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ade4 (version 1.7-18)

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

48,431

Version

1.7-18

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

September 16th, 2021

Functions in ade4 (1.7-18)

Deprecated functions

Deprecated functions in ade4

Internal ade4 functions

Phylogenies and quantitative traits from Abouheif

RVdist.randtest

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

Small Ecological Dataset

Fauna Table with double (row and column) partitioning

Spatial pattern analysis in plant communities

The ade4 package

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Arrivals at an intensive care unit

Analysis of molecular variance

Distribution of Alpine plants in Aravo (Valloire, France)

Add graphics to an existing plot

Graphical Display of Areas

Between-class coinertia analysis

Between-Class RLQ analysis

Ecological Tables Triplet

Fauna Table for Constrained Ordinations

Genetic variability of Cacadors

African Estuary Fishes

Bird species distribution

Between-Class Analysis

Genetics-Ecology-Environment Triple

Enzymatic polymorphism in Leuciscus cephalus

Phylogeny and quantative trait of carnivora

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

Charolais-Zebus

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Import data files from Phylogenetic Independance Package

Pair of Variables

Apportionment of Quadratic Entropy

Double Weighted Centring

Phylogeny and quantitative traits of carnivora

Cubic Ecological Data

Ecological and Biological Traits

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Corvus morphology

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

Rao's dissimilarity coefficient

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

Exam marks for some students

Enzymatic polymorphism in Mus musculus

Fruit Production

Qualitative Weighted Variables

Computation of Distance Matrices for Binary Data

Computation of Distance Matrices on Quantitative Variables

Discriminant Correspondence Analysis

Computation of Distance Matrices of Percentage Data

Rao's diversity coefficient also called quadratic entropy

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Coinertia Analysis

Genomes of 43 Bacteria

Representation of n values on a circle

Table of Factors

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

Ordination of Tables mixing quantitative variables and factors

Between- and within-class double principal coordinate analysis

Transformation to make Euclidean a distance matrix

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Functions to compute the fourth-corner statistic

Ecomorphological Convergence

Pair of Ecological Tables

Non symmetric correspondence analysis

Table of Fuzzy Biological Traits

Ordination of Tables mixing quantitative variables and factors

Computation of the Distance Matrix from a Statistical Triplet

costatis.randtest

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

Dagnelie multinormality test

Geary's Irish Data

Duality Diagram

Double principal coordinate analysis

Faunistic K-tables

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

Mixed-variables coefficient of distance

Frequenting movie theaters in France in 2003

Linear Discriminant Analysis (descriptive statistic)

Phylogeny and quantitative traits of lizards

Dune Meadow Data

Is a Distance Matrix Euclidean?

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

K-tables of wine-tasting

Triangular Data

Multiple Graphs for Separated Analyses in a K-tables

Multiple Correspondence Analysis

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

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Fission pattern and heritable morphological traits

Correspondence Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

Tests of randomization between distances applied to 'kdist' objetcs

Contingency Table

K-tables Multi-Regions

Electrocardiogram data

Multiple Graphs for the Foucart's Correspondence Analysis

Complete regular grid analysis

Point sampling of fish community

Class of the Permutation Tests (in C).

Computation of the Distance Matrix associated to a Neighbouring Graph

loocv.discrimin

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

human mitochondrial DNA restriction data

Transformation of a Distance Matrix for becoming Euclidean

Principal Coordinates Analysis

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

Multiple Graphs for a Partial Triadic Analysis

A table of Qualitative Variables

Genetic/Environment and types of variables

Decentred Correspondence Analysis

Microsatellites of Galapagos tortoises populations

Principal Component Analysis

Multiblock partial least squares

Multiple Graphs for a Multiple Co-inertia Analysis

Multiple Graphs for a Multiple Factorial Analysis

Genetic Variation In Human Populations

Granulometric Curves

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

Ponds in a nature reserve

Global State of the World in 1984

Leave-one-out cross-validation for a dudi

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

Athletes' Morphology

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

Leave-one-out cross-validation for a bca

a way to obtain Euclidean distance matrices

Contingency Table with a partition in Molecular Biology

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

Phylogeny and quantitative traits of flowers

Multiblock principal component analysis with instrumental variables

Assemblages of Macroinvertebrates in the Loire River (France)

Faunistic Communities and Sampling Experiment

Phyto-Ecological Survey

Phylogenetic and quantitative traits of amazonian palm trees

Plot of the factorial maps in a Multiple Correspondence Analysis

Within-Class Analysis

Multiple Graphs of a STATIS Analysis

Correspondence Analysis Table

Genetic Relationships between cattle breeds with microsatellites

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

randtest.discrimin

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

Multivariate spatial analysis

Partial Triadic Analysis of a K-tables

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

Display and summarize multiblock objects

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

Multiple Factorial Analysis

Neighbourhood Graphs

Multi Level Decomposition of unidimensional data

mantel.randtest

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

Plant traits response to grazing

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

Phylogeny and trait of bacteria

Olympic Decathlon

Phylogenetic trees in Newick format

Average temperatures of 30 French cities

ktab.match2ktabs

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

Reconstitution of Data from a Duality Diagram

Transformation of a distance matrice to a Euclidean one

Distribution of of tropical trees along the Panama canal

Representation of an object in a graph by a picture

Function to perform a test of dimensionality

Results of the French presidential elections of 2002

Permutation test for double principal coordinate analysis (DPCoA)

Class of the Permutation Tests (in R).

Two-fold cross-validation

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

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

Minimal Spanning Tree

ktab.data.frame

Creation of K-tables from a data frame

Plot of Paired Coordinates

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

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

Indirect Ordination

Plot of the factorial maps of a correlation circle

Array of Recapture of Rings

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

Plot of a frequency distribution

Plot of factorial maps with representation of point classes

1D plot of a pair of numeric scores with labels

Simplified Analysis in Principal Coordinates

Bootstrap simulations

randboot.multiblock

Bootstraped simulations for multiblock methods

Principal Component Analysis with respect to orthogonal instrumental variables

Phylogeny and quantitative traits of birds

Plot phylogenies

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Phylogeny and quantitative traits of teleos fishes

Originality of a species

Between-Class Analysis

multispati.rtest

Multivariate spatial autocorrelation test

Orthonormal basis for orthonormal transform

Graphs for One Dimension

Scatterplot of two sets of coordinates and a partionning into classes

Avifauna and Vegetation

Tinto and Odiel estuary geochemistry

Scatter Plot with Kernel Density Estimate

Graph to Analyse the Relation between a Score and Quantitative Variables

testdim.multiblock

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

Reciprocal scaling after a correspondence analysis

Multiple CO-inertia Analysis

Multiple Double Principal Coordinate Analysis

Create phylogeny

Graphs to Analyse a factor in PCA

Ordination Table

Taxonomy and quantitative traits of carnivora

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

Representation of a quantitative variable in front of a phylogenetic tree

Elimination of Duplicated Rows in a Array

Graphs to Analyse a factor in a Mixed Analysis

Transect in the Vegetation

Principal component analysis with respect to instrumental variables

procuste.randtest

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

Display of a scatterplot and its two marginal histograms

rtest.discrimin

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

Relationships between one score and qualitative variables

Simple Procruste Rotation between two sets of points

Class of the Permutation Tests (in C).

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

Representation of a value in a graph

Plot of the factorial maps for a correspondence analysis

Trajectory Plot

Graph of frequency profiles (useful for instance in genetic)

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

Plot of Contingency Tables

variance.phylog

The phylogenetic ANOVA

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

1D plot of a numeric score with labels

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

Projections of Supplementary Columns

Internal Correspondence Analysis

STATIS, a method for analysing K-tables

Vegetation in Trois-Fontaines

Projection of additional items in a PCO analysis

Freshwater fish zoogeography in west Africa

Phylogeny and quantitative traits of flowers

Normed within principal component analysis

Graphical representation of the outputs of a multivariate analysis

Mountain Avifauna

Students and Subjects

Examples of taxonomy

Graphs to study one factor in a Multiple Correspondence Analysis

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

Projections of Supplementary Rows

Triangular Representation and Groups of points

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

randtest.coinertia

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

Within-class coinertia analysis

Physico-Chemistry Data

Separated Analyses in a K-tables

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

randtest.between

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

Graphical utility functions

Morphometric Evolution

Graph of a variable using image and contour

Plot of the factorial maps for a fuzzy correspondence analysis

Plot of the Factorial Maps

Example for Centring in PCA

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

French Worker Survey (1970)

Triangular Plotting

Within-Class RLQ analysis

Graph Display for Distance Matrices

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

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

Plot of the arrays by grey levels

Morphological Study of the Painted Turtle

Homogeneous Table

Plot of the Arrays

Two Questions asked on a Sample of 1000 Respondents

Road distances in New-Zealand

statico.krandtest

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

Pair of Ecological Data

Within-Class Analysis

Distance Matrices

Plot arrays in front of a phylogenetic tree

Phylogeny and quantitative traits of ungulates.

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