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ade4 (version 1.7-23)

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

30,716

Version

1.7-23

License

GPL (>= 2)

Homepage

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

Maintainer

Aurélie Siberchicot

Last Published

February 14th, 2025

Functions in ade4 (1.7-23)

Apportionment of Quadratic Entropy

Analysis of molecular variance

adegraphicsLoaded

Utility function to test if the adegraphics package is loaded

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Distribution of Alpine plants in Aravo (Valloire, France)

Graphical Display of Areas

Arrivals at an intensive care unit

The ade4 package

Fauna Table with double (row and column) partitioning

Fauna Table for Constrained Ordinations

African Estuary Fishes

Genetic variability of Cacadors

Genomes of 43 Bacteria

Bird species distribution

Between-Class Analysis

Table of Factors

Cubic Ecological Data

Double Weighted Centring

Between-Class RLQ analysis

Between- and within-class double principal coordinate analysis

Between-class coinertia analysis

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

Phylogeny and quantative trait of carnivora

Small Ecological Dataset

Transformation to make Euclidean a distance matrix

Table of Fuzzy Biological Traits

Ecological and Biological Traits

Pair of Variables

Enzymatic polymorphism in Leuciscus cephalus

Coinertia Analysis

Ecological Tables Triplet

Charolais-Zebus

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

costatis.randtest

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

Enzymatic polymorphism in Mus musculus

Genetics-Ecology-Environment Triple

Computation of Distance Matrices on Quantitative Variables

Computation of Distance Matrices of Percentage Data

Qualitative Weighted Variables

Decentred Correspondence Analysis

Mixed-variables coefficient of distance

Correspondence Analysis

Computation of the Distance Matrix associated to a Neighbouring Graph

Representation of n values on a circle

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Computation of Distance Matrices for Binary Data

Electrocardiogram data

Dune Meadow Data

Multiple Correspondence Analysis

Duality Diagram

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

Corvus morphology

Dagnelie multinormality test

Computation of the Distance Matrix from a Statistical Triplet

Tests of randomization between distances applied to 'kdist' objetcs

Phylogeny and quantitative traits of carnivora

Exam marks for some students

Ordination of Tables mixing quantitative variables and factors

Pair of Ecological Tables

Fruit Production

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Frequenting movie theaters in France in 2003

Linear Discriminant Analysis (descriptive statistic)

Double principal coordinate analysis

Non symmetric correspondence analysis

Rao's diversity coefficient also called quadratic entropy

Discriminant Correspondence Analysis

Rao's dissimilarity coefficient

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

Principal Component Analysis

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Functions to compute the fourth-corner statistic

Ecomorphological Convergence

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

Fission pattern and heritable morphological traits

Contingency Table

Morphometric data set

Principal Coordinates Analysis

Faunistic K-tables

Ordination of Tables mixing quantitative variables and factors

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

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

Multiple Graphs for a Multiple Factorial Analysis

Complete regular grid analysis

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

Geary's Irish Data

K-tables of wine-tasting

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

Triangular Data

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

Multiple Graphs of a STATIS Analysis

Multiple Graphs for a Partial Triadic Analysis

Multiple Graphs for Separated Analyses in a K-tables

ktab.match2ktabs

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

human mitochondrial DNA restriction data

Genetic Variation In Human Populations

Point sampling of fish community

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

Multiple Graphs for the Foucart's Correspondence Analysis

Multiple Graphs for a Multiple Co-inertia Analysis

K-tables Multi-Regions

Assemblages of Macroinvertebrates in the Loire River (France)

Leave-one-out cross-validation for a bca

Microsatellites of Galapagos tortoises populations

Genetic/Environment and types of variables

Leave-one-out cross-validation for a dudi

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

Multiblock partial least squares

Ponds in a nature reserve

Multiple Double Principal Coordinate Analysis

Class of the Permutation Tests (in C).

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

Multiple CO-inertia Analysis

Phylogeny and quantitative traits of flowers

Neighbourhood Graphs

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

Phylogenetic trees in Newick format

Minimal Spanning Tree

loocv.discrimin

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

Granulometric Curves

Create phylogeny

Display and summarize multiblock objects

A table of Qualitative Variables

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

Multiple Factorial Analysis

Phylogeny and quantitative traits of lizards

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

Originality of a species

Transformation of a Distance Matrix for becoming Euclidean

Is a Distance Matrix Euclidean?

Genetic Relationships between cattle breeds with microsatellites

Phylogeny and quantitative traits of teleos fishes

Multi Level Decomposition of unidimensional data

Faunistic Communities and Sampling Experiment

Olympic Decathlon

Orthonormal basis for orthonormal transform

Plot phylogenies

Phylogenetic and quantitative traits of amazonian palm trees

Between-Class Analysis

Plant traits response to grazing

a way to obtain Euclidean distance matrices

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

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Class of the Permutation Tests (in C).

Phylogeny and trait of bacteria

ktab.data.frame

Creation of K-tables from a data frame

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

Generic Function for Multiple Graphs in a K-tables Analysis

Phylogeny and quantitative traits of birds

Distribution of of tropical trees along the Panama canal

Simple Procruste Rotation between two sets of points

Contingency Table with a partition in Molecular Biology

Class of the Permutation Tests (in R).

Phyto-Ecological Survey

randtest.discrimin

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

mantel.randtest

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

Principal Component Analysis with respect to orthogonal instrumental variables

Simplified Analysis in Principal Coordinates

Permutation test for double principal coordinate analysis (DPCoA)

Correspondence Analysis Table

Multiblock principal component analysis with instrumental variables

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

Transformation of a distance matrice to a Euclidean one

Partial Triadic Analysis of a K-tables

Athletes' Morphology

Global State of the World in 1984

Bootstrap simulations

Within-Class Analysis

Results of the French presidential elections of 2002

Taxonomy and quantitative traits of carnivora

randboot.multiblock

Bootstraped simulations for multiblock methods

randtest.between

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

Principal component analysis with respect to instrumental variables

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

Two-fold cross-validation

Avifauna and Vegetation

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

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

Plot of Paired Coordinates

Representation of an object in a graph by a picture

Plot of the Factorial Maps

Graphical representation of the outputs of a multivariate analysis

procuste.randtest

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

Plot of the factorial maps for a fuzzy correspondence analysis

Plot of factorial maps with representation of point classes

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

Plot of the factorial maps of a correlation circle

1D plot of a pair of numeric scores with labels

Ordination Table

Plot of a frequency distribution

randtest.coinertia

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

Reconstitution of Data from a Duality Diagram

Scatterplot of two sets of coordinates and a partionning into classes

Graph of frequency profiles (useful for instance in genetic)

Graph to Analyse the Relation between a Score and Quantitative Variables

Plot of the factorial maps for a correspondence analysis

Plot of the factorial maps in a Multiple Correspondence Analysis

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

rtest.discrimin

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

Trajectory Plot

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

Reciprocal scaling after a correspondence analysis

Graphs to Analyse a factor in a Mixed Analysis

Representation of a value in a graph

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

Graphs for One Dimension

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

Physico-Chemistry Data

Representation of a quantitative variable in front of a phylogenetic tree

Graphs to study one factor in a Multiple Correspondence Analysis

Scatter Plot with Kernel Density Estimate

Two Questions asked on a Sample of 1000 Respondents

Display of a scatterplot and its two marginal histograms

Graph of a variable using image and contour

Graphical utility functions

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

Graph Display for Distance Matrices

Indirect Ordination

Array of Recapture of Rings

Separated Analyses in a K-tables

Plot of the arrays by grey levels

Morphometric Evolution

Relationships between one score and qualitative variables

Graphs to Analyse a factor in PCA

Projections of Supplementary Rows

Students and Subjects

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

1D plot of a numeric score with labels

Plot arrays in front of a phylogenetic tree

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

Plot of the Arrays

STATIS, a method for analysing K-tables

Transect in the Vegetation

Vegetation in Trois-Fontaines

Function to perform a test of dimensionality

Projections of Supplementary Columns

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

Projection of additional items in a PCO analysis

statico.krandtest

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

Morphological Study of the Painted Turtle

testdim.multiblock

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

Homogeneous Table

Freshwater fish zoogeography in west Africa

Tinto and Odiel estuary geochemistry

Normed within principal component analysis

Average temperatures of 30 French cities

Triangular Representation and Groups of points

Phylogeny and quantitative traits of flowers

Triangular Plotting

Plot of Contingency Tables

Mountain Avifauna

Elimination of Duplicated Rows in a Array

variance.phylog

The phylogenetic ANOVA

Pair of Ecological Data

Internal Correspondence Analysis

Examples of taxonomy

Example for Centring in PCA

Phylogeny and quantitative traits of ungulates.

Road distances in New-Zealand

Within-Class Analysis

French Worker Survey (1970)

Distance Matrices

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

Within-class coinertia analysis

Within-Class RLQ analysis

Spatial pattern analysis in plant communities

Internal ade4 functions

Deprecated functions

Deprecated functions in ade4

RVintra.randtest

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

Import data files from Phylogenetic Independance Package

Phylogenies and quantitative traits from Abouheif

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

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

Add graphics to an existing plot

RVdist.randtest

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