Learn R Programming

⚠️There's a newer version (1.7-23) of this package.Take me there.

ade4 (version 1.7-10)

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) .

Copy Link

Version

Install

install.packages('ade4')

Monthly Downloads

38,204

Version

1.7-10

License

GPL (>= 2)

Homepage

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

Maintainer

Aurélie Siberchicot

Last Published

December 15th, 2017

Functions in ade4 (1.7-10)

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

Add graphics to an existing plot

Internal ade4 functions

Deprecated functions

Deprecated functions in ade4

Amount of Evolutionary History

Phylogenies and quantitative traits from Abouheif

Fauna Table with double (row and column) partitioning

Spatial pattern analysis in plant communities

Graphical Display of Areas

Analysis of molecular variance

The ade4 package

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Import data files from Phylogenetic Independance Package

Apportionment of Quadratic Entropy

RVdist.randtest

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

Distribution of Alpine plants in Aravo (Valloire, France)

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Arrivals at an intensive care unit

Bird species distribution

Fauna Table for Constrained Ordinations

Small Ecological Dataset

Genetic variability of Cacadors

Table of Factors

Genetics-Ecology-Environment Triple

Between- and within-class double principal coordinate analysis

Between-Class Analysis

Transformation to make Euclidean a distance matrix

Ecological Tables Triplet

Between-class coinertia analysis

Enzymatic polymorphism in Leuciscus cephalus

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

Between-Class RLQ analysis

Fruit Production

Table of Fuzzy Biological Traits

Cubic Ecological Data

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Genomes of 43 Bacteria

Discriminant Correspondence Analysis

Ecological and Biological Traits

Computation of Distance Matrices for Binary Data

Computation of Distance Matrices on Quantitative Variables

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Charolais-Zebus

Enzymatic polymorphism in Mus musculus

Rao's dissimilarity coefficient

African Estuary Fishes

Linear Discriminant Analysis (descriptive statistic)

Tests of randomization between distances applied to 'kdist' objetcs

Pair of Ecological Tables

Corvus morphology

Double principal coordinate analysis

Computation of Distance Matrices of Percentage Data

Rao's diversity coefficient also called quadratic entropy

Double Weighted Centring

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

Phylogeny and quantative trait of carnivora

Principal Component Analysis

Phylogeny and quantitative traits of carnivora

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

Principal Coordinates Analysis

costatis.randtest

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

Computation of the Distance Matrix from a Statistical Triplet

Duality Diagram

Dagnelie multinormality test

Exam marks for some students

Multiple Correspondence Analysis

Mixed-variables coefficient of distance

Dune Meadow Data

Electrocardiogram data

Reading a table of genetic data (diploid individuals)

Microsatellites of Galapagos tortoises populations

Computation of the Distance Matrix associated to a Neighbouring Graph

Granulometric Curves

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Geary's Irish Data

Is a Distance Matrix Euclidean?

Ordination of Tables mixing quantitative variables and factors

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

Genetic distances from gene frequencies

Functions to compute the fourth-corner statistic

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Faunistic K-tables

Contingency Table

Representation of n values on a circle

human mitochondrial DNA restriction data

Ordination of Tables mixing quantitative variables and factors

a way to obtain Euclidean distance matrices

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

Non symmetric correspondence analysis

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

Fission pattern and heritable morphological traits

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

Multiblock partial least squares

Multiple CO-inertia Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

Phyto-Ecological Survey

Multiple Graphs for the Foucart's Correspondence Analysis

mantel.randtest

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

Correspondence Analysis Table

Phylogeny and quantitative traits of lizards

K-tables of wine-tasting

K-tables Multi-Regions

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

Triangular Data

Multiple Graphs for a Partial Triadic Analysis

Complete regular grid analysis

Multiple Graphs for Separated Analyses in a K-tables

Genetic Variation In Human Populations

Qualitative Weighted Variables

Ponds in a nature reserve

Pair of Variables

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

Frequenting movie theaters in France in 2003

ktab.data.frame

Creation of K-tables from a data frame

ktab.match2ktabs

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

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

Minimal Spanning Tree

Multiblock principal component analysis with instrumental variables

Assemblages of Macroinvertebrates in the Loire River (France)

Multi Level Decomposition of unidimensional data

Multiple Double Principal Coordinate Analysis

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

Faunistic Communities and Sampling Experiment

Multivariate spatial analysis

Genetic/Environment and types of variables

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Transformation of a Distance Matrix for becoming Euclidean

Phylogenetic trees in Newick format

Create phylogeny

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

Principal component analysis with respect to instrumental variables

Multiple Factorial Analysis

Principal Component Analysis with respect to orthogonal instrumental variables

Coinertia Analysis

Global State of the World in 1984

Athletes' Morphology

Correspondence Analysis

Originality of a species

Decentred Correspondence Analysis

Simple Procruste Rotation between two sets of points

Ecomorphological Convergence

Bootstrap simulations

randboot.multiblock

Bootstraped simulations for multiblock methods

multispati.rtest

Multivariate spatial autocorrelation test

Display and summarize multiblock objects

Neighbourhood Graphs

Phylogenetic and quantitative traits of amazonian palm trees

Taxonomy and quantitative traits of carnivora

Phylogeny and trait of bacteria

Nee and May's optimizing process

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

Physico-Chemistry Data

Orthonormal basis for orthonormal transform

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

Representation of an object in a graph by a picture

randtest.discrimin

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

Plot of Paired Coordinates

Plot of the factorial maps in a Multiple Correspondence Analysis

Permutation test for double principal coordinate analysis (DPCoA)

Olympic Decathlon

Plot of the factorial maps of a correlation circle

Simplified Analysis in Principal Coordinates

Plot of a frequency distribution

Distribution of of tropical trees along the Panama canal

Plot phylogenies

A table of Qualitative Variables

Within-Class Analysis

Plant traits response to grazing

Class of the Permutation Tests (in C).

Between-Class Analysis

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

Ordination Table

Avifauna and Vegetation

Plot of the factorial maps for a correspondence analysis

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

Graphical representation of the outputs of a multivariate analysis

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

Graphs to Analyse a factor in PCA

Maximal or minimal amount of originality saved under optimal conditions

Students and Subjects

Contingency Table with a partition in Molecular Biology

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

Graph of a variable using image and contour

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

A class of data: tables of populations and alleles

Relationships between one score and qualitative variables

statico.krandtest

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

1D plot of a numeric score with labels

Plot of the Arrays

Mountain Avifauna

1D plot of a pair of numeric scores with labels

Reconstitution of Data from a Duality Diagram

Graph to Analyse the Relation between a Score and Quantitative Variables

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

Plot of factorial maps with representation of point classes

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

Homogeneous Table

randtest.between

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

Triangular Representation and Groups of points

Vegetation in Trois-Fontaines

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

Point sampling of fish community

Graphs for One Dimension

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

Graphs to study one factor in a Multiple Correspondence Analysis

Multiple Graphs for a Multiple Co-inertia Analysis

randtest.coinertia

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

STATIS, a method for analysing K-tables

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

Example for Centring in PCA

Two-fold cross-validation

rtest.discrimin

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

Partial Triadic Analysis of a K-tables

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

Morphometric Evolution

Trajectory Plot

Projections of Supplementary Rows

Representation of a value in a graph

Representation of a quantitative variable in front of a phylogenetic tree

Plot of the arrays by grey levels

Plot of the Factorial Maps

Multiple Graphs for a Multiple Factorial Analysis

Plot of the factorial maps for a fuzzy correspondence analysis

Multiple Graphs of a STATIS Analysis

Class of the Permutation Tests (in C).

Separated Analyses in a K-tables

Scatterplot of two sets of coordinates and a partionning into classes

Transect in the Vegetation

Graph of frequency profiles (useful for instance in genetic)

testdim.multiblock

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

Reciprocal scaling after a correspondence analysis

Phylogeny and quantitative traits of flowers

Tinto and Odiel estuary geochemistry

Phylogeny and quantitative traits of ungulates.

Morphological Study of the Painted Turtle

Plot arrays in front of a phylogenetic tree

Normed within principal component analysis

Internal Correspondence Analysis

Genetic Relationships between cattle breeds with microsatellites

Transformation of a distance matrice to a Euclidean one

Phylogeny and quantitative traits of teleos fishes

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

Nee and May's random process

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Class of the Permutation Tests (in R).

Results of the French presidential elections of 2002

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

Phylogeny and quantitative traits of birds

Scatter Plot with Kernel Density Estimate

Array of Recapture of Rings

Graphical utility functions

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

Indirect Ordination

Two Questions asked on a Sample of 1000 Respondents

Average temperatures of 30 French cities

Graphs to Analyse a factor in a Mixed Analysis

Plot of Contingency Tables

Projections of Supplementary Columns

Graph Display for Distance Matrices

Projection of additional items in a PCO analysis

Function to perform a test of dimensionality

Triangular Plotting

Examples of taxonomy

Pair of Ecological Data

Elimination of Duplicated Rows in a Array

Distance Matrices

Within-Class Analysis

Road distances in New-Zealand

variance.phylog

The phylogenetic ANOVA

Within-class coinertia analysis

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

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

Within-Class RLQ analysis

Freshwater fish zoogeography in west Africa

French Worker Survey (1970)