Learn R Programming

⚠️There's a newer version (1.7-22) of this package.Take me there.

ade4 (version 1.7-13)

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

33,243

Version

1.7-13

License

GPL (>= 2)

Homepage

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

Maintainer

Aurélie Siberchicot

Last Published

August 31st, 2018

Functions in ade4 (1.7-13)

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

Apportionment of Quadratic Entropy

Distribution of Alpine plants in Aravo (Valloire, France)

Ecological Tables Triplet

Phylogenies and quantitative traits from Abouheif

Genomes of 43 Bacteria

Spatial pattern analysis in plant communities

Between-Class RLQ analysis

Cubic Ecological Data

Table of Fuzzy Biological Traits

Arrivals at an intensive care unit

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Mixed-variables coefficient of distance

Computation of the Distance Matrix associated to a Neighbouring Graph

Table of Factors

African Estuary Fishes

Ordination of Tables mixing quantitative variables and factors

Qualitative Weighted Variables

Non symmetric correspondence analysis

Fission pattern and heritable morphological traits

Pair of Variables

Tests of randomization between distances applied to 'kdist' objetcs

Corvus morphology

Discriminant Correspondence Analysis

Computation of Distance Matrices for Binary Data

Correspondence Analysis

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

Microsatellites of Galapagos tortoises populations

Granulometric Curves

Decentred Correspondence Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Multiple Graphs of a STATIS Analysis

Multiple Graphs for the Foucart's Correspondence Analysis

Class of the Permutation Tests (in C).

Ordination of Tables mixing quantitative variables and factors

Phylogeny and quantitative traits of lizards

Genetic Relationships between cattle breeds with microsatellites

Phylogeny and quantitative traits of teleos fishes

Phylogenetic trees in Newick format

Create phylogeny

Reading a table of genetic data (diploid individuals)

Contingency Table with a partition in Molecular Biology

Geary's Irish Data

Is a Distance Matrix Euclidean?

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

Plot phylogenies

Within-Class Analysis

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).

a way to obtain Euclidean distance matrices

ktab.match2ktabs

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

Add graphics to an existing plot

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

Two-fold cross-validation

Amount of Evolutionary History

Import data files from Phylogenetic Independance Package

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

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Small Ecological Dataset

Genetic variability of Cacadors

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)

Transformation to make Euclidean a distance matrix

Deprecated functions

Deprecated functions in ade4

Graphical utility functions

Graphical representation of the outputs of a multivariate analysis

Analysis of molecular variance

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

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

Between-Class Analysis

Assemblages of Macroinvertebrates in the Loire River (France)

Graphs for One Dimension

Graphs to study one factor in a Multiple Correspondence Analysis

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Phylogeny and quantative trait of carnivora

Between-class coinertia analysis

testdim.multiblock

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

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

Phylogeny and quantitative traits of carnivora

Dagnelie multinormality test

Tinto and Odiel estuary geochemistry

Fauna Table for Constrained Ordinations

Vegetation in Trois-Fontaines

Bird species distribution

Ecological and Biological Traits

Example for Centring in PCA

Exam marks for some students

Double Weighted Centring

Computation of the Distance Matrix from a Statistical Triplet

Distance Matrices

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

Multiple Factorial Analysis

Fruit Production

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Road distances in New-Zealand

Multi Level Decomposition of unidimensional data

Genetic distances from gene frequencies

Rao's dissimilarity coefficient

Duality Diagram

Linear Discriminant Analysis (descriptive statistic)

Multiple Correspondence Analysis

Dune Meadow Data

Faunistic Communities and Sampling Experiment

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

Electrocardiogram data

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Rao's diversity coefficient also called quadratic entropy

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

Simplified Analysis in Principal Coordinates

K-tables of wine-tasting

Triangular Data

Distribution of of tropical trees along the Panama canal

Point sampling of fish community

Internal ade4 functions

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

Enzymatic polymorphism in Mus musculus

Plant traits response to grazing

Ecomorphological Convergence

The ade4 package

Fauna Table with double (row and column) partitioning

Ponds in a nature reserve

Multiblock partial least squares

Multiple CO-inertia Analysis

Between-Class Analysis

Frequenting movie theaters in France in 2003

randtest.discrimin

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

Permutation test for double principal coordinate analysis (DPCoA)

Coinertia Analysis

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Graphical Display of Areas

Genetics-Ecology-Environment Triple

Between- and within-class double principal coordinate analysis

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

Global State of the World in 1984

Charolais-Zebus

Principal Component Analysis

Physico-Chemistry Data

Representation of n values on a circle

Principal Coordinates Analysis

Athletes' Morphology

Faunistic K-tables

Plot of the factorial maps of a correlation circle

Functions to compute the fourth-corner statistic

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

Plot of a frequency distribution

Nee and May's optimizing process

Scatterplot of two sets of coordinates and a partionning into classes

Complete regular grid analysis

Enzymatic polymorphism in Leuciscus cephalus

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

Computation of Distance Matrices of Percentage Data

Graph of frequency profiles (useful for instance in genetic)

costatis.randtest

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

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

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

Computation of Distance Matrices on Quantitative Variables

Principal component analysis with respect to instrumental variables

Principal Component Analysis with respect to orthogonal instrumental variables

Genetic Variation In Human Populations

Simple Procruste Rotation between two sets of points

Genetic/Environment and types of variables

1D plot of a pair of numeric scores with labels

Graph to Analyse the Relation between a Score and Quantitative Variables

K-tables Multi-Regions

procuste.randtest

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

STATIS, a method for analysing K-tables

Transect in the Vegetation

Transformation of a Distance Matrix for becoming Euclidean

Minimal Spanning Tree

Pair of Ecological Tables

Multiple Graphs for a Partial Triadic Analysis

Examples of taxonomy

Function to perform a test of dimensionality

Multiple Graphs for Separated Analyses in a K-tables

Transformation of a distance matrice to a Euclidean one

Phylogeny and quantitative traits of flowers

Morphological Study of the Painted Turtle

Double principal coordinate analysis

Nee and May's random process

Display and summarize multiblock objects

Class of the Permutation Tests (in R).

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

Within-Class RLQ analysis

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

Orthonormal basis for orthonormal transform

A table of Qualitative Variables

Results of the French presidential elections of 2002

Phylogeny and quantitative traits of birds

Scatter Plot with Kernel Density Estimate

Phyto-Ecological Survey

Avifauna and Vegetation

Contingency Table

Freshwater fish zoogeography in west Africa

A class of data: tables of populations and alleles

Display of a scatterplot and its two marginal histograms

human mitochondrial DNA restriction data

Graph of a variable using image and contour

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

Trajectory Plot

Representation of a value in a graph

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

Separated Analyses in a K-tables

mantel.randtest

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

Morphometric Evolution

Plot of the factorial maps in a Multiple Correspondence Analysis

Multiple Double Principal Coordinate Analysis

Projections of Supplementary Rows

Representation of a quantitative variable in front of a phylogenetic tree

Multiple Graphs for a Multiple Co-inertia Analysis

Plot of the factorial maps for a correspondence analysis

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

Multiple Graphs for a Multiple Factorial Analysis

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

ktab.data.frame

Creation of K-tables from a data frame

Neighbourhood Graphs

multispati.rtest

Multivariate spatial autocorrelation test

Plot of the Arrays

Mountain Avifauna

Homogeneous Table

Originality of a species

Reciprocal scaling after a correspondence analysis

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

Graphs to Analyse a factor in a Mixed Analysis

Maximal or minimal amount of originality saved under optimal conditions

Two Questions asked on a Sample of 1000 Respondents

Bootstrap simulations

Within-Class Analysis

Within-class coinertia analysis

Phylogeny and quantitative traits of flowers

Average temperatures of 30 French cities

Triangular Representation and Groups of points

Plot of Contingency Tables

Correspondence Analysis Table

randboot.multiblock

Bootstraped simulations for multiblock methods

Multivariate spatial analysis

Multiblock principal component analysis with instrumental variables

Graph Display for Distance Matrices

Triangular Plotting

Phylogeny and trait of bacteria

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Pair of Ecological Data

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

Olympic Decathlon

French Worker Survey (1970)

Phylogenetic and quantitative traits of amazonian palm trees

Ordination Table

Taxonomy and quantitative traits of carnivora

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

Reconstitution of Data from a Duality Diagram

Partial Triadic Analysis of a K-tables

Class of the Permutation Tests (in C).

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

rtest.discrimin

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

Indirect Ordination

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

Array of Recapture of Rings

Plot of the Factorial Maps

Representation of an object in a graph by a picture

Plot of the factorial maps for a fuzzy correspondence analysis

Plot of Paired Coordinates

Relationships between one score and qualitative variables

1D plot of a numeric score with labels

Graphs to Analyse a factor in PCA

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

Students and Subjects

Projections of Supplementary Columns

Phylogeny and quantitative traits of ungulates.

Elimination of Duplicated Rows in a Array

statico.krandtest

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

Projection of additional items in a PCO analysis

Plot of the arrays by grey levels

Plot arrays in front of a phylogenetic tree

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

variance.phylog

The phylogenetic ANOVA

Internal Correspondence Analysis

Normed within principal component analysis

RVdist.randtest

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