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ade4 (version 1.7-19)

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

39,219

Version

1.7-19

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

April 19th, 2022

Functions in ade4 (1.7-19)

Deprecated functions

Deprecated functions in ade4

Analysis of molecular variance

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Small Ecological Dataset

Genomes of 43 Bacteria

The ade4 package

Add graphics to an existing plot

Table of Factors

Between-Class Analysis

RVdist.randtest

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

Pair of Variables

African Estuary Fishes

Import data files from Phylogenetic Independance Package

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Ecological and Biological Traits

Phylogenies and quantitative traits from Abouheif

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

Charolais-Zebus

Graphical Display of Areas

Apportionment of Quadratic Entropy

Dagnelie multinormality test

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

Corvus morphology

Genetic variability of Cacadors

Bird species distribution

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Phylogeny and quantitative traits of carnivora

Distribution of Alpine plants in Aravo (Valloire, France)

costatis.randtest

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

Fauna Table with double (row and column) partitioning

Computation of Distance Matrices of Percentage Data

Transformation to make Euclidean a distance matrix

Ecological Tables Triplet

Fauna Table for Constrained Ordinations

Between- and within-class double principal coordinate analysis

Coinertia Analysis

Table of Fuzzy Biological Traits

Computation of the Distance Matrix from a Statistical Triplet

Computation of Distance Matrices for Binary Data

Genetics-Ecology-Environment Triple

Computation of Distance Matrices on Quantitative Variables

Arrivals at an intensive care unit

Linear Discriminant Analysis (descriptive statistic)

Discriminant Correspondence Analysis

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Genetic Variation In Human Populations

Complete regular grid analysis

Morphometric data set

Representation of n values on a circle

Contingency Table

Dune Meadow Data

Duality Diagram

Electrocardiogram data

Cubic Ecological Data

Enzymatic polymorphism in Mus musculus

Double Weighted Centring

Qualitative Weighted Variables

Mixed-variables coefficient of distance

Between-Class RLQ analysis

Functions to compute the fourth-corner statistic

Principal Component Analysis

Faunistic K-tables

Multiple Correspondence Analysis

Between-class coinertia analysis

Computation of the Distance Matrix associated to a Neighbouring Graph

Enzymatic polymorphism in Leuciscus cephalus

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

a way to obtain Euclidean distance matrices

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

ktab.data.frame

Creation of K-tables from a data frame

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

Generic Function for Multiple Graphs in a K-tables Analysis

Principal Coordinates Analysis

K-tables Multi-Regions

Exam marks for some students

Phylogeny and quantitative traits of flowers

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

Minimal Spanning Tree

Multiple Factorial Analysis

Phylogeny and quantative trait of carnivora

Decentred Correspondence Analysis

Correspondence Analysis

K-tables of wine-tasting

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Ponds in a nature reserve

Fruit Production

Pair of Ecological Tables

Frequenting movie theaters in France in 2003

Rao's dissimilarity coefficient

Rao's diversity coefficient also called quadratic entropy

Triangular Data

Double principal coordinate analysis

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

Genetic/Environment and types of variables

Tests of randomization between distances applied to 'kdist' objetcs

Leave-one-out cross-validation for a dudi

Display and summarize multiblock objects

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

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

Ordination of Tables mixing quantitative variables and factors

Multiple Graphs for Separated Analyses in a K-tables

Multiple Graphs of a STATIS Analysis

Genetic Relationships between cattle breeds with microsatellites

Originality of a species

Ecomorphological Convergence

Global State of the World in 1984

Athletes' Morphology

Ordination of Tables mixing quantitative variables and factors

Phylogeny and quantitative traits of teleos fishes

Is a Distance Matrix Euclidean?

Assemblages of Macroinvertebrates in the Loire River (France)

Microsatellites of Galapagos tortoises populations

Granulometric Curves

Non symmetric correspondence analysis

Fission pattern and heritable morphological traits

multispati.rtest

Multivariate spatial autocorrelation test

Phylogenetic trees in Newick format

Create phylogeny

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

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

Simple Procruste Rotation between two sets of points

Contingency Table with a partition in Molecular Biology

procuste.randtest

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

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

Two-fold cross-validation

Avifauna and Vegetation

Plant traits response to grazing

Class of the Permutation Tests (in R).

Between-Class Analysis

Ordination Table

Plot of the factorial maps for a correspondence analysis

Graph to Analyse the Relation between a Score and Quantitative Variables

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

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

Plot of the Factorial Maps

human mitochondrial DNA restriction data

ktab.match2ktabs

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

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

Partial Triadic Analysis of a K-tables

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

Point sampling of fish community

Neighbourhood Graphs

Multiple Graphs for the Foucart's Correspondence Analysis

loocv.discrimin

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

Leave-one-out cross-validation for a bca

Multiblock partial least squares

Geary's Irish Data

Olympic Decathlon

Phylogeny and trait of bacteria

Transformation of a Distance Matrix for becoming Euclidean

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs for a Partial Triadic Analysis

Phylogenetic and quantitative traits of amazonian palm trees

Class of the Permutation Tests (in C).

Taxonomy and quantitative traits of carnivora

Multiple Graphs for a Multiple Co-inertia Analysis

Permutation test for double principal coordinate analysis (DPCoA)

Multiple CO-inertia Analysis

Bootstrap simulations

Graphs for One Dimension

Transformation of a distance matrice to a Euclidean one

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

Phylogeny and quantitative traits of lizards

Plot phylogenies

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Multivariate spatial analysis

Morphometric Evolution

rtest.discrimin

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

randboot.multiblock

Bootstraped simulations for multiblock methods

Transect in the Vegetation

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

Phyto-Ecological Survey

Within-Class Analysis

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

Representation of an object in a graph by a picture

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

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

Representation of a value in a graph

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Multiple Double Principal Coordinate Analysis

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

mantel.randtest

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

Correspondence Analysis Table

Multiblock principal component analysis with instrumental variables

Class of the Permutation Tests (in C).

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

Projections of Supplementary Columns

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

Indirect Ordination

Faunistic Communities and Sampling Experiment

Simplified Analysis in Principal Coordinates

Graphs to Analyse a factor in a Mixed Analysis

Two Questions asked on a Sample of 1000 Respondents

Average temperatures of 30 French cities

Phylogeny and quantitative traits of flowers

Graphs to Analyse a factor in PCA

Distribution of of tropical trees along the Panama canal

randtest.between

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

Multi Level Decomposition of unidimensional data

Results of the French presidential elections of 2002

Graph of a variable using image and contour

Array of Recapture of Rings

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

Scatter Plot with Kernel Density Estimate

testdim.multiblock

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

Plot of the factorial maps for a fuzzy correspondence analysis

Plot of the factorial maps of a correlation circle

1D plot of a numeric score with labels

Plot of factorial maps with representation of point classes

Phylogeny and quantitative traits of birds

Principal component analysis with respect to instrumental variables

A table of Qualitative Variables

Orthonormal basis for orthonormal transform

Graph Display for Distance Matrices

Plot of Contingency Tables

Phylogeny and quantitative traits of ungulates.

Principal Component Analysis with respect to orthogonal instrumental variables

Morphological Study of the Painted Turtle

Graphical utility functions

Plot of the arrays by grey levels

Tinto and Odiel estuary geochemistry

Reconstitution of Data from a Duality Diagram

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

1D plot of a pair of numeric scores with labels

Freshwater fish zoogeography in west Africa

Elimination of Duplicated Rows in a Array

Within-Class RLQ analysis

Students and Subjects

Representation of a quantitative variable in front of a phylogenetic tree

Separated Analyses in a K-tables

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

randtest.coinertia

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

randtest.discrimin

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

Trajectory Plot

Scatterplot of two sets of coordinates and a partionning into classes

Homogeneous Table

Plot arrays in front of a phylogenetic tree

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

Plot of Paired Coordinates

Graph of frequency profiles (useful for instance in genetic)

Triangular Representation and Groups of points

Reciprocal scaling after a correspondence analysis

Relationships between one score and qualitative variables

Triangular Plotting

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

Graphs to study one factor in a Multiple Correspondence Analysis

Within-class coinertia analysis

Distance Matrices

Within-Class Analysis

Pair of Ecological Data

variance.phylog

The phylogenetic ANOVA

Physico-Chemistry Data

Road distances in New-Zealand

Examples of taxonomy

Function to perform a test of dimensionality

Example for Centring in PCA

Normed within principal component analysis

Vegetation in Trois-Fontaines

Internal Correspondence Analysis

Display of a scatterplot and its two marginal histograms

Plot of a frequency distribution

Graphical representation of the outputs of a multivariate analysis

Plot of the factorial maps in a Multiple Correspondence Analysis

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

statico.krandtest

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

STATIS, a method for analysing K-tables

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

Projections of Supplementary Rows

Projection of additional items in a PCO analysis

Plot of the Arrays

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

Mountain Avifauna

French Worker Survey (1970)

Spatial pattern analysis in plant communities

Internal ade4 functions