Display and summarize multiblock objects

the class of objects 'kdist' (K distance matrices)

Mantel test (correlation between two distance matrices (in R).)

mantel.randtest

Mantel test (correlation between two distance matrices (in C).)

Transformation of a Distance Matrix for becoming Euclidean

Neighbourhood Graphs

Faunistic Communities and Sampling Experiment

Global State of the World in 1984

Multiblock partial least squares

Multiple Factorial Analysis

Create phylogeny

Phylogenetic trees in Newick format

Minimal Spanning Tree

Method to Analyse a pair of tables : Environmental and Faunistic Data

Athletes' Morphology

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Phylogeny and quantitative traits of lizards

Correspondence Analysis Table

Phylogeny and quantitative traits of teleos fishes

Phylogeny and quantitative traits of flowers

Leave-one-out cross-validation for a bca

Multi Level Decomposition of unidimensional data

Plant traits response to grazing

Genetic Relationships between cattle breeds with microsatellites

Principal component analysis with respect to instrumental variables

Principal Component Analysis with respect to orthogonal instrumental variables

Olympic Decathlon

Phylogeny and trait of bacteria

Orthonormal basis for orthonormal transform

Distribution of of tropical trees along the Panama canal

Simplified Analysis in Principal Coordinates

Originality of a species

A table of Qualitative Variables

Contingency Table with a partition in Molecular Biology

Phylogenetic and quantitative traits of amazonian palm trees

Taxonomy and quantitative traits of carnivora

Between-Class Analysis

Simple Procruste Rotation between two sets of points

Results of the French presidential elections of 2002

Bootstrap simulations

Phylogeny and quantitative traits of birds

Transformation of a distance matrice to a Euclidean one

procuste.randtest

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).

Permutation test for double principal coordinate analysis (DPCoA)

Ordination Table

Two-fold cross-validation

Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia

Partial Triadic Analysis of a K-tables

randboot.multiblock

Bootstraped simulations for multiblock methods

Class of the Permutation Tests (in C).

Reconstitution of Data from a Duality Diagram

Within-Class Analysis

rtest.discrimin

Monte-Carlo Test on a Discriminant Analysis (in R).

randtest.coinertia

Monte-Carlo test on a Co-inertia analysis (in C).

Plot phylogenies

Monte-Carlo Test on the between-groups inertia percentage (in R).

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).

Permutation tests on an analysis of molecular variance (in C).

randtest.between

Monte-Carlo Test on the between-groups inertia percentage (in C).

Plot of the factorial maps for the projection of a vector basis

randtest.discrimin

Monte-Carlo Test on a Discriminant Analysis (in C).

Avifauna and Vegetation

Physico-Chemistry Data

Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization

Plot of factorial maps with representation of point classes

Plot of the factorial maps with polygons of contour by level of a factor

Plot of the factorial maps of a correlation circle

Scatterplot of two sets of coordinates and a partionning into classes

Graph of a variable using image and contour

Plot of Paired Coordinates

Scatter Plot with Kernel Density Estimate

Class of the Permutation Tests (in R).

Indirect Ordination

Representation of an object in a graph by a picture

Plot of the Factorial Maps

Plot of the factorial maps for a correspondence analysis

Array of Recapture of Rings

Representation of a value in a graph

Display of a scatterplot and its two marginal histograms

Graph of frequency profiles (useful for instance in genetic)

Plot of a frequency distribution

Trajectory Plot

Representation of the link between a variable and a set of qualitative variables

Graph to Analyse the Relation between a Score and Quantitative Variables

Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)

1D plot of a numeric score with labels

Graphs for One Dimension

1D plot of a pair of numeric scores with labels

Representation by mean- standard deviation of a set of weight distributions on a numeric score

Relationships between one score and qualitative variables

Separated Analyses in a K-tables

Graphs to Analyse a factor in a Mixed Analysis

Students and Subjects

Reciprocal scaling after a correspondence analysis

Graphs to study one factor in a Multiple Correspondence Analysis

Graphs to Analyse a factor in PCA

Plot of the factorial maps for a fuzzy correspondence analysis

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

Two Questions asked on a Sample of 1000 Respondents

statico.krandtest

Monte-Carlo test on a Statico analysis (in C).

Morphometric Evolution

1D plot of a numeric score and a factor with labels

Graphical representation of the outputs of a multivariate analysis

Graphical utility functions

Plot of the factorial maps in a Multiple Correspondence Analysis

Projections of Supplementary Rows for a Partial Triadic Analysis of K-tables

STATIS, a method for analysing K-tables

Representation of a quantitative variable in front of a phylogenetic tree

Average temperatures of 30 French cities

Projections of Supplementary Columns

Transect in the Vegetation

Phylogeny and quantitative traits of flowers

Tinto and Odiel estuary geochemistry

testdim.multiblock

Selection of the number of dimension by two-fold cross-validation for multiblock methods

Graph Display for Distance Matrices

Morphological Study of the Painted Turtle

Plot of Contingency Tables

Plot arrays in front of a phylogenetic tree

Plot of the arrays by grey levels

Plot of the Arrays

Mountain Avifauna

Triangular Representation and Groups of points

Elimination of Duplicated Rows in a Array

Homogeneous Table

Phylogeny and quantitative traits of ungulates.

Vegetation in Trois-Fontaines

Partition of the variation of a response multivariate table by 2 explanatory tables

Examples of taxonomy

Projection of additional items in a PCO analysis

Function to perform a test of dimensionality

Example for Centring in PCA

variance.phylog

The phylogenetic ANOVA

Projections of Supplementary Rows

Freshwater fish zoogeography in west Africa

Within-Class RLQ analysis

Within-Class Analysis

Internal Correspondence Analysis

Within-class coinertia analysis

Normed within principal component analysis

Plant assemblages in woodlands of the conurbation of Angers (France)

French Worker Survey (1970)

Distance Matrices

Triangular Plotting

Road distances in New-Zealand

Pair of Ecological Data

Phylogenies and quantitative traits from Abouheif

Deprecated functions

Deprecated functions in ade4

Import data files from Phylogenetic Independance Package

Internal ade4 functions

Spatial pattern analysis in plant communities

Add graphics to an existing plot

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).

RVdist.randtest

Tests of randomization on the correlation between two distance matrices (in R).

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in C++ with Rcpp).

RVintra.randtest

Monte-Carlo Test on the sum of eigenvalues of a within-class co-inertia analysis (in C++ with Rcpp).