This package is considered a duplicate. The official version of this package is found at:https://adeverse.r-universe.dev/ade4

Package: ade4 1.7-24

Aurélie Siberchicot

ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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) <doi:10.18637/jss.v022.i04>.

Authors:Stéphane Dray [aut], Anne-Béatrice Dufour [aut], Jean Thioulouse [aut], Daniel Chessel [ant], Thibaut Jombart [ctb], Sandrine Pavoine [ctb], Jean R. Lobry [ctb], Sébastien Ollier [ctb], Daniel Borcard [ctb], Pierre Legendre [ctb], Stéphanie Bougeard [ctb], Aurélie Siberchicot [ctb, cre]

ade4_1.7-24.tar.gz
ade4_1.7-24.zip(r-4.7)ade4_1.7-24.zip(r-4.6)ade4_1.7-24.zip(r-4.5)
ade4_1.7-24.tgz(r-4.6-x86_64)ade4_1.7-24.tgz(r-4.6-arm64)ade4_1.7-24.tgz(r-4.5-x86_64)ade4_1.7-24.tgz(r-4.5-arm64)
ade4_1.7-24.tar.gz(r-4.7-arm64)ade4_1.7-24.tar.gz(r-4.7-x86_64)ade4_1.7-24.tar.gz(r-4.6-arm64)ade4_1.7-24.tar.gz(r-4.6-x86_64)
ade4_1.7-24.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
ade4/json (API)

# Install 'ade4' in R:

install.packages('ade4', repos = c('https://thioulouse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeverse/ade4/issues

Pkgdown/docs site:https://adeverse.github.io

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

abouheif.eg - Phylogenies and quantitative traits from Abouheif
acacia - Spatial pattern analysis in plant communities
aminoacyl - Codon usage
apis108 - Allelic frequencies in ten honeybees populations at eight microsatellites loci
aravo - Distribution of Alpine plants in Aravo
ardeche - Fauna Table with double (row and column) partitioning
arrival - Arrivals at an intensive care unit
atlas - Small Ecological Dataset
atya - Genetic variability of Cacadors
avijons - Bird species distribution
avimedi - Fauna Table for Constrained Ordinations
aviurba - Ecological Tables Triplet
bacteria - Genomes of 43 Bacteria
banque - Table of Factors
baran95 - African Estuary Fishes
bf88 - Cubic Ecological Data
bordeaux - Wine Tasting
bsetal97 - Ecological and Biological Traits
buech - Buech basin
butterfly - Genetics-Ecology-Environment Triple
capitales - Road Distances
carni19 - Phylogeny and quantative trait of carnivora
carni70 - Phylogeny and quantitative traits of carnivora
carniherbi49 - Taxonomy, phylogenies and quantitative traits of carnivora and herbivora
casitas - Enzymatic polymorphism in Mus musculus
chatcat - Qualitative Weighted Variables
chats - Pair of Variables
chazeb - Charolais-Zebus
chevaine - Enzymatic polymorphism in Leuciscus cephalus
chickenk - Veterinary epidemiological study to assess the risk factors for losses in broiler chickens
clementines - Fruit Production
cnc2003 - Frequenting movie theaters in France in 2003
coleo - Table of Fuzzy Biological Traits
corvus - Corvus morphology
deug - Exam marks for some students
doubs - Pair of Ecological Tables
dunedata - Dune Meadow Data
ecg - Electrocardiogram data
ecomor - Ecomorphological Convergence
elec88 - Electoral Data
escopage - K-tables of wine-tasting
euro123 - Triangular Data
fission - Fission pattern and heritable morphological traits
friday87 - Faunistic K-tables
fruits - Pair of Tables
ggtortoises - Microsatellites of Galapagos tortoises populations
granulo - Granulometric Curves
hdpg - Genetic Variation In Human Populations
houmousr - Morphometric data set
housetasks - Contingency Table
humDNAm - Human mitochondrial DNA restriction data
ichtyo - Point sampling of fish community
irishdata - Geary's Irish Data
julliot - Seed dispersal
jv73 - K-tables Multi-Regions
kcponds - Ponds in a nature reserve
lascaux - Genetic/Environment and types of variables
lizards - Phylogeny and quantitative traits of lizards
macaca - Landmarks
macon - Wine Tasting
macroloire - Assemblages of Macroinvertebrates in the Loire River
mafragh - Phyto-Ecological Survey
maples - Phylogeny and quantitative traits of flowers
mariages - Correspondence Analysis Table
meau - Ecological Data : sites-variables, sites-species, where and when
meaudret - Ecological Data : sites-variables, sites-species, where and when
microsatt - Genetic Relationships between cattle breeds with microsatellites
mjrochet - Phylogeny and quantitative traits of teleos fishes
mollusc - Faunistic Communities and Sampling Experiment
monde84 - Global State of the World in 1984
morphosport - Athletes' Morphology
newick.eg - Phylogenetic trees in Newick format
njplot - Phylogeny and trait of bacteria
olympic - Olympic Decathlon
oribatid - Oribatid mite
ours - A table of Qualitative Variables
palm - Phylogenetic and quantitative traits of amazonian palm trees
pap - Taxonomy and quantitative traits of carnivora
pcw - Distribution of of tropical trees along the Panama canal
perthi02 - Contingency Table with a partition in Molecular Biology
piosphere - Plant traits response to grazing
presid2002 - Results of the French presidential elections of 2002
procella - Phylogeny and quantitative traits of birds
rankrock - Ordination Table
rhizobium - Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization
rhone - Physico-Chemistry Data
rpjdl - Avifauna and Vegetation
santacatalina - Indirect Ordination
sarcelles - Array of Recapture of Rings
seconde - Students and Subjects
skulls - Morphometric Evolution
steppe - Transect in the Vegetation
syndicats - Two Questions asked on a Sample of 1000 Respondents
t3012 - Average temperatures of 30 French cities
tarentaise - Mountain Avifauna
taxo.eg - Examples of taxonomy
tintoodiel - Tinto and Odiel estuary geochemistry
tithonia - Phylogeny and quantitative traits of flowers
tortues - Morphological Study of the Painted Turtle
toxicity - Homogeneous Table
trichometeo - Pair of Ecological Data
ungulates - Phylogeny and quantitative traits of ungulates.
vegtf - Vegetation in Trois-Fontaines
veuvage - Example for Centring in PCA
westafrica - Freshwater fish zoogeography in west Africa
woangers - Plant assemblages in woodlands of the conurbation of Angers
worksurv - French Worker Survey
yanomama - Distance Matrices
zealand - Road distances in New-Zealand

On CRAN:

openblas cpp

15.02 score 45 stars 286 packages 5.5k scripts 55k downloads 809 mentions 229 exports 6 dependencies

Last updated from:4bfb05bea6. Checks:11 NOTE, 2 OK. Indexed: no.

Target	Result	Time
linux-devel-arm64	NOTE	323
linux-devel-x86_64	NOTE	367
source / vignettes	OK	316
linux-release-arm64	NOTE	326
linux-release-x86_64	NOTE	346
macos-release-arm64	NOTE	230
macos-release-x86_64	NOTE	437
macos-oldrel-arm64	NOTE	196
macos-oldrel-x86_64	NOTE	329
windows-devel	NOTE	297
windows-release	NOTE	287
windows-oldrel	NOTE	267
wasm-release	OK	229

Exports:acm.burt acm.disjonctif add.scatter add.scatter.eig adegraphicsLoaded amova apqe area.plot area2link area2poly as.dudi as.krandboot as.krandtest as.krandxval as.randboot as.randtest as.randxval as.taxo bca betweenvarCpp bicenter.wt bwca.dpcoa cailliez coinertia col.names col.names<-combine.4thcorner combine.randtest.rlq costatis costatis.randtest covfacwt covwt dagnelie.test disc discrimin discrimin.coa dist.binary dist.dudi dist.ktab dist.neig dist.prop dist.quant dist.taxo divc divcmax dotchart.phylog dotcircle dpcaiv dpcoa dudi.acm dudi.coa dudi.dec dudi.fca dudi.fpca dudi.hillsmith dudi.mix dudi.nsc dudi.pca dudi.pco dudi.type dvaripart enum.phylog foucart fourthcorner fourthcorner.rlq fourthcorner2 gearymoran gridrowcol haar2level hclust2phylog inerbetweenCpp inertia inertia.dudi is.dudi is.euclid is.ktab is.orthobasis kdist kdist.cor kdist2ktab kdisteuclid kplot kplotsepan.coa kplotX.mdpcoa ktab.data.frame ktab.list.df ktab.list.dudi ktab.match2ktabs ktab.within ldist.ktab lingoes loocv mantel.randtest mantel.rtest mantelkdist mbpcaiv mbpls mcoa mdpcoa meanfacwt mfa mld mstree nb2neig neig neig2mat neig2nb newick2phylog niche niche.param nipals originality orthobasis.circ orthobasis.haar orthobasis.line orthobasis.mat orthobasis.neig p.adjust.4thcorner pcaiv pcaivortho pcoscaled phylog.extract phylog.permut PI2newick poly2area prep.binary prep.circular prep.fuzzy prep.fuzzy.var prep.mdpcoa procuste procuste.randtest procuste.rtest procusterandtestCpp pta quasieuclid radial.phylog randboot randtest reciprocal.coa reconst redo.dudi rlq rtest RV.randtest RV.rtest RVdist.randtest RVintra.randtest RVintrarandtestCpp RVkdist RVrandtestCpp s.arrow s.chull s.class s.corcircle s.distri s.hist s.image s.kde2d s.label s.logo s.match s.match.class s.multinom s.traject s.value scalefacwt scalewt scatter scatterutil.base scatterutil.chull scatterutil.convrot90 scatterutil.eigen scatterutil.ellipse scatterutil.eti scatterutil.eti.circ scatterutil.grid scatterutil.legend.bw.square scatterutil.legend.square.grey scatterutil.legendgris scatterutil.logo scatterutil.scaling scatterutil.sco scatterutil.star scatterutil.sub sco.boxplot sco.class sco.distri sco.gauss sco.label sco.match sco.quant score scores.neig sepan statico statico.krandtest statis supcol supdist suprow symbols.phylog tab.names tab.names<-table.cont table.dist table.paint table.phylog table.value taxo2phylog testdim testdiscriminCpp testertraceCpp testertracenubisCpp testertracenuCpp testinterCpp testmantelCpp triangle.biplot triangle.class triangle.plot uniquewt.df varfacwt variance.phylog varipart varwt wca withinpca witwit.coa witwitsepan

Dependencies:lattice MASS pixmap Rcpp RcppArmadillo sp

FAQ

Rendered fromfaq.Rmdusingknitr::rmarkdown

Last update: 2024-07-12
Started: 2023-05-17

Help page	Topics
The ade4 package	ade4-package ade4
Phylogenies and quantitative traits from Abouheif	abouheif.eg
Spatial pattern analysis in plant communities	acacia
Add graphics to an existing plot	add.scatter add.scatter.eig
Codon usage	aminoacyl
Analysis of molecular variance	amova print.amova
Allelic frequencies in ten honeybees populations at eight microsatellites loci	apis108
Apportionment of Quadratic Entropy	apqe print.apqe
Distribution of Alpine plants in Aravo (Valloire, France)	aravo
Fauna Table with double (row and column) partitioning	ardeche
Graphical Display of Areas	area.plot area.util.class area.util.contour area.util.xy area2link area2poly poly2area
Arrivals at an intensive care unit	arrival
Taxonomy	as.taxo dist.taxo
Small Ecological Dataset	atlas
Genetic variability of Cacadors	atya
Bird species distribution	avijons
Fauna Table for Constrained Ordinations	avimedi
Ecological Tables Triplet	aviurba
Genomes of 43 Bacteria	bacteria
Table of Factors	banque
African Estuary Fishes	baran95
Between-Class Analysis	bca bca.dudi
Between-class coinertia analysis	bca.coinertia
Between-Class RLQ analysis	bca.rlq plot.betrlq print.betrlq
Between-Class Analysis	plot.betcoi plot.between print.betcoi print.between summary.between
Cubic Ecological Data	bf88
Double Weighted Centring	bicenter.wt
Wine Tasting	bordeaux
Ecological and Biological Traits	bsetal97
Buech basin	buech
Genetics-Ecology-Environment Triple	butterfly
Between- and within-class double principal coordinate analysis	bca.dpcoa bwca.dpcoa print.betdpcoa print.witdpcoa randtest.betwit summary.betwit wca.dpcoa
Transformation to make Euclidean a distance matrix	cailliez
Road Distances	capitales
Phylogeny and quantative trait of carnivora	carni19
Phylogeny and quantitative traits of carnivora	carni70
Taxonomy, phylogenies and quantitative traits of carnivora and herbivora	carniherbi49
Enzymatic polymorphism in Mus musculus	casitas
Qualitative Weighted Variables	chatcat
Pair of Variables	chats
Charolais-Zebus	chazeb
Enzymatic polymorphism in Leuciscus cephalus	chevaine
Veterinary epidemiological study to assess the risk factors for losses in broiler chickens	chickenk
Fruit Production	clementines
Frequenting movie theaters in France in 2003	cnc2003
Coinertia Analysis	coinertia plot.coinertia print.coinertia summary.coinertia
Table of Fuzzy Biological Traits	coleo
Functions to combine and adjust the outputs 3-table methods	combine.4thcorner combine.randtest.rlq p.adjust.4thcorner
Tests of randomization between distances applied to 'kdist' objetcs	corkdist mantelkdist plot.corkdist print.corkdist RVkdist summary.corkdist
Corvus morphology	corvus
STATIS and Co-Inertia : Analysis of a series of paired ecological tables	costatis
Monte-Carlo test on a Costatis analysis (in C).	costatis.randtest
Dagnelie multinormality test	dagnelie.test
Deprecated functions in ade4	ade4-deprecated
Exam marks for some students	deug
Rao's dissimilarity coefficient	disc
Linear Discriminant Analysis (descriptive statistic)	discrimin plot.discrimin print.discrimin
Discriminant Correspondence Analysis	discrimin.coa
Computation of Distance Matrices for Binary Data	dist.binary
Computation of the Distance Matrix from a Statistical Triplet	dist.dudi
Mixed-variables coefficient of distance	dist.ktab kdist.cor ldist.ktab prep.binary prep.circular prep.fuzzy
Computation of the Distance Matrix associated to a Neighbouring Graph	dist.neig
Computation of Distance Matrices of Percentage Data	dist.prop
Computation of Distance Matrices on Quantitative Variables	dist.quant
Rao's diversity coefficient also called quadratic entropy	divc
Maximal value of Rao's diversity coefficient also called quadratic entropy	divcmax
Representation of many quantitative variables in front of a phylogenetic tree	dotchart.phylog
Representation of n values on a circle	dotcircle
Pair of Ecological Tables	doubs
Double principal component analysis with respect to instrumental variables	dpcaiv dvaripart plot.dpcaiv print.dpcaiv print.dvaripart randtest.dpcaiv summary.dpcaiv
Double principal coordinate analysis	dpcoa plot.dpcoa print.dpcoa summary.dpcoa
Duality Diagram	as.dudi dudi is.dudi print.dudi redo.dudi summary.dudi t.dudi [.dudi
Multiple Correspondence Analysis	acm.burt acm.disjonctif boxplot.acm dudi.acm
Correspondence Analysis	dudi.coa
Decentred Correspondence Analysis	dudi.dec
Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis	dudi.fca dudi.fpca prep.fuzzy.var
Ordination of Tables mixing quantitative variables and factors	dudi.hillsmith
Ordination of Tables mixing quantitative variables and factors	dudi.mix
Non symmetric correspondence analysis	dudi.nsc
Principal Component Analysis	dudi.pca
Principal Coordinates Analysis	dudi.pco scatter.pco
Dune Meadow Data	dunedata
Electrocardiogram data	ecg
Ecomorphological Convergence	ecomor
Electoral Data	elec88
K-tables of wine-tasting	escopage
Triangular Data	euro123
Fission pattern and heritable morphological traits	fission
K-tables Correspondence Analysis with the same rows and the same columns	foucart plot.foucart print.foucart
Functions to compute the fourth-corner statistic	fourthcorner fourthcorner.rlq fourthcorner2 plot.4thcorner print.4thcorner summary.4thcorner
Faunistic K-tables	friday87
Pair of Tables	fruits
Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation	gearymoran
Microsatellites of Galapagos tortoises populations	ggtortoises
Granulometric Curves	granulo
Complete regular grid analysis	gridrowcol
Genetic Variation In Human Populations	hdpg
Morphometric data set	houmousr
Contingency Table	housetasks
human mitochondrial DNA restriction data	humDNAm
Point sampling of fish community	ichtyo
Decomposition of inertia (i.e. contributions) in multivariate methods	inertia inertia.dudi print.inertia summary.inertia
Geary's Irish Data	irishdata
Is a Distance Matrix Euclidean?	is.euclid summary.dist
Seed dispersal	julliot
K-tables Multi-Regions	jv73
Ponds in a nature reserve	kcponds
the class of objects 'kdist' (K distance matrices)	as.data.frame.kdist c.kdist kdist print.kdist [.kdist
Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')	kdist2ktab
a way to obtain Euclidean distance matrices	kdisteuclid
Generic Function for Multiple Graphs in a K-tables Analysis	kplot
Multiple Graphs for the Foucart's Correspondence Analysis	kplot.foucart
Multiple Graphs for a Multiple Co-inertia Analysis	kplot.mcoa
Multiple Graphs for a Multiple Factorial Analysis	kplot.mfa
Multiple Graphs for a Partial Triadic Analysis	kplot.pta
Multiple Graphs for Separated Analyses in a K-tables	kplot.sepan kplotsepan.coa
Multiple Graphs of a STATIS Analysis	kplot.statis
Class of the Permutation Tests (in C).	as.krandtest krandtest plot.krandtest print.krandtest [.krandtest [[.krandtest
the class of objects 'ktab' (K-tables)	c.ktab col.names col.names.ktab col.names<- col.names<-.ktab is.ktab ktab ktab.util.addfactor ktab.util.names print.ktab row.names.ktab row.names<-.ktab t.ktab tab.names tab.names.ktab tab.names<- tab.names<-.ktab [.ktab
Creation of K-tables from a data frame	ktab.data.frame
Creating a K-tables from a list of data frames.	ktab.list.df
Creation of a K-tables from a list of duality diagrams	ktab.list.dudi
STATIS and Co-Inertia : Analysis of a series of paired ecological tables	ktab.match2ktabs
Process to go from a Within Analysis to a K-tables	ktab.within
Genetic/Environment and types of variables	lascaux
Transformation of a Distance Matrix for becoming Euclidean	lingoes
Phylogeny and quantitative traits of lizards	lizards
Leave-one-out cross-validation for a 'bca'	loocv.between plot.bcaloocv print.bcaloocv
Leave-one-out cross-validation for a 'discrimin' analysis	loocv.discrimin plot.discloocv print.discloocv
Leave-one-out cross-validation for a 'dudi'	loocv loocv.dudi
Landmarks	macaca
Wine Tasting	macon
Assemblages of Macroinvertebrates in the Loire River (France)	macroloire
Phyto-Ecological Survey	mafragh
Mantel test (correlation between two distance matrices (in C).)	mantel.randtest
Mantel test (correlation between two distance matrices (in R).)	mantel.rtest
Phylogeny and quantitative traits of flowers	maples
Correspondence Analysis Table	mariages
Multiblock principal component analysis with instrumental variables	mbpcaiv
Multiblock partial least squares	mbpls
Multiple CO-inertia Analysis	mcoa plot.mcoa print.mcoa summary.mcoa
Multiple Double Principal Coordinate Analysis	kplotX.mdpcoa mdpcoa prep.mdpcoa
Ecological Data : sites-variables, sites-species, where and when	meau
Ecological Data : sites-variables, sites-species, where and when	meaudret
Multiple Factorial Analysis	mfa plot.mfa print.mfa summary.mfa
Genetic Relationships between cattle breeds with microsatellites	microsatt
Phylogeny and quantitative traits of teleos fishes	mjrochet
Multi Level Decomposition of unidimensional data	haar2level mld
Faunistic Communities and Sampling Experiment	mollusc
Global State of the World in 1984	monde84
Athletes' Morphology	morphosport
Minimal Spanning Tree	mstree
Display and summarize multiblock objects	print.multiblock summary.multiblock
Neighbourhood Graphs	nb2neig neig neig.util.GtoL neig.util.LtoG neig2mat neig2nb print.neig scores.neig summary.neig
Phylogenetic trees in Newick format	newick.eg
Create phylogeny	hclust2phylog newick2phylog newick2phylog.addtools taxo2phylog
Method to Analyse a pair of tables : Environmental and Faunistic Data	niche niche.param plot.niche print.niche rtest.niche
Non-linear Iterative Partial Least Squares (NIPALS) algorithm	nipals print.nipals scatter.nipals
Phylogeny and trait of bacteria	njplot
Olympic Decathlon	olympic
Oribatid mite	oribatid
Originality of a species	originality
Orthonormal basis for orthonormal transform	is.orthobasis orthobasis orthobasis.circ orthobasis.haar orthobasis.line orthobasis.mat orthobasis.neig plot.orthobasis print.orthobasis summary.orthobasis
A table of Qualitative Variables	ours
Phylogenetic and quantitative traits of amazonian palm trees	palm
Taxonomy and quantitative traits of carnivora	pap
Principal component analysis with respect to instrumental variables	pcaiv plot.pcaiv print.pcaiv summary.pcaiv
Principal Component Analysis with respect to orthogonal instrumental variables	pcaivortho summary.pcaivortho
Simplified Analysis in Principal Coordinates	pcoscaled
Distribution of of tropical trees along the Panama canal	pcw
Contingency Table with a partition in Molecular Biology	perthi02
Phylogeny	phylog phylog.extract phylog.permut print.phylog
Import data files from Phylogenetic Independance Package	PI2newick
Plant traits response to grazing	piosphere
Plot phylogenies	enum.phylog plot.phylog radial.phylog
Results of the French presidential elections of 2002	presid2002
Phylogeny and quantitative traits of birds	procella
Simple Procruste Rotation between two sets of points	plot.procuste print.procuste procuste randtest.procuste
Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).	procuste.randtest
Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).	procuste.rtest
Partial Triadic Analysis of a K-tables	plot.pta print.pta pta
Transformation of a distance matrice to a Euclidean one	quasieuclid
Bootstrap simulations	as.krandboot as.randboot print.krandboot print.randboot randboot
Bootstraped simulations for multiblock methods	randboot.multiblock
Class of the Permutation Tests (in C).	as.randtest plot.randtest print.randtest randtest
Permutation tests on an analysis of molecular variance (in C).	randtest.amova
Monte-Carlo Test on the between-groups inertia percentage (in C).	randtest.between
Monte-Carlo test on a Co-inertia analysis (in C).	randtest.coinertia
Monte-Carlo Test on a Discriminant Analysis (in C).	randtest.discrimin
Permutation test for double principal coordinate analysis (DPCoA)	randtest.dpcoa
Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia	randtest.pcaiv randtest.pcaivortho
Two-fold cross-validation	as.krandxval as.randxval krandxval print.krandxval print.randxval randxval
Ordination Table	rankrock
Reconstitution of Data from a Duality Diagram	reconst reconst.coa reconst.pca
Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization	rhizobium
Physico-Chemistry Data	rhone
RLQ analysis	plot.rlq print.rlq randtest.rlq rlq summary.rlq
Avifauna and Vegetation	rpjdl
Class of the Permutation Tests (in R).	rtest
Monte-Carlo Test on the between-groups inertia percentage (in R).	rtest.between
Monte-Carlo Test on a Discriminant Analysis (in R).	rtest.discrimin
Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in C++ with Rcpp).	RV.randtest
Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).	RV.rtest
Tests of randomization on the correlation between two distance matrices (in R).	RVdist.randtest
Monte-Carlo Test on the sum of eigenvalues of a within-class co-inertia analysis (in C++ with Rcpp).	RVintra.randtest
Plot of the factorial maps for the projection of a vector basis	s.arrow
Plot of the factorial maps with polygons of contour by level of a factor	s.chull
Plot of factorial maps with representation of point classes	s.class
Plot of the factorial maps of a correlation circle	s.corcircle
Plot of a frequency distribution	s.distri
Display of a scatterplot and its two marginal histograms	s.hist
Graph of a variable using image and contour	s.image
Scatter Plot with Kernel Density Estimate	s.kde2d
Scatter Plot	s.label
Representation of an object in a graph by a picture	s.logo scatterutil.logo
Plot of Paired Coordinates	s.match
Scatterplot of two sets of coordinates and a partionning into classes	s.match.class
Graph of frequency profiles (useful for instance in genetic)	s.multinom
Trajectory Plot	s.traject
Representation of a value in a graph	s.value
Indirect Ordination	santacatalina
Array of Recapture of Rings	sarcelles
Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)	covfacwt covwt meanfacwt scalefacwt scalewt varfacwt varwt
Graphical representation of the outputs of a multivariate analysis	biplot.dudi scatter screeplot.dudi
Plot of the factorial maps in a Multiple Correspondence Analysis	scatter.acm
Plot of the factorial maps for a correspondence analysis	scatter.coa
Plot of the Factorial Maps	scatter.dudi
Plot of the factorial maps for a fuzzy correspondence analysis	scatter.fca
Graphical utility functions	scatterutil scatterutil.base scatterutil.chull scatterutil.convrot90 scatterutil.eigen scatterutil.ellipse scatterutil.eti scatterutil.eti.circ scatterutil.grid scatterutil.legend.bw.square scatterutil.legend.square.grey scatterutil.legendgris scatterutil.scaling scatterutil.sco scatterutil.star scatterutil.sub
Representation of the link between a variable and a set of qualitative variables	sco.boxplot
1D plot of a numeric score and a factor with labels	sco.class
Representation by mean- standard deviation of a set of weight distributions on a numeric score	sco.distri
Relationships between one score and qualitative variables	sco.gauss
1D plot of a numeric score with labels	sco.label
1D plot of a pair of numeric scores with labels	sco.match
Graph to Analyse the Relation between a Score and Quantitative Variables	sco.quant
Graphs for One Dimension	score scoreutil.base
Graphs to study one factor in a Multiple Correspondence Analysis	score.acm
Reciprocal scaling after a correspondence analysis	reciprocal.coa score.coa
Graphs to Analyse a factor in a Mixed Analysis	score.mix
Graphs to Analyse a factor in PCA	score.pca
Students and Subjects	seconde
Separated Analyses in a K-tables	plot.sepan print.sepan sepan summary.sepan
Morphometric Evolution	skulls
STATIS and Co-Inertia : Analysis of a series of paired ecological tables	statico
Monte-Carlo test on a Statico analysis (in C).	statico.krandtest
STATIS, a method for analysing K-tables	plot.statis print.statis statis
Transect in the Vegetation	steppe
Projections of Supplementary Columns	supcol supcol.coa supcol.dudi
Projection of additional items in a PCO analysis	supdist
Projections of Supplementary Rows	predict.dudi suprow suprow.acm suprow.coa suprow.dudi suprow.fca suprow.mix suprow.pca
Projections of Supplementary Rows for a Partial Triadic Analysis of K-tables	suprow.pta
Representation of a quantitative variable in front of a phylogenetic tree	symbols.phylog
Two Questions asked on a Sample of 1000 Respondents	syndicats
Average temperatures of 30 French cities	t3012
Plot of Contingency Tables	table.cont
Graph Display for Distance Matrices	table.dist
Plot of the arrays by grey levels	table.paint
Plot arrays in front of a phylogenetic tree	table.phylog
Plot of the Arrays	table.prepare table.value
Mountain Avifauna	tarentaise
Examples of taxonomy	taxo.eg
Function to perform a test of dimensionality	testdim testdim.pca
Selection of the number of dimension by two-fold cross-validation for multiblock methods	testdim.multiblock
Tinto and Odiel estuary geochemistry	tintoodiel
Phylogeny and quantitative traits of flowers	tithonia
Morphological Study of the Painted Turtle	tortues
Homogeneous Table	toxicity
Triangular Representation and Groups of points	triangle.class
Triangular Plotting	add.position.triangle triangle.biplot triangle.param triangle.plot triangle.posipoint
Pair of Ecological Data	trichometeo
Phylogeny and quantitative traits of ungulates.	ungulates
Elimination of Duplicated Rows in a Array	uniquewt.df
The phylogenetic ANOVA	variance.phylog
Partition of the variation of a response multivariate table by 2 explanatory tables	print.varipart varipart
Vegetation in Trois-Fontaines	vegtf
Example for Centring in PCA	veuvage
Within-Class Analysis	wca wca.dudi
Within-class coinertia analysis	wca.coinertia
Within-Class RLQ analysis	plot.witrlq print.witrlq wca.rlq
Freshwater fish zoogeography in west Africa	westafrica
Within-Class Analysis	plot.witcoi plot.within print.witcoi print.within summary.within
Normed within principal component analysis	withinpca
Internal Correspondence Analysis	summary.witwit witwit.coa witwitsepan
Plant assemblages in woodlands of the conurbation of Angers (France)	woangers
French Worker Survey (1970)	worksurv
Distance Matrices	yanomama
Road distances in New-Zealand	zealand

Package: ade4 1.7-24

ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

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