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ade4 (version 1.7-15)

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

38,204

Version

1.7-15

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

February 13th, 2020

Functions in ade4 (1.7-15)

Deprecated functions

Deprecated functions in ade4

Spatial pattern analysis in plant communities

Graphical Display of Areas

Internal ade4 functions

Arrivals at an intensive care unit

Add graphics to an existing plot

Small Ecological Dataset

Genetic variability of Cacadors

The ade4 package

adegraphicsLoaded

Utility function to test if the package adegraphics is loaded

Bird species distribution

Analysis of molecular variance

RVdist.randtest

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

Fauna Table for Constrained Ordinations

Ecological Tables Triplet

Genomes of 43 Bacteria

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

Table of Factors

Import data files from Phylogenetic Independance Package

Ecological and Biological Traits

Phylogeny and quantative trait of carnivora

Genetics-Ecology-Environment Triple

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

Corvus morphology

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

Phylogeny and quantitative traits of carnivora

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

Allelic frequencies in ten honeybees populations at eight microsatellites loci

Rao's diversity coefficient also called quadratic entropy

Charolais-Zebus

Phylogenies and quantitative traits from Abouheif

Duality Diagram

Apportionment of Quadratic Entropy

Enzymatic polymorphism in Leuciscus cephalus

Distribution of Alpine plants in Aravo (Valloire, France)

Pair of Variables

Fauna Table with double (row and column) partitioning

Exam marks for some students

Rao's dissimilarity coefficient

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

Ordination of Tables mixing quantitative variables and factors

costatis.randtest

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

African Estuary Fishes

Computation of the Distance Matrix from a Statistical Triplet

Computation of Distance Matrices for Binary Data

Functions to compute the fourth-corner statistic

Multiple Correspondence Analysis

Non symmetric correspondence analysis

Dagnelie multinormality test

Between-Class Analysis

Geary's Irish Data

Faunistic K-tables

Decentred Correspondence Analysis

Triangular Data

K-tables of wine-tasting

Correspondence Analysis

Class of the Permutation Tests (in C).

Is a Distance Matrix Euclidean?

Linear Discriminant Analysis (descriptive statistic)

Microsatellites of Galapagos tortoises populations

Cubic Ecological Data

Multiple Graphs of a STATIS Analysis

Double Weighted Centring

Multiple Graphs for a Partial Triadic Analysis

Multiple Graphs for Separated Analyses in a K-tables

ktab.data.frame

Creation of K-tables from a data frame

Ponds in a nature reserve

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

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

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

Enzymatic polymorphism in Mus musculus

Phylogeny and quantitative traits of flowers

Granulometric Curves

Global State of the World in 1984

Phylogeny and quantitative traits of lizards

Discriminant Correspondence Analysis

Athletes' Morphology

Between-Class Analysis

Multivariate spatial analysis

Originality of a species

multispati.randtest

Multivariate spatial autocorrelation test (in C)

Plant traits response to grazing

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

Between-Class RLQ analysis

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

Tests of randomization between distances applied to 'kdist' objetcs

Mixed-variables coefficient of distance

Computation of the Distance Matrix associated to a Neighbouring Graph

Pair of Ecological Tables

Double principal coordinate analysis

Between-class coinertia analysis

Multiple CO-inertia Analysis

Dune Meadow Data

Multiblock partial least squares

Principal Component Analysis

Qualitative Weighted Variables

Ordination of Tables mixing quantitative variables and factors

Principal Coordinates Analysis

Bootstrap simulations

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

Between- and within-class double principal coordinate analysis

Genetic Variation In Human Populations

Display of a scatterplot and its two marginal histograms

Plot of a frequency distribution

Transformation to make Euclidean a distance matrix

Complete regular grid analysis

Reconstitution of Data from a Duality Diagram

Plot of Paired Coordinates

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

Fission pattern and heritable morphological traits

K-tables Multi-Regions

Multiple Double Principal Coordinate Analysis

Frequenting movie theaters in France in 2003

Transformation of a distance matrice to a Euclidean one

Multiple Graphs for a Multiple Factorial Analysis

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

Fruit Production

Electrocardiogram data

Table of Fuzzy Biological Traits

Scatterplot of two sets of coordinates and a partionning into classes

Multiple Graphs for a Multiple Co-inertia Analysis

ktab.match2ktabs

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

Phyto-Ecological Survey

Coinertia Analysis

Computation of Distance Matrices of Percentage Data

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

Computation of Distance Matrices on Quantitative Variables

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

Point sampling of fish community

Phylogenetic trees in Newick format

Representation of n values on a circle

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

mantel.randtest

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

Ecomorphological Convergence

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

Orthonormal basis for orthonormal transform

Graphical representation of the outputs of a multivariate analysis

Plot of the factorial maps in a Multiple Correspondence Analysis

Create phylogeny

Genetic/Environment and types of variables

a way to obtain Euclidean distance matrices

A table of Qualitative Variables

Plot phylogenies

Display and summarize multiblock objects

Graphs to study one factor in a Multiple Correspondence Analysis

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

STATIS, a method for analysing K-tables

Multi Level Decomposition of unidimensional data

Faunistic Communities and Sampling Experiment

Minimal Spanning Tree

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

Representation of a quantitative variable in front of a phylogenetic tree

Reciprocal scaling after a correspondence analysis

Within-Class Analysis

Principal component analysis with respect to instrumental variables

statico.krandtest

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

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

Tinto and Odiel estuary geochemistry

testdim.multiblock

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

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

Assemblages of Macroinvertebrates in the Loire River (France)

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

Phylogeny and quantitative traits of teleos fishes

Results of the French presidential elections of 2002

Within-class coinertia analysis

Phylogeny and quantitative traits of birds

Transformation of a Distance Matrix for becoming Euclidean

Principal Component Analysis with respect to orthogonal instrumental variables

Contingency Table

Genetic Relationships between cattle breeds with microsatellites

Within-Class Analysis

randtest.between

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

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

rtest.discrimin

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

Multiple Graphs for the Foucart's Correspondence Analysis

Generic Function for Multiple Graphs in a K-tables Analysis

randtest.discrimin

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

Phylogeny and trait of bacteria

human mitochondrial DNA restriction data

procuste.randtest

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

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

Representation of a value in a graph

Ordination Table

Simple Procruste Rotation between two sets of points

Indirect Ordination

Array of Recapture of Rings

Two-fold cross-validation

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

randtest.coinertia

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

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

Avifauna and Vegetation

1D plot of a numeric score with labels

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

1D plot of a pair of numeric scores with labels

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

Average temperatures of 30 French cities

Morphometric Evolution

Two Questions asked on a Sample of 1000 Respondents

Pair of Ecological Data

Class of the Permutation Tests (in R).

Graph of frequency profiles (useful for instance in genetic)

Correspondence Analysis Table

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

Within-Class RLQ analysis

randboot.multiblock

Bootstraped simulations for multiblock methods

Olympic Decathlon

Multiblock principal component analysis with instrumental variables

Triangular Plotting

Simplified Analysis in Principal Coordinates

Distribution of of tropical trees along the Panama canal

French Worker Survey (1970)

Trajectory Plot

Physico-Chemistry Data

multispati.rtest

Multivariate spatial autocorrelation test

Multiple Factorial Analysis

Class of the Permutation Tests (in C).

Plot of the factorial maps for a correspondence analysis

Freshwater fish zoogeography in west Africa

Graphs to Analyse a factor in PCA

Plot of the Factorial Maps

Plot of factorial maps with representation of point classes

Phylogenetic and quantitative traits of amazonian palm trees

Plot of the factorial maps of a correlation circle

Neighbourhood Graphs

Taxonomy and quantitative traits of carnivora

Plot arrays in front of a phylogenetic tree

Transect in the Vegetation

Projections of Supplementary Columns

Plot of the arrays by grey levels

Contingency Table with a partition in Molecular Biology

Graphs to Analyse a factor in a Mixed Analysis

Normed within principal component analysis

Partial Triadic Analysis of a K-tables

Representation of an object in a graph by a picture

Phylogeny and quantitative traits of ungulates.

Homogeneous Table

Permutation test for double principal coordinate analysis (DPCoA)

Triangular Representation and Groups of points

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

Internal Correspondence Analysis

Elimination of Duplicated Rows in a Array

Graph to Analyse the Relation between a Score and Quantitative Variables

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

Road distances in New-Zealand

Distance Matrices

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

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

Graphs for One Dimension

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

Projection of additional items in a PCO analysis

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

Graph of a variable using image and contour

Projections of Supplementary Rows

Scatter Plot with Kernel Density Estimate

Example for Centring in PCA

Function to perform a test of dimensionality

Mountain Avifauna

Vegetation in Trois-Fontaines

Plot of the Arrays

Plot of the factorial maps for a fuzzy correspondence analysis

Examples of taxonomy

Graphical utility functions

Relationships between one score and qualitative variables

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

Students and Subjects

Plot of Contingency Tables

Separated Analyses in a K-tables

Phylogeny and quantitative traits of flowers

Graph Display for Distance Matrices

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

variance.phylog

The phylogenetic ANOVA

Morphological Study of the Painted Turtle