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ade4 (version 1.7-8)

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

33,243

Version

1.7-8

License

GPL (>= 2)

Homepage

http://pbil.univ-lyon1.fr/ADE-4

Maintainer

Aurélie Siberchicot

Last Published

August 9th, 2017

Functions in ade4 (1.7-8)

Phylogenies and quantitative traits from Abouheif

Spatial pattern analysis in plant communities

Internal ade4 functions

The ade4 package

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

RVdist.randtest

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

Add graphics to an existing plot

Deprecated functions

Deprecated functions in ade4

Amount of Evolutionary History

Import data files from Phylogenetic Independance Package

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Analysis of molecular variance

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Bird species distribution

Between-Class RLQ analysis

Between-Class Analysis

Genetics-Ecology-Environment Triple

Between- and within-class double principal coordinate analysis

Fauna Table with double (row and column) partitioning

Graphical Display of Areas

Table of Factors

African Estuary Fishes

Arrivals at an intensive care unit

Small Ecological Dataset

Genetic variability of Cacadors

Double Weighted Centring

Charolais-Zebus

Enzymatic polymorphism in Leuciscus cephalus

Qualitative Weighted Variables

Pair of Variables

Table of Fuzzy Biological Traits

Tests of randomization between distances applied to 'kdist' objetcs

Corvus morphology

Computation of Distance Matrices on Quantitative Variables

Rao's diversity coefficient also called quadratic entropy

Apportionment of Quadratic Entropy

Distribution of Alpine plants in Aravo (Valloire, France)

Ecological Tables Triplet

Genomes of 43 Bacteria

Representation of n values on a circle

Pair of Ecological Tables

Principal Coordinates Analysis

Dune Meadow Data

Transformation to make Euclidean a distance matrix

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Enzymatic polymorphism in Mus musculus

Ecological and Biological Traits

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

Fruit Production

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Computation of Distance Matrices for Binary Data

Computation of the Distance Matrix from a Statistical Triplet

Decentred Correspondence Analysis

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

Functions to compute the fourth-corner statistic

human mitochondrial DNA restriction data

Exam marks for some students

Rao's dissimilarity coefficient

Genetic distances from gene frequencies

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

K-tables of wine-tasting

Triangular Data

Fauna Table for Constrained Ordinations

Between-class coinertia analysis

Cubic Ecological Data

Phylogeny and quantative trait of carnivora

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

costatis.randtest

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

Linear Discriminant Analysis (descriptive statistic)

Discriminant Correspondence Analysis

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

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Electrocardiogram data

Phylogeny and quantitative traits of carnivora

Frequenting movie theaters in France in 2003

Coinertia Analysis

Computation of the Distance Matrix associated to a Neighbouring Graph

Mixed-variables coefficient of distance

Multiple Correspondence Analysis

Correspondence Analysis

Ordination of Tables mixing quantitative variables and factors

Ordination of Tables mixing quantitative variables and factors

Faunistic K-tables

Point sampling of fish community

Multiple Graphs for the Foucart's Correspondence Analysis

ktab.data.frame

Creation of K-tables from a data frame

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

Geary's Irish Data

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

Ecomorphological Convergence

A class of data: tables of populations and alleles

Microsatellites of Galapagos tortoises populations

Is a Distance Matrix Euclidean?

Multiple Graphs for a Multiple Co-inertia Analysis

Fission pattern and heritable morphological traits

Granulometric Curves

Complete regular grid analysis

a way to obtain Euclidean distance matrices

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

Phylogeny and quantitative traits of flowers

Correspondence Analysis Table

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

Computation of Distance Matrices of Percentage Data

Double principal coordinate analysis

Duality Diagram

Non symmetric correspondence analysis

Multiple Graphs for a Multiple Factorial Analysis

Multiple Graphs for a Partial Triadic Analysis

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

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

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

ktab.match2ktabs

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

Transformation of a Distance Matrix for becoming Euclidean

Phylogeny and quantitative traits of lizards

Phylogeny and quantitative traits of teleos fishes

Multi Level Decomposition of unidimensional data

Display and summarize multiblock objects

Principal Component Analysis

Reading a table of genetic data (diploid individuals)

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

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

multispati.randtest

Multivariate spatial autocorrelation test (in C)

multispati.rtest

Multivariate spatial autocorrelation test

Maximal or minimal amount of originality saved under optimal conditions

Genetic/Environment and types of variables

Assemblages of Macroinvertebrates in the Loire River (France)

Phyto-Ecological Survey

Multiple CO-inertia Analysis

Multiple Double Principal Coordinate Analysis

Faunistic Communities and Sampling Experiment

Global State of the World in 1984

Originality of a species

Phylogenetic and quantitative traits of amazonian palm trees

Taxonomy and quantitative traits of carnivora

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

Genetic Variation In Human Populations

Contingency Table

K-tables Multi-Regions

Ponds in a nature reserve

Multivariate spatial analysis

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Phylogeny and trait of bacteria

Orthonormal decomposition of variance

Partial Triadic Analysis of a K-tables

Bootstrap simulations

randboot.multiblock

Bootstraped simulations for multiblock methods

Class of the Permutation Tests (in C).

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

Orthonormal basis for orthonormal transform

Simplified Analysis in Principal Coordinates

Distribution of of tropical trees along the Panama canal

Simple Procruste Rotation between two sets of points

Generic Function for Multiple Graphs in a K-tables Analysis

Multiple Graphs for Separated Analyses in a K-tables

Multiple Graphs of a STATIS Analysis

mantel.randtest

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

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

Multiple Factorial Analysis

Genetic Relationships between cattle breeds with microsatellites

Neighbourhood Graphs

Multiblock principal component analysis with instrumental variables

Multiblock partial least squares

Athletes' Morphology

Minimal Spanning Tree

procuste.randtest

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

Transformation of a distance matrice to a Euclidean one

Nee and May's random process

A table of Qualitative Variables

Plant traits response to grazing

Between-Class Analysis

Class of the Permutation Tests (in C).

Ordination Table

Reconstitution of Data from a Duality Diagram

Display of a scatterplot and its two marginal histograms

Graph of a variable using image and contour

Avifauna and Vegetation

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

Plot of factorial maps with representation of point classes

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

Graphical utility functions

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

Separated Analyses in a K-tables

Morphometric Evolution

Projections of Supplementary Rows

Indirect Ordination

Array of Recapture of Rings

Plot of the Factorial Maps

Plot of the factorial maps for a fuzzy correspondence analysis

Graphical representation of the outputs of a multivariate analysis

1D plot of a pair of numeric scores with labels

Graph to Analyse the Relation between a Score and Quantitative Variables

Projections of Supplementary Columns

Projection of additional items in a PCO analysis

Phylogenetic trees in Newick format

Olympic Decathlon

Nee and May's optimizing process

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

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

Physico-Chemistry Data

Representation of a quantitative variable in front of a phylogenetic tree

Plot of the arrays by grey levels

Plot arrays in front of a phylogenetic tree

Plot of the Arrays

Mountain Avifauna

Triangular Plotting

Pair of Ecological Data

Scatter Plot with Kernel Density Estimate

Scatterplot of two sets of coordinates and a partionning into classes

Graph of frequency profiles (useful for instance in genetic)

Phylogeny and quantitative traits of flowers

Morphological Study of the Painted Turtle

Within-Class RLQ analysis

Freshwater fish zoogeography in west Africa

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

French Worker Survey (1970)

Distance Matrices

Road distances in New-Zealand

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

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

Reciprocal scaling after a correspondence analysis

Graphs to Analyse a factor in a Mixed Analysis

Create phylogeny

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

Principal component analysis with respect to instrumental variables

Contingency Table with a partition in Molecular Biology

Plot phylogenies

Within-Class Analysis

Principal Component Analysis with respect to orthogonal instrumental variables

Results of the French presidential elections of 2002

Phylogeny and quantitative traits of birds

randtest.between

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

randtest.coinertia

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

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

Two-fold cross-validation

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

statico.krandtest

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

Plot of Contingency Tables

Graph Display for Distance Matrices

variance.phylog

The phylogenetic ANOVA

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

Within-Class Analysis

randtest.discrimin

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

Permutation test for double principal coordinate analysis (DPCoA)

Class of the Permutation Tests (in R).

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

Plot of the factorial maps of a correlation circle

rtest.discrimin

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

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

Trajectory Plot

Representation of a value in a graph

Relationships between one score and qualitative variables

1D plot of a numeric score with labels

withincoinertia

Within-class coinertia analysis

Graphs to Analyse a factor in PCA

Students and Subjects

STATIS, a method for analysing K-tables

Transect in the Vegetation

Plot of a frequency distribution

Representation of an object in a graph by a picture

Plot of Paired Coordinates

Plot of the factorial maps in a Multiple Correspondence Analysis

Plot of the factorial maps for a correspondence analysis

Graphs for One Dimension

Graphs to study one factor in a Multiple Correspondence Analysis

testdim.multiblock

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

Tinto and Odiel estuary geochemistry

Phylogeny and quantitative traits of ungulates.

Elimination of Duplicated Rows in a Array

Vegetation in Trois-Fontaines

Example for Centring in PCA

Two Questions asked on a Sample of 1000 Respondents

Average temperatures of 30 French cities

Examples of taxonomy

Function to perform a test of dimensionality

Homogeneous Table

Triangular Representation and Groups of points

Normed within principal component analysis

Internal Correspondence Analysis