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ade4 (version 1.3-3)

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

40,590

Version

1.3-3

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 (1.3-3)

score.pca

Graphs to Analyse a factor in PCA

Projections of Supplementary Columns

scatter.dudi

Plot of the Factorial Maps

table.dist

Graph Display for Distance Matrices

yanomama

Distance Matrices

score.mix

Graphs to Analyse a factor in a Mixed Analysis

syndicats

Two Questions asked on a Sample of 1000 Respondents

uniquewt.df

Elimination of Duplicated Rows in a Array

ungulates

Phylogeny and quantitative traits of ungulates.

table.phylog

Plot arrays in front of a phylogenetic tree

variance.phylog

The phylogenetic ANOVA

t3012

Average temperatures of 30 French cities

triangle.plot

Triangular Plotting

score.coa

Graphs to analyse a factor in a correspondence analysis

tortues

Morphological Study of the Painted Turtle

seconde

Students and Subjects

scatter.coa

Plot of the factorial maps for a correspondence analysis

sco.boxplot

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

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

score

Graphs for One Dimension

worksurv

French Worker Survey (1970)

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

zealand

Road distances in New-Zealand

within

Within Analyses

table.paint

Plot of the arrays by grey levels

scatter.acm

Plot of the factorial maps in multiple correspondence analysis

suprow

Projections of Supplementary Rows

statis

STATIS, a method for analysing K-tables

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

tarentaise

Mountain Avifauna

tintoodiel

Tinto and Odiel estuary geochemistry

table.cont

Plot of Contingency Tables

table.value

Plot of the Arrays

trichometeo

Pair of Ecological Data

triangle.class

Triangular Representation and Groups of points

westafrica

Freshwater fish zoogeography in west Africa

as.taxo

Taxonomy

casitas

Enzymatic polymorphism in Mus musculus

atya

Genetic variability of Cacadors

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

coleo

Table of Fuzzy Biological Traits

bsetal97

Ecological and Biological Traits

kdist

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

abouheif.eg

Phylogenies and quantitative traits from Abouheif

multispati

Multivariate spatial analysis

rtest

Class of the Permutation Tests (in R).

s.arrow

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

Phylogenetic and quantitative traits of amazonian palm trees

mcoa

Multiple CO-inertia Analysis

atlas

Small Ecological Dataset

arrival

Arrivals at an intensive care unit

ktab.match2ktabs

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

euro123

Triangular Data

orthobasis

Orthonormal basis for orthonormal transform

randtest

Class of the Permutation Tests (in C).

bicenter.wt

Double Weighted Centring

genet

A class of data: tables of populations and alleles

niche

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

Bird species distribution

inertia.dudi

Statistics of inertia in a one-table analysis

chazeb

Charolais-Zebus

pap

Taxonomy and quantitative traits of carnivora

dudi.acm

Multiple Correspondence Analysis

PI2newick

Import data files from Phylogenetic Independance Package

between

Between-Class Analysis

cnc2003

Frequenting movie theaters in France in 2003

ardeche

Fauna Table with double (row and column) partitioning

rpjdl

Avifauna and Vegetation

area.plot

Graphical Display of Areas

avimedi

Fauna Table for Constrained Ordinations

carni19

Phylogeny and quantative trait of carnivora

dudi.dec

Decentred Correspondence Analysis

mstree

Minimal Spanning Tree

dist.prop

Computation of Distance Matrices of Percentage Data

corvus

Corvus morphology

dudi.fca

Fuzzy Correspondence Analysis

dist.binary

Computation of Distance Matrices for Binary Data

tithonia

Phylogeny and quantitative traits of flowers

olympic

Olympic Decathlon

kdisteuclid

a way to obtain Euclidean distance matrices

phylog

Phylogeny

procella

Phylogeny and quantitative traits of birds

perthi02

Contingency Table with a partition in Molecular Biology

julliot

Seed dispersal

s.chull

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

bacteria

Genomes of 43 Bacteria

s.match

Plot of Paired Coordinates

ecomor

Ecomorphological Convergence

njplot

Phylogeny and trait of bacteria

macon

Wine Tasting

mantel.rtest

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

orthogram

Orthonormal decomposition of variance

housetasks

Contingency Table

dudi.nsc

Non symmetric correspondence analysis

ours

A table of Qualitative Variables

s.distri

Plot of a frequency distribution

ecg

Electrocardiogram data

ade4toR

Format Change Utility

dist.quant

Computation of Distance Matrices on Quantitative Variables

s.hist

Display of a scatterplot and its two marginal histograms

elec88

Electoral Data

is.euclid

Is a Distance Matrix Euclidean ?

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

s.corcircle

Plot of the factorial maps of a correlation circle

jv73

K-tables Multi-Regions

sarcelles

Array of Recapture of Rings

dpcoa

Double principal coordinate analysis

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

fuzzygenet

Reading a table of genetic data (diploid individuals)

lizards

Phylogeny and quantitative traits of lizards

coinertia

Coinertia Analysis

s.value

Representation of a value in a graph

ktab.list.dudi

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

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

aviurba

Ecological Tables Triplet

s.kde2d

Scatter Plot with Kernel Density Estimate

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

mafragh

Phyto-Ecological Survey

RV.rtest

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

procuste.rtest

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

quasieuclid

Transformation of a distance matrice to a Euclidean one

dudi.pca

Principal Component Analysis

clementines

Fruit Production

dudi.pco

Principal Coordinates Analysis

dudi.coa

Correspondence Analysis

rlq

RLQ analysis

randtest.amova

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

irishdata

Geary's Irish Data

foucart

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

rhone

Physico-Chemistry Data

procuste

Simple Procruste Rotation between two sets of points

ichtyo

Point sampling of fish community

s.label

Scatter Plot

procuste.randtest

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

chevaine

Enzymatic polymorphism in Leuciscus cephalus

s.image

Graph of a variable using image and contour

rtest.discrimin

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

rtest.between

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

plot.phylog

Plot phylogenies

randtest.discrimin

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

newick2phylog

Create phylogeny

pcoscaled

Simplified Analysis in Principal Coordinates

kplot.statis

Multiple Graphs of a STATIS Analysis

microsatt

Genetic Relationships between cattle breeds with microsatellites

acacia

Spatial pattern analysis in plant communities

pcaiv

Principal component analysis with respect to instrumental variables

discrimin

Linear Discriminant Analysis (descriptive statistic)

dist.dudi

Computation of the Distance Matrix of a Statistical Triplet

mantel.randtest

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

bf88

Cubic Ecological Data

gridrowcol

Complete regular grid analysis

morphosport

Athletes' Morphology

escopage

K-tables of wine-tasting

maples

Phylogeny and quantitative traits of flowers

randtest.coinertia

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

divcmax

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

pta

Partial Triadic Analysis of a K-tables

cca

Canonical Correspondence Analysis

oribatid

Oribatid mite

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

mollusc

Faunistic Communities and Sampling Experiment

s.class

Plot of factorial maps with representation of point classes

mld

Multi Level Decomposition of unidimensional data

deug

Exam marks for some students

ktab.list.df

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

ktab.data.frame

Creation of K-tables from a data frame

witwit.coa

Internal Correspondence Analysis

mariages

Correspondence Analysis Table

chatcat

Qualitative Weighted Variables

bordeaux

Wine Tasting

monde84

Global State of the World in 1984

doubs

Pair of Ecological Tables

dotcircle

Representation of n values on a circle

fruits

Pair of Tables

meau

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

dist.genet

Genetic distances from gene frequencies

gearymoran

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

veuvage

Example for Centring in PCA

sco.distri

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

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

lascaux

Genetic/Environment and types of variables

kdist2ktab

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

mfa

Multiple Factorial Analysis

meaudret

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

multispati.rtest

Multivariate spatial autocorrelation test

carni70

Phylogeny and quantitative traits of carnivora

amova

Analysis of molecular variance

African Estuary Fishes

multispati.randtest

Multivariate spatial autocorrelation test (in C)

macaca

Landmarks

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

butterfly

Genetics-Ecology-Environment Triple

scatter

Scatter Plot

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

RVdist.randtest

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

newick.eg

Phylogenetic trees in Newick format

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

rankrock

Ordination Table

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

skulls

Morphometric Evolution

within.pca

Normed within Principal Component Analysis

humDNAm

human mitochondrial DNA restriction data

randtest.between

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

neig

Neighbourhood Graphs

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

krandtest

Class of the Permutation Tests (in C).

kcponds

Ponds in a nature reserve

ktab.within

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

randtest-internal

Internal Permutation Tests functions (in C).

ktab

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

presid2002

Results of the French presidential elections of 2002

fission

Fission pattern and heritable morphological traits

mjrochet

Phylogeny and quantitative traits of teleos fishes

dudi.mix

Ordination of Tables mixing quantitative variables and factors

divc

Rao's diversity coefficient also called quadratic entropy

discrimin.coa

Discriminant Correspondence Analysis

disc

Rao's dissimilarity coefficient

cailliez

Transformation to make Euclidean a distance matrix

lingoes

Transformation of a Distance Matrix for becoming Euclidean

banque

Table of Factors

reconst

Reconstitution of Data from a Duality Diagram

aminoacyl

Codon usage

sepan

Separated Analyses in a K-tables

taxo.eg

Examples of taxonomy

scalewt

Centring and Scaling a Matrix of Any Weighting

dudi

Duality Diagram

steppe

Transect in the Vegetation

dunedata

Dune Meadow Data