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ade4 (version 1.7-20)

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

62,618

Version

1.7-20

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

November 1st, 2022

Functions in ade4 (1.7-20)

Deprecated functions

Deprecated functions in ade4

Internal ade4 functions

Distribution of Alpine plants in Aravo (Valloire, France)

The ade4 package

RVdist.randtest

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

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Phylogenies and quantitative traits from Abouheif

Between-class coinertia analysis

Fauna Table with double (row and column) partitioning

Fauna Table for Constrained Ordinations

Ecological Tables Triplet

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Between-Class RLQ analysis

Apportionment of Quadratic Entropy

Import data files from Phylogenetic Independance Package

Ecological and Biological Traits

Phylogeny and quantative trait of carnivora

Fruit Production

Graphical Display of Areas

Pair of Variables

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

Charolais-Zebus

Arrivals at an intensive care unit

African Estuary Fishes

Frequenting movie theaters in France in 2003

Genomes of 43 Bacteria

Coinertia Analysis

Between-Class Analysis

Spatial pattern analysis in plant communities

Add graphics to an existing plot

Exam marks for some students

Enzymatic polymorphism in Leuciscus cephalus

Table of Fuzzy Biological Traits

Rao's dissimilarity coefficient

Table of Factors

Correspondence Analysis

Small Ecological Dataset

Decentred Correspondence Analysis

Cubic Ecological Data

Dune Meadow Data

Computation of Distance Matrices for Binary Data

Genetic variability of Cacadors

Bird species distribution

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

Double Weighted Centring

Between- and within-class double principal coordinate analysis

Computation of the Distance Matrix from a Statistical Triplet

Enzymatic polymorphism in Mus musculus

Qualitative Weighted Variables

Analysis of molecular variance

Ordination of Tables mixing quantitative variables and factors

Rao's diversity coefficient also called quadratic entropy

Electrocardiogram data

Transformation to make Euclidean a distance matrix

costatis.randtest

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

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

Non symmetric correspondence analysis

Genetics-Ecology-Environment Triple

Phylogeny and quantitative traits of carnivora

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Complete regular grid analysis

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

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Genetic Variation In Human Populations

a way to obtain Euclidean distance matrices

Corvus morphology

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

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Computation of Distance Matrices of Percentage Data

Generic Function for Multiple Graphs in a K-tables Analysis

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

Tests of randomization between distances applied to 'kdist' objetcs

Mixed-variables coefficient of distance

ktab.match2ktabs

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

Morphometric data set

Ordination of Tables mixing quantitative variables and factors

Contingency Table

Multiple Graphs for the Foucart's Correspondence Analysis

Functions to compute the fourth-corner statistic

Computation of the Distance Matrix associated to a Neighbouring Graph

Faunistic K-tables

Computation of Distance Matrices on Quantitative Variables

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Dagnelie multinormality test

Multiple Graphs for a Multiple Co-inertia Analysis

Phyto-Ecological Survey

mantel.randtest

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

Pair of Ecological Tables

Linear Discriminant Analysis (descriptive statistic)

Discriminant Correspondence Analysis

Double principal coordinate analysis

Multiblock partial least squares

Duality Diagram

Multiple Correspondence Analysis

Principal Component Analysis

Principal Coordinates Analysis

Is a Distance Matrix Euclidean?

Multiple CO-inertia Analysis

Ecomorphological Convergence

Orthonormal basis for orthonormal transform

Fission pattern and heritable morphological traits

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

K-tables Multi-Regions

Ponds in a nature reserve

human mitochondrial DNA restriction data

Create phylogeny

A table of Qualitative Variables

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs for a Partial Triadic Analysis

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

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

Phylogeny and quantitative traits of flowers

Point sampling of fish community

Representation of n values on a circle

Multiple Graphs for Separated Analyses in a K-tables

ktab.data.frame

Creation of K-tables from a data frame

Multivariate spatial analysis

Multi Level Decomposition of unidimensional data

Multiple Graphs of a STATIS Analysis

Genetic/Environment and types of variables

K-tables of wine-tasting

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

Genetic Relationships between cattle breeds with microsatellites

Leave-one-out cross-validation for a dudi

Correspondence Analysis Table

Triangular Data

Leave-one-out cross-validation for a bca

Microsatellites of Galapagos tortoises populations

Phylogeny and quantitative traits of teleos fishes

Granulometric Curves

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

multispati.rtest

Multivariate spatial autocorrelation test

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

loocv.discrimin

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

Transformation of a Distance Matrix for becoming Euclidean

Phylogeny and quantitative traits of lizards

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

Multiple Factorial Analysis

Plot phylogenies

Minimal Spanning Tree

Assemblages of Macroinvertebrates in the Loire River (France)

Geary's Irish Data

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

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

Multiblock principal component analysis with instrumental variables

Display and summarize multiblock objects

Neighbourhood Graphs

Phylogeny and trait of bacteria

Multiple Double Principal Coordinate Analysis

Reconstitution of Data from a Duality Diagram

Originality of a species

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

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

Olympic Decathlon

Class of the Permutation Tests (in C).

Phylogenetic trees in Newick format

Plant traits response to grazing

Faunistic Communities and Sampling Experiment

Display of a scatterplot and its two marginal histograms

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

Plot of the factorial maps in a Multiple Correspondence Analysis

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Simplified Analysis in Principal Coordinates

Distribution of of tropical trees along the Panama canal

Representation of an object in a graph by a picture

Global State of the World in 1984

Between-Class Analysis

Trajectory Plot

Distance Matrices

Athletes' Morphology

Within-Class Analysis

Contingency Table with a partition in Molecular Biology

Transformation of a distance matrice to a Euclidean one

Bootstrap simulations

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

Graph of frequency profiles (useful for instance in genetic)

Projections of Supplementary Rows

Taxonomy and quantitative traits of carnivora

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Principal component analysis with respect to instrumental variables

Avifauna and Vegetation

Plot of the factorial maps for a correspondence analysis

Phylogeny and quantitative traits of birds

Simple Procruste Rotation between two sets of points

randtest.coinertia

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

Representation of a quantitative variable in front of a phylogenetic tree

Phylogenetic and quantitative traits of amazonian palm trees

procuste.randtest

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

Plot of the factorial maps of a correlation circle

Vegetation in Trois-Fontaines

Graphs to study one factor in a Multiple Correspondence Analysis

Principal Component Analysis with respect to orthogonal instrumental variables

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

Physico-Chemistry Data

Example for Centring in PCA

Projection of additional items in a PCO analysis

Reciprocal scaling after a correspondence analysis

Road distances in New-Zealand

Plot arrays in front of a phylogenetic tree

Plot of the arrays by grey levels

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

randtest.discrimin

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

Class of the Permutation Tests (in R).

Permutation test for double principal coordinate analysis (DPCoA)

Plot of Paired Coordinates

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

Results of the French presidential elections of 2002

statico.krandtest

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

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

Triangular Representation and Groups of points

Scatterplot of two sets of coordinates and a partionning into classes

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

Plot of a frequency distribution

Relationships between one score and qualitative variables

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

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

Plot of the factorial maps for a fuzzy correspondence analysis

Representation of a value in a graph

Partial Triadic Analysis of a K-tables

Plot of factorial maps with representation of point classes

Separated Analyses in a K-tables

randboot.multiblock

Bootstraped simulations for multiblock methods

Homogeneous Table

STATIS, a method for analysing K-tables

Indirect Ordination

testdim.multiblock

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

Graphical representation of the outputs of a multivariate analysis

Examples of taxonomy

Tinto and Odiel estuary geochemistry

Class of the Permutation Tests (in C).

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

Graphical utility functions

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

Graphs to Analyse a factor in a Mixed Analysis

randtest.between

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

1D plot of a pair of numeric scores with labels

Two-fold cross-validation

Ordination Table

Morphometric Evolution

Array of Recapture of Rings

rtest.discrimin

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

Transect in the Vegetation

Scatter Plot with Kernel Density Estimate

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

variance.phylog

The phylogenetic ANOVA

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

Function to perform a test of dimensionality

1D plot of a numeric score with labels

Graph to Analyse the Relation between a Score and Quantitative Variables

Freshwater fish zoogeography in west Africa

Normed within principal component analysis

Graph of a variable using image and contour

Morphological Study of the Painted Turtle

Graphs for One Dimension

Plot of the Factorial Maps

Plot of the Arrays

Two Questions asked on a Sample of 1000 Respondents

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

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

Graph Display for Distance Matrices

Phylogeny and quantitative traits of flowers

French Worker Survey (1970)

Students and Subjects

Plot of Contingency Tables

Average temperatures of 30 French cities

Phylogeny and quantitative traits of ungulates.

Elimination of Duplicated Rows in a Array

Internal Correspondence Analysis

Graphs to Analyse a factor in PCA

Within-Class RLQ analysis

Triangular Plotting

Mountain Avifauna

Projections of Supplementary Columns

Pair of Ecological Data

Within-Class Analysis

Within-class coinertia analysis