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ade4 (version 1.7-22)

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

37,956

Version

1.7-22

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

February 6th, 2023

Functions in ade4 (1.7-22)

RVdist.randtest

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

Arrivals at an intensive care unit

The ade4 package

Deprecated functions

Deprecated functions in ade4

African Estuary Fishes

Spatial pattern analysis in plant communities

Add graphics to an existing plot

Internal ade4 functions

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Small Ecological Dataset

Between-Class Analysis

Genetic variability of Cacadors

Import data files from Phylogenetic Independance Package

Analysis of molecular variance

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in C++ with Rcpp).

Genomes of 43 Bacteria

Table of Factors

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Phylogeny and quantative trait of carnivora

Cubic Ecological Data

Ecological and Biological Traits

Bird species distribution

Coinertia Analysis

Genetics-Ecology-Environment Triple

Table of Fuzzy Biological Traits

Double Weighted Centring

Enzymatic polymorphism in Leuciscus cephalus

Fruit Production

Rao's diversity coefficient also called quadratic entropy

Frequenting movie theaters in France in 2003

Computation of Distance Matrices of Percentage Data

Apportionment of Quadratic Entropy

Fauna Table for Constrained Ordinations

Computation of Distance Matrices on Quantitative Variables

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

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

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

Ecological Tables Triplet

Representation of n values on a circle

Dune Meadow Data

Electrocardiogram data

Microsatellites of Galapagos tortoises populations

Granulometric Curves

Computation of Distance Matrices for Binary Data

Complete regular grid analysis

Genetic Variation In Human Populations

Computation of the Distance Matrix from a Statistical Triplet

Phylogeny and quantitative traits of carnivora

a way to obtain Euclidean distance matrices

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

RVintra.randtest

Monte-Carlo Test on the sum of eigenvalues of a within-class co-inertia analysis (in C++ with Rcpp).

Phylogenies and quantitative traits from Abouheif

Distribution of Alpine plants in Aravo (Valloire, France)

Generic Function for Multiple Graphs in a K-tables Analysis

Correspondence Analysis

Decentred Correspondence Analysis

Fauna Table with double (row and column) partitioning

Between-class coinertia analysis

costatis.randtest

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

Ordination of Tables mixing quantitative variables and factors

Dagnelie multinormality test

Non symmetric correspondence analysis

Linear Discriminant Analysis (descriptive statistic)

Between-Class RLQ analysis

Multiple Graphs for Separated Analyses in a K-tables

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

Functions to compute the fourth-corner statistic

Morphometric data set

Contingency Table

Faunistic K-tables

Multiple Graphs of a STATIS Analysis

Pair of Variables

Between- and within-class double principal coordinate analysis

K-tables Multi-Regions

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

Transformation to make Euclidean a distance matrix

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

Leave-one-out cross-validation for a dudi

Ponds in a nature reserve

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

Discriminant Correspondence Analysis

ktab.match2ktabs

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

Correspondence Analysis Table

Assemblages of Macroinvertebrates in the Loire River (France)

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

Multiple Double Principal Coordinate Analysis

Genetic/Environment and types of variables

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

Enzymatic polymorphism in Mus musculus

Charolais-Zebus

Principal Component Analysis

Phylogeny and quantitative traits of flowers

Phylogeny and quantitative traits of teleos fishes

Genetic Relationships between cattle breeds with microsatellites

Multiblock principal component analysis with instrumental variables

Minimal Spanning Tree

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

Multivariate spatial analysis

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Display and summarize multiblock objects

Principal Coordinates Analysis

Originality of a species

Qualitative Weighted Variables

Corvus morphology

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

Principal component analysis with respect to instrumental variables

Principal Component Analysis with respect to orthogonal instrumental variables

Fission pattern and heritable morphological traits

Reconstitution of Data from a Duality Diagram

Exam marks for some students

Phylogenetic trees in Newick format

Rao's dissimilarity coefficient

Phylogenetic and quantitative traits of amazonian palm trees

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

Is a Distance Matrix Euclidean?

Taxonomy and quantitative traits of carnivora

Create phylogeny

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Tests of randomization between distances applied to 'kdist' objetcs

Duality Diagram

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

Multiple Correspondence Analysis

Contingency Table with a partition in Molecular Biology

Plant traits response to grazing

Plot of factorial maps with representation of point classes

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Mixed-variables coefficient of distance

Plot phylogenies

Ordination of Tables mixing quantitative variables and factors

Plot of the factorial maps of a correlation circle

Representation of a value in a graph

Computation of the Distance Matrix associated to a Neighbouring Graph

Between-Class Analysis

Transformation of a distance matrice to a Euclidean one

Multiple Graphs for the Foucart's Correspondence Analysis

Within-Class Analysis

Bootstrap simulations

Two-fold cross-validation

Pair of Ecological Tables

Multiple Graphs for a Multiple Co-inertia Analysis

Permutation test for double principal coordinate analysis (DPCoA)

K-tables of wine-tasting

Indirect Ordination

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

Triangular Data

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

Geary's Irish Data

ktab.data.frame

Creation of K-tables from a data frame

Class of the Permutation Tests (in C).

Double principal coordinate analysis

Ordination Table

Ecomorphological Convergence

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

Plot of a frequency distribution

Display of a scatterplot and its two marginal histograms

human mitochondrial DNA restriction data

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

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

Graphs to study one factor in a Multiple Correspondence Analysis

Phyto-Ecological Survey

Transformation of a Distance Matrix for becoming Euclidean

mantel.randtest

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

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

Graphical representation of the outputs of a multivariate analysis

Avifauna and Vegetation

Point sampling of fish community

Multiple Graphs for a Multiple Factorial Analysis

Phylogeny and quantitative traits of lizards

Multiple Factorial Analysis

Plot of the factorial maps in a Multiple Correspondence Analysis

Relationships between one score and qualitative variables

Multiblock partial least squares

Class of the Permutation Tests (in R).

Distance Matrices

Multiple CO-inertia Analysis

Global State of the World in 1984

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

Graphs to Analyse a factor in a Mixed Analysis

Athletes' Morphology

Phylogeny and trait of bacteria

Morphometric Evolution

Olympic Decathlon

Graphs to Analyse a factor in PCA

Plot of the factorial maps for a correspondence analysis

statico.krandtest

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

Multiple Graphs for a Partial Triadic Analysis

Leave-one-out cross-validation for a bca

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

loocv.discrimin

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

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

Partial Triadic Analysis of a K-tables

Representation of an object in a graph by a picture

Plot of the Factorial Maps

STATIS, a method for analysing K-tables

Faunistic Communities and Sampling Experiment

Multi Level Decomposition of unidimensional data

Simplified Analysis in Principal Coordinates

Homogeneous Table

Distribution of of tropical trees along the Panama canal

Triangular Representation and Groups of points

Results of the French presidential elections of 2002

randboot.multiblock

Bootstraped simulations for multiblock methods

Within-Class Analysis

Phylogeny and quantitative traits of birds

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

Phylogeny and quantitative traits of flowers

Within-class coinertia analysis

Plot of Paired Coordinates

Scatterplot of two sets of coordinates and a partionning into classes

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

Within-Class RLQ analysis

Graph to Analyse the Relation between a Score and Quantitative Variables

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

randtest.between

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

Class of the Permutation Tests (in C).

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

multispati.rtest

Multivariate spatial autocorrelation test

Graph of frequency profiles (useful for instance in genetic)

Physico-Chemistry Data

rtest.discrimin

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

Representation of a quantitative variable in front of a phylogenetic tree

Road distances in New-Zealand

testdim.multiblock

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

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

Neighbourhood Graphs

Plot of the factorial maps for a fuzzy correspondence analysis

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

Graph of a variable using image and contour

Scatter Plot with Kernel Density Estimate

Orthonormal basis for orthonormal transform

A table of Qualitative Variables

Freshwater fish zoogeography in west Africa

Simple Procruste Rotation between two sets of points

Graphical utility functions

Tinto and Odiel estuary geochemistry

procuste.randtest

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

Morphological Study of the Painted Turtle

Examples of taxonomy

Students and Subjects

Reciprocal scaling after a correspondence analysis

Triangular Plotting

randtest.coinertia

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

randtest.discrimin

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

Array of Recapture of Rings

Graphs for One Dimension

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

Two Questions asked on a Sample of 1000 Respondents

Projections of Supplementary Rows

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

Trajectory Plot

1D plot of a numeric score with labels

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

Projection of additional items in a PCO analysis

Average temperatures of 30 French cities

Mountain Avifauna

1D plot of a pair of numeric scores with labels

Function to perform a test of dimensionality

Transect in the Vegetation

Normed within principal component analysis

Vegetation in Trois-Fontaines

Separated Analyses in a K-tables

Plot of the Arrays

Pair of Ecological Data

Projections of Supplementary Columns

Example for Centring in PCA

Plot of Contingency Tables

Graph Display for Distance Matrices

Plot of the arrays by grey levels

Plot arrays in front of a phylogenetic tree

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

variance.phylog

The phylogenetic ANOVA

Phylogeny and quantitative traits of ungulates.

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

Elimination of Duplicated Rows in a Array

French Worker Survey (1970)

Internal Correspondence Analysis

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

Graphical Display of Areas