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ade4 (version 1.7-11)

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

40,590

Version

1.7-11

License

GPL (>= 2)

Homepage

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

Maintainer

Aurélie Siberchicot

Last Published

April 5th, 2018

Functions in ade4 (1.7-11)

Frequenting movie theaters in France in 2003

Principal Component Analysis

Is a Distance Matrix Euclidean?

Amount of Evolutionary History

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

Enzymatic polymorphism in Leuciscus cephalus

Phyto-Ecological Survey

Computation of Distance Matrices on Quantitative Variables

Analysis of molecular variance

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

Table of Factors

RVdist.randtest

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

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Multiple Correspondence Analysis

African Estuary Fishes

Corvus morphology

Duality Diagram

Double Weighted Centring

Import data files from Phylogenetic Independance Package

Correspondence Analysis

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Charolais-Zebus

Exam marks for some students

Computation of Distance Matrices for Binary Data

Discriminant Correspondence Analysis

Coinertia Analysis

Fauna Table for Constrained Ordinations

Principal Coordinates Analysis

Bird species distribution

Ecological and Biological Traits

Dune Meadow Data

Rao's diversity coefficient also called quadratic entropy

Decentred Correspondence Analysis

Enzymatic polymorphism in Mus musculus

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Minimal Spanning Tree

Internal ade4 functions

Geary's Irish Data

Dagnelie multinormality test

The ade4 package

Tests of randomization between distances applied to 'kdist' objetcs

Apportionment of Quadratic Entropy

Distribution of Alpine plants in Aravo (Valloire, France)

Small Ecological Dataset

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

Genetic variability of Cacadors

Genetics-Ecology-Environment Triple

Reading a table of genetic data (diploid individuals)

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Between- and within-class double principal coordinate analysis

Contingency Table

Genetic distances from gene frequencies

Qualitative Weighted Variables

Pair of Variables

Fission pattern and heritable morphological traits

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

Electrocardiogram data

Generic Function for Multiple Graphs in a K-tables Analysis

Rao's dissimilarity coefficient

Fruit Production

Assemblages of Macroinvertebrates in the Loire River (France)

Computation of Distance Matrices of Percentage Data

Add graphics to an existing plot

Correspondence Analysis Table

Multiple Graphs for the Foucart's Correspondence Analysis

ktab.match2ktabs

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

Multiple Graphs for a Partial Triadic Analysis

Linear Discriminant Analysis (descriptive statistic)

K-tables of wine-tasting

Multiple Graphs of a STATIS Analysis

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

Deprecated functions

Deprecated functions in ade4

Triangular Data

Arrivals at an intensive care unit

Nee and May's optimizing process

Class of the Permutation Tests (in C).

Ecomorphological Convergence

Multiple CO-inertia Analysis

Point sampling of fish community

Faunistic K-tables

Scatter Plot with Kernel Density Estimate

Phylogenies and quantitative traits from Abouheif

Multiblock principal component analysis with instrumental variables

Between-Class Analysis

K-tables Multi-Regions

Pair of Ecological Tables

Multiblock partial least squares

Phylogeny and quantitative traits of lizards

Multiple Graphs for Separated Analyses in a K-tables

Olympic Decathlon

Display and summarize multiblock objects

Between-class coinertia analysis

Class of the Permutation Tests (in C).

Functions to compute the fourth-corner statistic

human mitochondrial DNA restriction data

Array of Recapture of Rings

Phylogeny and trait of bacteria

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Projections of Supplementary Columns

Faunistic Communities and Sampling Experiment

Between-Class RLQ analysis

Multi Level Decomposition of unidimensional data

Plant traits response to grazing

Phylogeny and quantitative traits of teleos fishes

Ordination Table

Computation of the Distance Matrix associated to a Neighbouring Graph

Cubic Ecological Data

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

a way to obtain Euclidean distance matrices

Partial Triadic Analysis of a K-tables

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

Simplified Analysis in Principal Coordinates

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

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

Distribution of of tropical trees along the Panama canal

Computation of the Distance Matrix from a Statistical Triplet

testdim.multiblock

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

Phylogeny and quantitative traits of carnivora

costatis.randtest

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

A class of data: tables of populations and alleles

Global State of the World in 1984

Principal Component Analysis with respect to orthogonal instrumental variables

mantel.randtest

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

Principal component analysis with respect to instrumental variables

Create phylogeny

Complete regular grid analysis

Avifauna and Vegetation

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

Representation of n values on a circle

Spatial pattern analysis in plant communities

Between-Class Analysis

Transformation of a Distance Matrix for becoming Euclidean

Representation of an object in a graph by a picture

Plot of the factorial maps for a fuzzy correspondence analysis

Ponds in a nature reserve

Bootstrap simulations

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

randboot.multiblock

Bootstraped simulations for multiblock methods

Students and Subjects

Fauna Table with double (row and column) partitioning

Ordination of Tables mixing quantitative variables and factors

Reconstitution of Data from a Duality Diagram

Graphical Display of Areas

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

Ecological Tables Triplet

Genetic Variation In Human Populations

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

Athletes' Morphology

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

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

Genomes of 43 Bacteria

Transformation to make Euclidean a distance matrix

Genetic Relationships between cattle breeds with microsatellites

Indirect Ordination

Neighbourhood Graphs

Projections of Supplementary Rows

Phylogeny and quantative trait of carnivora

Genetic/Environment and types of variables

Display of a scatterplot and its two marginal histograms

Plot of Paired Coordinates

Graph of a variable using image and contour

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

Projection of additional items in a PCO analysis

Reciprocal scaling after a correspondence analysis

Phylogenetic trees in Newick format

multispati.rtest

Multivariate spatial autocorrelation test

Taxonomy and quantitative traits of carnivora

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

Graphs to Analyse a factor in PCA

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

Originality of a species

Graphs to Analyse a factor in a Mixed Analysis

Plot of the arrays by grey levels

Phylogenetic and quantitative traits of amazonian palm trees

Internal Correspondence Analysis

Pair of Ecological Data

Plot arrays in front of a phylogenetic tree

Triangular Plotting

Table of Fuzzy Biological Traits

ktab.data.frame

Creation of K-tables from a data frame

Mixed-variables coefficient of distance

Plot of the Factorial Maps

Tinto and Odiel estuary geochemistry

Normed within principal component analysis

Distance Matrices

Triangular Representation and Groups of points

Multiple Factorial Analysis

randtest.discrimin

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

Road distances in New-Zealand

Physico-Chemistry Data

Ordination of Tables mixing quantitative variables and factors

Permutation test for double principal coordinate analysis (DPCoA)

Multiple Graphs for a Multiple Co-inertia Analysis

Results of the French presidential elections of 2002

Transformation of a distance matrice to a Euclidean one

Representation of a quantitative variable in front of a phylogenetic tree

Scatterplot of two sets of coordinates and a partionning into classes

Phylogeny and quantitative traits of birds

Non symmetric correspondence analysis

Double principal coordinate analysis

Simple Procruste Rotation between two sets of points

Microsatellites of Galapagos tortoises populations

Multiple Graphs for a Multiple Factorial Analysis

Maximal or minimal amount of originality saved under optimal conditions

Two-fold cross-validation

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

Contingency Table with a partition in Molecular Biology

Plot of the factorial maps in a Multiple Correspondence Analysis

Granulometric Curves

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

Homogeneous Table

Nee and May's random process

Mountain Avifauna

Graph Display for Distance Matrices

Within-Class RLQ analysis

procuste.randtest

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

Freshwater fish zoogeography in west Africa

A table of Qualitative Variables

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

Plot phylogenies

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

rtest.discrimin

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

Plot of factorial maps with representation of point classes

Example for Centring in PCA

Morphometric Evolution

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

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

Plot of the factorial maps for a correspondence analysis

Graphical representation of the outputs of a multivariate analysis

Graph of frequency profiles (useful for instance in genetic)

Plot of the factorial maps of a correlation circle

Separated Analyses in a 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)

Morphological Study of the Painted Turtle

Graph to Analyse the Relation between a Score and Quantitative Variables

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Phylogeny and quantitative traits of flowers

Average temperatures of 30 French cities

Multiple Double Principal Coordinate Analysis

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

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

Multivariate spatial analysis

Graphical utility functions

STATIS, a method for analysing K-tables

Plot of the Arrays

Vegetation in Trois-Fontaines

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

1D plot of a pair of numeric scores with labels

Plot of Contingency Tables

Within-Class Analysis

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Transect in the Vegetation

Phylogeny and quantitative traits of flowers

Orthonormal basis for orthonormal transform

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

Within-Class Analysis

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

Within-class coinertia analysis

variance.phylog

The phylogenetic ANOVA

Trajectory Plot

randtest.between

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

Graphs to study one factor in a Multiple Correspondence Analysis

Representation of a value in a graph

Class of the Permutation Tests (in R).

Relationships between one score and qualitative variables

randtest.coinertia

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

Plot of a frequency distribution

French Worker Survey (1970)

statico.krandtest

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

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

1D plot of a numeric score with labels

Graphs for One Dimension

Phylogeny and quantitative traits of ungulates.

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

Examples of taxonomy

Function to perform a test of dimensionality

Elimination of Duplicated Rows in a Array