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ade4 (version 1.7-16)

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

51,023

Version

1.7-16

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

October 28th, 2020

Functions in ade4 (1.7-16)

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

The ade4 package

RVdist.randtest

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

Phylogenies and quantitative traits from Abouheif

Small Ecological Dataset

Enzymatic polymorphism in Mus musculus

Between- and within-class double principal coordinate analysis

Transformation to make Euclidean a distance matrix

Qualitative Weighted Variables

Fauna Table for Constrained Ordinations

Ecological Tables Triplet

Graphical Display of Areas

Spatial pattern analysis in plant communities

Import data files from Phylogenetic Independance Package

Add graphics to an existing plot

Deprecated functions

Deprecated functions in ade4

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

Phylogeny and quantative trait of carnivora

Arrivals at an intensive care unit

Genetic variability of Cacadors

Internal ade4 functions

Corvus morphology

Distribution of Alpine plants in Aravo (Valloire, France)

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

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Fruit Production

Frequenting movie theaters in France in 2003

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Fauna Table with double (row and column) partitioning

Apportionment of Quadratic Entropy

Between-Class RLQ analysis

Between-class coinertia analysis

Cubic Ecological Data

Double Weighted Centring

Bird species distribution

Ordination of Tables mixing quantitative variables and factors

African Estuary Fishes

Pair of Variables

Analysis of molecular variance

Computation of Distance Matrices for Binary Data

Computation of the Distance Matrix from a Statistical Triplet

Between-Class Analysis

Duality Diagram

Charolais-Zebus

Multiple Correspondence Analysis

Coinertia Analysis

Genetics-Ecology-Environment Triple

Phylogeny and quantitative traits of carnivora

Table of Fuzzy Biological Traits

Genomes of 43 Bacteria

Table of Factors

Ecomorphological Convergence

Principal Component Analysis

Principal Coordinates Analysis

Ecological and Biological Traits

Rao's diversity coefficient also called quadratic entropy

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

Representation of n values on a circle

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Rao's dissimilarity coefficient

Exam marks for some students

Functions to compute the fourth-corner statistic

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

Enzymatic polymorphism in Leuciscus cephalus

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Complete regular grid analysis

Genetic Variation In Human Populations

Faunistic K-tables

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

Point sampling of fish community

Tests of randomization between distances applied to 'kdist' objetcs

Dagnelie multinormality test

Mixed-variables coefficient of distance

costatis.randtest

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

Computation of the Distance Matrix associated to a Neighbouring Graph

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs for a Multiple Co-inertia Analysis

Phylogeny and quantitative traits of flowers

Correspondence Analysis Table

Fission pattern and heritable morphological traits

Genetic/Environment and types of variables

Dune Meadow Data

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

Electrocardiogram data

Geary's Irish Data

Is a Distance Matrix Euclidean?

Multiple Factorial Analysis

Genetic Relationships between cattle breeds with microsatellites

Discriminant Correspondence Analysis

Linear Discriminant Analysis (descriptive statistic)

Athletes' Morphology

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

Minimal Spanning Tree

Correspondence Analysis

Multiple Graphs for a Partial Triadic Analysis

Multiple Graphs for Separated Analyses in a K-tables

Transformation of a Distance Matrix for becoming Euclidean

mantel.randtest

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

Olympic Decathlon

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

Computation of Distance Matrices of Percentage Data

Computation of Distance Matrices on Quantitative Variables

Decentred Correspondence Analysis

Contingency Table

Pair of Ecological Tables

Plant traits response to grazing

human mitochondrial DNA restriction data

Ordination of Tables mixing quantitative variables and factors

Double principal coordinate analysis

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

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

Non symmetric correspondence analysis

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

K-tables of wine-tasting

K-tables Multi-Regions

a way to obtain Euclidean distance matrices

Phylogeny and quantitative traits of birds

Simple Procruste Rotation between two sets of points

Within-Class RLQ analysis

Array of Recapture of Rings

randtest.coinertia

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

randtest.between

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

Class of the Permutation Tests (in C).

Multiple Graphs of a STATIS Analysis

Triangular Data

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

Plot of factorial maps with representation of point classes

Microsatellites of Galapagos tortoises populations

Granulometric Curves

Ponds in a nature reserve

variance.phylog

The phylogenetic ANOVA

Indirect Ordination

Students and Subjects

Graphs to Analyse a factor in PCA

loocv.discrimin

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

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

Phylogeny and quantitative traits of lizards

Leave-one-out cross-validation for a dudi

Leave-one-out cross-validation for a bca

Mountain Avifauna

Within-class coinertia analysis

Multiple Graphs for the Foucart's Correspondence Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

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

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

ktab.match2ktabs

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

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

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

ktab.data.frame

Creation of K-tables from a data frame

Examples of taxonomy

Elimination of Duplicated Rows in a Array

Multiblock principal component analysis with instrumental variables

Multiblock partial least squares

Display and summarize multiblock objects

Multivariate spatial analysis

Phylogeny and quantitative traits of teleos fishes

Assemblages of Macroinvertebrates in the Loire River (France)

Multi Level Decomposition of unidimensional data

A table of Qualitative Variables

Phylogenetic and quantitative traits of amazonian palm trees

Phylogenetic trees in Newick format

Create phylogeny

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

Neighbourhood Graphs

Between-Class Analysis

Contingency Table with a partition in Molecular Biology

Distribution of of tropical trees along the Panama canal

Plot phylogenies

procuste.randtest

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

Phyto-Ecological Survey

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

randtest.discrimin

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

Permutation test for double principal coordinate analysis (DPCoA)

Faunistic Communities and Sampling Experiment

Transformation of a distance matrice to a Euclidean one

Partial Triadic Analysis of a K-tables

Reconstitution of Data from a Duality Diagram

Ordination Table

rtest.discrimin

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

Global State of the World in 1984

Multiple CO-inertia Analysis

Principal Component Analysis with respect to orthogonal instrumental variables

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

Multiple Double Principal Coordinate Analysis

Scatterplot of two sets of coordinates and a partionning into classes

Simplified Analysis in Principal Coordinates

Graphical utility functions

Graph of frequency profiles (useful for instance in genetic)

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

multispati.randtest

Multivariate spatial autocorrelation test (in C)

multispati.rtest

Multivariate spatial autocorrelation test

Originality of a species

Graph of a variable using image and contour

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

Representation of an object in a graph by a picture

Separated Analyses in a K-tables

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

Representation of a quantitative variable in front of a phylogenetic tree

Plot of the factorial maps for a correspondence analysis

Class of the Permutation Tests (in R).

Plot of Paired Coordinates

Morphological Study of the Painted Turtle

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

Taxonomy and quantitative traits of carnivora

Tinto and Odiel estuary geochemistry

Physico-Chemistry Data

Orthonormal basis for orthonormal transform

Principal component analysis with respect to instrumental variables

Phylogeny and trait of bacteria

Plot of Contingency Tables

Display of a scatterplot and its two marginal histograms

Reciprocal scaling after a correspondence analysis

Plot of the Factorial Maps

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

Average temperatures of 30 French cities

Plot of the factorial maps for a fuzzy correspondence analysis

Morphometric Evolution

Projections of Supplementary Columns

Phylogeny and quantitative traits of ungulates.

Projection of additional items in a PCO analysis

Relationships between one score and qualitative variables

Graphs to study one factor in a Multiple Correspondence Analysis

Within-Class Analysis

1D plot of a numeric score with labels

Plot of the factorial maps in a Multiple Correspondence Analysis

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

randboot.multiblock

Bootstraped simulations for multiblock methods

Results of the French presidential elections of 2002

Bootstrap simulations

Two-fold cross-validation

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

Internal Correspondence Analysis

Function to perform a test of dimensionality

testdim.multiblock

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

Class of the Permutation Tests (in C).

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

Vegetation in Trois-Fontaines

STATIS, a method for analysing K-tables

Two Questions asked on a Sample of 1000 Respondents

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

Scatter Plot with Kernel Density Estimate

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

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

Homogeneous Table

Phylogeny and quantitative traits of flowers

Road distances in New-Zealand

Trajectory Plot

Example for Centring in PCA

Freshwater fish zoogeography in west Africa

Transect in the Vegetation

Graph to Analyse the Relation between a Score and Quantitative Variables

Avifauna and Vegetation

Graph Display for Distance Matrices

Graphs for One Dimension

Plot of the factorial maps of a correlation circle

Projections of Supplementary Rows

statico.krandtest

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

Within-Class Analysis

Graphical representation of the outputs of a multivariate analysis

Plot of a frequency distribution

Distance Matrices

1D plot of a pair of numeric scores with labels

Representation of a value in a graph

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

Graphs to Analyse a factor in a Mixed Analysis

Pair of Ecological Data

Normed within principal component analysis

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

Plot of the arrays by grey levels

Plot of the Arrays

Triangular Plotting

Plot arrays in front of a phylogenetic tree

French Worker Survey (1970)

Triangular Representation and Groups of points