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ade4 (version 1.3-2)

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

Description

Multivariate data analysis and graphical display.

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Version

Install

install.packages('ade4')

Monthly Downloads

38,204

Version

1.3-2

License

GPL version 2 or newer

Homepage

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

Maintainer

Jean Thioulouse

Last Published

February 14th, 2025

Functions in ade4 (1.3-2)

acacia

Spatial pattern analysis in plant communities

randtest.amova

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

discrimin.coa

Discriminant Correspondence Analysis

area.plot

Graphical Display of Areas

scatter

Scatter Plot

atlas

Small Ecological Dataset

arrival

Arrivals at an intensive care unit

Computation of Distance Matrices of Percentage Data

dudi.dec

Decentred Correspondence Analysis

ktab.list.dudi

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

mariages

Correspondence Analysis Table

carni70

Phylogeny and quantitative traits of carnivora

rtest

Class of the Permutation Tests (in R).

ardeche

Fauna Table with double (row and column) partitioning

score.coa

Graphs to analyse a factor in a correspondence analysis

dist.genet

Genetic distances from gene frequencies

casitas

Enzymatic polymorphism in Mus musculus

humDNAm

human mitochondrial DNA restriction data

multispati.rtest

Multivariate spatial autocorrelation test

bsetal97

Ecological and Biological Traits

RVdist.randtest

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

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

as.taxo

Taxonomy

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

s.match

Plot of Paired Coordinates

avimedi

Fauna Table for Constrained Ordinations

ichtyo

Point sampling of fish community

Ecological Tables Triplet

divcmax

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

ktab.match2ktabs

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

dudi

Duality Diagram

randtest-internal

Internal Permutation Tests functions (in C).

bf88

Cubic Ecological Data

niche

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

fruits

Pair of Tables

s.kde2d

Scatter Plot with Kernel Density Estimate

s.traject

Trajectory Plot

deug

Exam marks for some students

cca

Canonical Correspondence Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

between

Between-Class Analysis

ecg

Electrocardiogram data

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

kdisteuclid

a way to obtain Euclidean distance matrices

rpjdl

Avifauna and Vegetation

s.hist

Display of a scatterplot and its two marginal histograms

krandtest

Class of the Permutation Tests (in C).

mstree

Minimal Spanning Tree

suprow

Projections of Supplementary Rows

maples

Phylogeny and quantitative traits of flowers

ours

A table of Qualitative Variables

ade4toR

Format Change Utility

procuste.randtest

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

perthi02

Contingency Table with a partition in Molecular Biology

randtest

Class of the Permutation Tests (in C).

multispati.randtest

Multivariate spatial autocorrelation test (in C)

rtest.discrimin

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

plot.phylog

Plot phylogenies

uniquewt.df

Elimination of Duplicated Rows in a Array

dudi.fca

Fuzzy Correspondence Analysis

dudi.pca

Principal Component Analysis

pap

Taxonomy and quantitative traits of carnivora

mantel.rtest

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

gearymoran

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

quasieuclid

Transformation of a distance matrice to a Euclidean one

reconst

Reconstitution of Data from a Duality Diagram

RV.rtest

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

mcoa

Multiple CO-inertia Analysis

mantel.randtest

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

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

table.cont

Plot of Contingency Tables

sepan

Separated Analyses in a K-tables

aminoacyl

Codon usage

skulls

Morphometric Evolution

bicenter.wt

Double Weighted Centring

coinertia

Coinertia Analysis

atya

Genetic variability of Cacadors

olympic

Olympic Decathlon

tintoodiel

Tinto and Odiel estuary geochemistry

PI2newick

Import data files from Phylogenetic Independance Package

randtest.between

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

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

abouheif.eg

Phylogenies and quantitative traits from Abouheif

carni19

Phylogeny and quantative trait of carnivora

banque

Table of Factors

dist.dudi

Computation of the Distance Matrix of a Statistical Triplet

lingoes

Transformation of a Distance Matrix for becoming Euclidean

rankrock

Ordination Table

s.distri

Plot of a frequency distribution

s.image

Graph of a variable using image and contour

mafragh

Phyto-Ecological Survey

doubs

Pair of Ecological Tables

inertia.dudi

Statistics of inertia in a one-table analysis

dudi.pco

Principal Coordinates Analysis

variance.phylog

The phylogenetic ANOVA

cnc2003

Frequenting movie theaters in France in 2003

procuste.rtest

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

within

Within Analyses

table.phylog

Plot arrays in front of a phylogenetic tree

s.value

Representation of a value in a graph

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

rhone

Physico-Chemistry Data

Graphs to Analyse a factor in PCA

coleo

Table of Fuzzy Biological Traits

bordeaux

Wine Tasting

table.dist

Graph Display for Distance Matrices

kdist2ktab

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

seconde

Students and Subjects

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

escopage

K-tables of wine-tasting

randtest.coinertia

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

dpcoa

Double principal coordinate analysis

t3012

Average temperatures of 30 French cities

score.mix

Graphs to Analyse a factor in a Mixed Analysis

taxo.eg

Examples of taxonomy

pta

Partial Triadic Analysis of a K-tables

avijons

Bird species distribution

chats

Pair of Variables

baran95

African Estuary Fishes

dist.quant

Computation of Distance Matrices on Quantitative Variables

corvus

Corvus morphology

fission

Fission pattern and heritable morphological traits

divc

Rao's diversity coefficient also called quadratic entropy

triangle.class

Triangular Representation and Groups of points

ecomor

Ecomorphological Convergence

foucart

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

tortues

Morphological Study of the Painted Turtle

dudi.mix

Ordination of Tables mixing quantitative variables and factors

chevaine

Enzymatic polymorphism in Leuciscus cephalus

dudi.acm

Multiple Correspondence Analysis

phylog

Phylogeny

s.corcircle

Plot of the factorial maps of a correlation circle

sarcelles

Array of Recapture of Rings

scatter.acm

Plot of the factorial maps in multiple correspondence analysis

ktab.within

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

yanomama

Distance Matrices

cailliez

Transformation to make Euclidean a distance matrix

chatcat

Qualitative Weighted Variables

worksurv

French Worker Survey (1970)

rlq

RLQ analysis

ungulates

Phylogeny and quantitative traits of ungulates.

disc

Rao's dissimilarity coefficient

lizards

Phylogeny and quantitative traits of lizards

dotcircle

Representation of n values on a circle

newick2phylog

Create phylogeny

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

genet

A class of data: tables of populations and alleles

s.class

Plot of factorial maps with representation of point classes

Normed within Principal Component Analysis

meaudret

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

s.chull

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

kdist

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

mollusc

Faunistic Communities and Sampling Experiment

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

procuste

Simple Procruste Rotation between two sets of points

dudi.coa

Correspondence Analysis

score

Graphs for One Dimension

monde84

Global State of the World in 1984

orthogram

Orthonormal decomposition of variance

witwit.coa

Internal Correspondence Analysis

table.paint

Plot of the arrays by grey levels

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

scalewt

Centring and Scaling a Matrix of Any Weighting

kcponds

Ponds in a nature reserve

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

jv73

K-tables Multi-Regions

kplot.statis

Multiple Graphs of a STATIS Analysis

westafrica

Freshwater fish zoogeography in west Africa

is.euclid

Is a Distance Matrix Euclidean ?

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

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

meau

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

presid2002

Results of the French presidential elections of 2002

mld

Multi Level Decomposition of unidimensional data

orthobasis

Orthonormal basis for orthonormal transform

statis

STATIS, a method for analysing K-tables

gridrowcol

Complete regular grid analysis

zealand

Road distances in New-Zealand

mjrochet

Phylogeny and quantitative traits of teleos fishes

procella

Phylogeny and quantitative traits of birds

njplot

Phylogeny and trait of bacteria

pcaiv

Principal component analysis with respect to instrumental variables

randtest.discrimin

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

neig

Neighbourhood Graphs

rtest.between

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

sco.distri

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

syndicats

Two Questions asked on a Sample of 1000 Respondents

Plot of the factorial maps for a fuzzy correspondence analysis

veuvage

Example for Centring in PCA

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

bacteria

Genomes of 43 Bacteria

Computation of Distance Matrices for Binary Data

ktab

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

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

newick.eg

Phylogenetic trees in Newick format

pcoscaled

Simplified Analysis in Principal Coordinates

butterfly

Genetics-Ecology-Environment Triple

discrimin

Linear Discriminant Analysis (descriptive statistic)

lascaux

Genetic/Environment and types of variables

mfa

Multiple Factorial Analysis

morphosport

Athletes' Morphology

scatter.dudi

Plot of the Factorial Maps

palm

Phylogenetic and quantitative traits of amazonian palm trees

tithonia

Phylogeny and quantitative traits of flowers

scatter.coa

Plot of the factorial maps for a correspondence analysis

fuzzygenet

Reading a table of genetic data (diploid individuals)

dudi.nsc

Non symmetric correspondence analysis

elec88

Electoral Data

amova

Analysis of molecular variance

microsatt

Genetic Relationships between cattle breeds with microsatellites

ktab.data.frame

Creation of K-tables from a data frame

multispati

Multivariate spatial analysis

sco.boxplot

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

trichometeo

Pair of Ecological Data

table.value

Plot of the Arrays

supcol

Projections of Supplementary Columns

dunedata

Dune Meadow Data

steppe

Transect in the Vegetation