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

ade4 (version 1.4-3)

Analysis of Ecological Data : Exploratory and Euclidean methods in Environmental sciences

Description

Multivariate data analysis and graphical display.

Copy Link

Version

Install

install.packages('ade4')

Monthly Downloads

51,023

Version

1.4-3

License

GPL version 2 or newer

Homepage

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

Maintainer

Simon Penel

Last Published

February 14th, 2025

Functions in ade4 (1.4-3)

avimedi

Fauna Table for Constrained Ordinations

score.coa

Graphs to analyse a factor in a correspondence analysis

table.phylog

Plot arrays in front of a phylogenetic tree

palm

Phylogenetic and quantitative traits of amazonian palm trees

randtest.amova

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

rankrock

Ordination Table

reconst

Reconstitution of Data from a Duality Diagram

ade4toR

Format Change Utility

coleo

Table of Fuzzy Biological Traits

ardeche

Fauna Table with double (row and column) partitioning

corvus

Corvus morphology

RV.rtest

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

dist.prop

Computation of Distance Matrices of Percentage Data

coinertia

Coinertia Analysis

dotcircle

Representation of n values on a circle

area.plot

Graphical Display of Areas

atlas

Small Ecological Dataset

divc

Rao's diversity coefficient also called quadratic entropy

friday87

Faunistic K-tables

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

RVdist.randtest

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

disc

Rao's dissimilarity coefficient

between

Between-Class Analysis

dudi.mix

Ordination of Tables mixing quantitative variables and factors

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

bsetal97

Ecological and Biological Traits

Amount of Evolutionary History

PI2newick

Import data files from Phylogenetic Independance Package

add.scatter

Add graphics to an existing plot

banque

Table of Factors

humDNAm

human mitochondrial DNA restriction data

discrimin.coa

Discriminant Correspondence Analysis

bicenter.wt

Double Weighted Centring

dist.genet

Genetic distances from gene frequencies

clementines

Fruit Production

mollusc

Faunistic Communities and Sampling Experiment

carni70

Phylogeny and quantitative traits of carnivora

capitales

Road Distances

dpcoa

Double principal coordinate analysis

ecg

Electrocardiogram data

cnc2003

Frequenting movie theaters in France in 2003

bacteria

Genomes of 43 Bacteria

bf88

Cubic Ecological Data

carni19

Phylogeny and quantative trait of carnivora

dist.quant

Computation of Distance Matrices on Quantitative Variables

discrimin

Linear Discriminant Analysis (descriptive statistic)

aviurba

Ecological Tables Triplet

lascaux

Genetic/Environment and types of variables

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

chatcat

Qualitative Weighted Variables

ggtortoises

Microsatellites of Galapagos tortoises populations

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

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

atya

Genetic variability of Cacadors

macon

Wine Tasting

dudi.acm

Multiple Correspondence Analysis

amova

Analysis of molecular variance

cailliez

Transformation to make Euclidean a distance matrix

divcmax

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

escopage

K-tables of wine-tasting

jv73

K-tables Multi-Regions

neig

Neighbourhood Graphs

orthogram

Orthonormal decomposition of variance

krandtest

Class of the Permutation Tests (in C).

cca

Canonical Correspondence Analysis

Fission pattern and heritable morphological traits

buech

Buech basin

kdist

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

s.logo

Representation of an object in a graph by a picture

is.euclid

Is a Distance Matrix Euclidean ?

ktab.list.df

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

lizards

Phylogeny and quantitative traits of lizards

Computation of the Distance Matrix associated to a Neighbouring Graph

rtest

Class of the Permutation Tests (in R).

dudi.pco

Principal Coordinates Analysis

gridrowcol

Complete regular grid analysis

gearymoran

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

chevaine

Enzymatic polymorphism in Leuciscus cephalus

deug

Exam marks for some students

baran95

African Estuary Fishes

butterfly

Genetics-Ecology-Environment Triple

casitas

Enzymatic polymorphism in Mus musculus

arrival

Arrivals at an intensive care unit

ecomor

Ecomorphological Convergence

dudi.nsc

Non symmetric correspondence analysis

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

kdisteuclid

a way to obtain Euclidean distance matrices

originality

Originality of a species

s.distri

Plot of a frequency distribution

orisaved

Maximal or minimal amount of originality saved under optimal conditions

sco.boxplot

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

genet

A class of data: tables of populations and alleles

kplot.statis

Multiple Graphs of a STATIS Analysis

plot.phylog

Plot phylogenies

inertia.dudi

Statistics of inertia in a one-table analysis

meaudret

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

procuste

Simple Procruste Rotation between two sets of points

dudi

Duality Diagram

pcaiv

Principal component analysis with respect to instrumental variables

ichtyo

Point sampling of fish community

s.match

Plot of Paired Coordinates

doubs

Pair of Ecological Tables

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

multispati.rtest

Multivariate spatial autocorrelation test

acacia

Spatial pattern analysis in plant communities

ours

A table of Qualitative Variables

multispati.randtest

Multivariate spatial autocorrelation test (in C)

s.multinom

Graph of frequency profiles (useful for instance in genetic)

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

rpjdl

Avifauna and Vegetation

tortues

Morphological Study of the Painted Turtle

abouheif.eg

Phylogenies and quantitative traits from Abouheif

ktab.within

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

mariages

Correspondence Analysis Table

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

procella

Phylogeny and quantitative traits of birds

dudi.coa

Correspondence Analysis

kcponds

Ponds in a nature reserve

mstree

Minimal Spanning Tree

rhone

Physico-Chemistry Data

syndicats

Two Questions asked on a Sample of 1000 Respondents

randtest

Class of the Permutation Tests (in C).

multispati

Multivariate spatial analysis

fruits

Pair of Tables

perthi02

Contingency Table with a partition in Molecular Biology

maples

Phylogeny and quantitative traits of flowers

procuste.rtest

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

sco.distri

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

lingoes

Transformation of a Distance Matrix for becoming Euclidean

scatter.coa

Plot of the factorial maps for a correspondence analysis

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

randtest.between

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

granulo

Granulometric Curves

s.hist

Display of a scatterplot and its two marginal histograms

randEH

Nee and May's random process

randtest-internal

Internal Permutation Tests functions (in C).

dudi.dec

Decentred Correspondence Analysis

ktab.match2ktabs

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

avijons

Bird species distribution

njplot

Phylogeny and trait of bacteria

hdpg

Genetic Variation In Human Populations

foucart

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

Average temperatures of 30 French cities

table.value

Plot of the Arrays

mcoa

Multiple CO-inertia Analysis

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

tarentaise

Mountain Avifauna

niche

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

table.cont

Plot of Contingency Tables

table.paint

Plot of the arrays by grey levels

irishdata

Geary's Irish Data

procuste.randtest

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

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

dist.binary

Computation of Distance Matrices for Binary Data

score.pca

Graphs to Analyse a factor in PCA

dudi.pca

Principal Component Analysis

newick.eg

Phylogenetic trees in Newick format

orthobasis

Orthonormal basis for orthonormal transform

ktab.list.dudi

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

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

mld

Multi Level Decomposition of unidimensional data

fuzzygenet

Reading a table of genetic data (diploid individuals)

olympic

Olympic Decathlon

skulls

Morphometric Evolution

ktab.data.frame

Creation of K-tables from a data frame

randtest.coinertia

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

newick2phylog

Create phylogeny

within.pca

Normed within Principal Component Analysis

meau

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

ktab

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

tintoodiel

Tinto and Odiel estuary geochemistry

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

s.arrow

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

scalewt

Centring and Scaling a Matrix of Any Weighting

pap

Taxonomy and quantitative traits of carnivora

mafragh

Phyto-Ecological Survey

mjrochet

Phylogeny and quantitative traits of teleos fishes

seconde

Students and Subjects

pcoscaled

Simplified Analysis in Principal Coordinates

microsatt

Genetic Relationships between cattle breeds with microsatellites

scatter.dudi

Plot of the Factorial Maps

s.image

Graph of a variable using image and contour

pta

Partial Triadic Analysis of a K-tables

quasieuclid

Transformation of a distance matrice to a Euclidean one

mantel.randtest

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

westafrica

Freshwater fish zoogeography in west Africa

presid2002

Results of the French presidential elections of 2002

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

ungulates

Phylogeny and quantitative traits of ungulates.

witwit.coa

Internal Correspondence Analysis

toxicity

Homogeneous Table

rtest.discrimin

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

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

Triangular Representation and Groups of points

statis

STATIS, a method for analysing K-tables

uniquewt.df

Elimination of Duplicated Rows in a Array

monde84

Global State of the World in 1984

score

Graphs for One Dimension

rtest.between

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

variance.phylog

The phylogenetic ANOVA

mantel.rtest

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

s.corcircle

Plot of the factorial maps of a correlation circle

suprow

Projections of Supplementary Rows

table.dist

Graph Display for Distance Matrices

supcol

Projections of Supplementary Columns

veuvage

Example for Centring in PCA

oribatid

Oribatid mite

s.value

Representation of a value in a graph

tithonia

Phylogeny and quantitative traits of flowers

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

yanomama

Distance Matrices

mfa

Multiple Factorial Analysis

zealand

Road distances in New-Zealand

trichometeo

Pair of Ecological Data

sarcelles

Array of Recapture of Rings

optimEH

Nee and May's optimizing process

s.chull

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

s.class

Plot of factorial maps with representation of point classes

s.kde2d

Scatter Plot with Kernel Density Estimate

s.label

Scatter Plot

score.mix

Graphs to Analyse a factor in a Mixed Analysis

within

Within Analyses

sepan

Separated Analyses in a K-tables

worksurv

French Worker Survey (1970)

dunedata

Dune Meadow Data

steppe

Transect in the Vegetation