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

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

## Documentation for package ‘ade4’ version 1.7-23

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W Y Z misc

ade4-package | The ade4 package

## -- A --

abouheif.eg | Phylogenies and quantitative traits from Abouheif
acacia | Spatial pattern analysis in plant communities
acm.burt | Multiple Correspondence Analysis
acm.disjonctif | Multiple Correspondence Analysis
add.position.triangle | Triangular Plotting
add.scatter | Add graphics to an existing plot
add.scatter.eig | Add graphics to an existing plot
ade4 | The ade4 package
ade4-deprecated | Deprecated functions in ade4
aminoacyl | Codon usage
amova | Analysis of molecular variance
apis108 | Allelic frequencies in ten honeybees populations at eight microsatellites loci
apqe | Apportionment of Quadratic Entropy
aravo | Distribution of Alpine plants in Aravo (Valloire, France)
ardeche | Fauna Table with double (row and column) partitioning
area.plot | Graphical Display of Areas
area.util.class | Graphical Display of Areas
area.util.contour | Graphical Display of Areas
area.util.xy | Graphical Display of Areas
area2link | Graphical Display of Areas
area2poly | Graphical Display of Areas
arrival | Arrivals at an intensive care unit
as.data.frame.kdist | the class of objects 'kdist' (K distance matrices)
as.dudi | Duality Diagram
as.krandboot | Bootstrap simulations
as.krandtest | Class of the Permutation Tests (in C).
as.krandxval | Two-fold cross-validation
as.randboot | Bootstrap simulations
as.randtest | Class of the Permutation Tests (in C).
as.randxval | Two-fold cross-validation
as.taxo | Taxonomy
atlas | Small Ecological Dataset
atya | Genetic variability of Cacadors
avijons | Bird species distribution
avimedi | Fauna Table for Constrained Ordinations
aviurba | Ecological Tables Triplet

## -- B --

bacteria | Genomes of 43 Bacteria
banque | Table of Factors
baran95 | African Estuary Fishes
bca | Between-Class Analysis
bca.coinertia | Between-class coinertia analysis
bca.dpcoa | Between- and within-class double principal coordinate analysis
bca.dudi | Between-Class Analysis
bca.rlq | Between-Class RLQ analysis
bf88 | Cubic Ecological Data
bicenter.wt | Double Weighted Centring
biplot.dudi | Graphical representation of the outputs of a multivariate analysis
bordeaux | Wine Tasting
boxplot.acm | Multiple Correspondence Analysis
bsetal97 | Ecological and Biological Traits
buech | Buech basin
butterfly | Genetics-Ecology-Environment Triple
bwca.dpcoa | Between- and within-class double principal coordinate analysis

## -- C --

c.kdist | the class of objects 'kdist' (K distance matrices)
c.ktab | the class of objects 'ktab' (K-tables)
cailliez | Transformation to make Euclidean a distance matrix
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
coinertia | Coinertia Analysis
col.names | the class of objects 'ktab' (K-tables)
col.names.ktab | the class of objects 'ktab' (K-tables)
col.names<- | the class of objects 'ktab' (K-tables)
col.names<-.ktab | the class of objects 'ktab' (K-tables)
coleo | Table of Fuzzy Biological Traits
combine.4thcorner | Functions to combine and adjust the outputs 3-table methods
combine.randtest.rlq | Functions to combine and adjust the outputs 3-table methods
corkdist | Tests of randomization between distances applied to 'kdist' objetcs
corvus | Corvus morphology
costatis | STATIS and Co-Inertia : Analysis of a series of paired ecological tables
costatis.randtest | Monte-Carlo test on a Costatis analysis (in C).
covfacwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
covwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)

## -- D --

dagnelie.test | Dagnelie multinormality test
deug | Exam marks for some students
disc | Rao's dissimilarity coefficient
discrimin | Linear Discriminant Analysis (descriptive statistic)
discrimin.coa | Discriminant Correspondence Analysis
dist.binary | Computation of Distance Matrices for Binary Data
dist.dudi | Computation of the Distance Matrix from a Statistical Triplet
dist.ktab | Mixed-variables coefficient of distance
dist.neig | Computation of the Distance Matrix associated to a Neighbouring Graph
dist.prop | Computation of Distance Matrices of Percentage Data
dist.quant | Computation of Distance Matrices on Quantitative Variables
dist.taxo | Taxonomy
divc | Rao's diversity coefficient also called quadratic entropy
divcmax | Maximal value of Rao's diversity coefficient also called quadratic entropy
dotchart.phylog | Representation of many quantitative variables in front of a phylogenetic tree
dotcircle | Representation of n values on a circle
doubs | Pair of Ecological Tables
dpcoa | Double principal coordinate analysis
dudi | Duality Diagram
dudi.acm | Multiple Correspondence Analysis
dudi.coa | Correspondence Analysis
dudi.dec | Decentred Correspondence Analysis
dudi.fca | Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
dudi.fpca | Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
dudi.hillsmith | Ordination of Tables mixing quantitative variables and factors
dudi.mix | Ordination of Tables mixing quantitative variables and factors
dudi.nsc | Non symmetric correspondence analysis
dudi.pca | Principal Component Analysis
dudi.pco | Principal Coordinates Analysis
dunedata | Dune Meadow Data

## -- E --

ecg | Electrocardiogram data
ecomor | Ecomorphological Convergence
elec88 | Electoral Data
enum.phylog | Plot phylogenies
escopage | K-tables of wine-tasting
euro123 | Triangular Data

## -- F --

fission | Fission pattern and heritable morphological traits
foucart | K-tables Correspondence Analysis with the same rows and the same columns
fourthcorner | Functions to compute the fourth-corner statistic
fourthcorner.rlq | Functions to compute the fourth-corner statistic
fourthcorner2 | Functions to compute the fourth-corner statistic
friday87 | Faunistic K-tables
fruits | Pair of Tables

## -- G --

gearymoran | Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation
ggtortoises | Microsatellites of Galapagos tortoises populations
granulo | Granulometric Curves
gridrowcol | Complete regular grid analysis

## -- H --

haar2level | Multi Level Decomposition of unidimensional data
hclust2phylog | Create phylogeny
hdpg | Genetic Variation In Human Populations
houmousr | Morphometric data set
housetasks | Contingency Table
humDNAm | human mitochondrial DNA restriction data

## -- I --

ichtyo | Point sampling of fish community
inertia | Decomposition of inertia (i.e. contributions) in multivariate methods
inertia.dudi | Decomposition of inertia (i.e. contributions) in multivariate methods
irishdata | Geary's Irish Data
is.dudi | Duality Diagram
is.euclid | Is a Distance Matrix Euclidean?
is.ktab | the class of objects 'ktab' (K-tables)
is.orthobasis | Orthonormal basis for orthonormal transform

## -- J --

julliot | Seed dispersal
jv73 | K-tables Multi-Regions

## -- K --

kcponds | Ponds in a nature reserve
kdist | the class of objects 'kdist' (K distance matrices)
kdist.cor | Mixed-variables coefficient of distance
kdist2ktab | Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')
kdisteuclid | a way to obtain Euclidean distance matrices
kplot | Generic Function for Multiple Graphs in a K-tables Analysis
kplot.foucart | Multiple Graphs for the Foucart's Correspondence Analysis
kplot.mcoa | Multiple Graphs for a Multiple Co-inertia Analysis
kplot.mfa | Multiple Graphs for a Multiple Factorial Analysis
kplot.pta | Multiple Graphs for a Partial Triadic Analysis
kplot.sepan | Multiple Graphs for Separated Analyses in a K-tables
kplot.statis | Multiple Graphs of a STATIS Analysis
kplotsepan.coa | Multiple Graphs for Separated Analyses in a K-tables
kplotX.mdpcoa | Multiple Double Principal Coordinate Analysis
krandtest | Class of the Permutation Tests (in C).
krandxval | Two-fold cross-validation
ktab | the class of objects 'ktab' (K-tables)
ktab.data.frame | Creation of K-tables from a data frame
ktab.list.df | Creating a K-tables from a list of data frames.
ktab.list.dudi | Creation of a K-tables from a list of duality diagrams
ktab.match2ktabs | STATIS and Co-Inertia : Analysis of a series of paired ecological tables
ktab.util.addfactor | the class of objects 'ktab' (K-tables)
ktab.util.names | the class of objects 'ktab' (K-tables)
ktab.within | Process to go from a Within Analysis to a K-tables

## -- L --

lascaux | Genetic/Environment and types of variables
ldist.ktab | Mixed-variables coefficient of distance
lingoes | Transformation of a Distance Matrix for becoming Euclidean
lizards | Phylogeny and quantitative traits of lizards
loocv | Leave-one-out cross-validation for a 'dudi'
loocv.between | Leave-one-out cross-validation for a 'bca'
loocv.discrimin | Leave-one-out cross-validation for a 'discrimin' analysis
loocv.dudi | Leave-one-out cross-validation for a 'dudi'

## -- M --

macaca | Landmarks
macon | Wine Tasting
macroloire | Assemblages of Macroinvertebrates in the Loire River (France)
mafragh | Phyto-Ecological Survey
mantel.randtest | Mantel test (correlation between two distance matrices (in C).)
mantel.rtest | Mantel test (correlation between two distance matrices (in R).)
mantelkdist | Tests of randomization between distances applied to 'kdist' objetcs
maples | Phylogeny and quantitative traits of flowers
mariages | Correspondence Analysis Table
mbpcaiv | Multiblock principal component analysis with instrumental variables
mbpls | Multiblock partial least squares
mcoa | Multiple CO-inertia Analysis
mdpcoa | Multiple Double Principal Coordinate Analysis
meanfacwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
meau | Ecological Data : sites-variables, sites-species, where and when
meaudret | Ecological Data : sites-variables, sites-species, where and when
mfa | Multiple Factorial Analysis
microsatt | Genetic Relationships between cattle breeds with microsatellites
mjrochet | Phylogeny and quantitative traits of teleos fishes
mld | Multi Level Decomposition of unidimensional data
mollusc | Faunistic Communities and Sampling Experiment
monde84 | Global State of the World in 1984
morphosport | Athletes' Morphology
mstree | Minimal Spanning Tree

## -- N --

nb2neig | Neighbourhood Graphs
neig | Neighbourhood Graphs
neig.util.GtoL | Neighbourhood Graphs
neig.util.LtoG | Neighbourhood Graphs
neig2mat | Neighbourhood Graphs
neig2nb | Neighbourhood Graphs
newick.eg | Phylogenetic trees in Newick format
newick2phylog | Create phylogeny
newick2phylog.addtools | Create phylogeny
niche | Method to Analyse a pair of tables : Environmental and Faunistic Data
niche.param | Method to Analyse a pair of tables : Environmental and Faunistic Data
nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm
njplot | Phylogeny and trait of bacteria

## -- O --

olympic | Olympic Decathlon
oribatid | Oribatid mite
originality | Originality of a species
orthobasis | Orthonormal basis for orthonormal transform
orthobasis.circ | Orthonormal basis for orthonormal transform
orthobasis.haar | Orthonormal basis for orthonormal transform
orthobasis.line | Orthonormal basis for orthonormal transform
orthobasis.mat | Orthonormal basis for orthonormal transform
orthobasis.neig | Orthonormal basis for orthonormal transform
ours | A table of Qualitative Variables

## -- P --

p.adjust.4thcorner | Functions to combine and adjust the outputs 3-table methods
palm | Phylogenetic and quantitative traits of amazonian palm trees
pap | Taxonomy and quantitative traits of carnivora
pcaiv | Principal component analysis with respect to instrumental variables
pcaivortho | Principal Component Analysis with respect to orthogonal instrumental variables
pcoscaled | Simplified Analysis in Principal Coordinates
pcw | Distribution of of tropical trees along the Panama canal
perthi02 | Contingency Table with a partition in Molecular Biology
phylog | Phylogeny
phylog.extract | Phylogeny
phylog.permut | Phylogeny
PI2newick | Import data files from Phylogenetic Independance Package
piosphere | Plant traits response to grazing
plot.4thcorner | Functions to compute the fourth-corner statistic
plot.bcaloocv | Leave-one-out cross-validation for a 'bca'
plot.betcoi | Between-Class Analysis
plot.betrlq | Between-Class RLQ analysis
plot.between | Between-Class Analysis
plot.coinertia | Coinertia Analysis
plot.corkdist | Tests of randomization between distances applied to 'kdist' objetcs
plot.discloocv | Leave-one-out cross-validation for a 'discrimin' analysis
plot.discrimin | Linear Discriminant Analysis (descriptive statistic)
plot.dpcoa | Double principal coordinate analysis
plot.foucart | K-tables Correspondence Analysis with the same rows and the same columns
plot.krandtest | Class of the Permutation Tests (in C).
plot.mcoa | Multiple CO-inertia Analysis
plot.mfa | Multiple Factorial Analysis
plot.niche | Method to Analyse a pair of tables : Environmental and Faunistic Data
plot.orthobasis | Orthonormal basis for orthonormal transform
plot.pcaiv | Principal component analysis with respect to instrumental variables
plot.phylog | Plot phylogenies
plot.procuste | Simple Procruste Rotation between two sets of points
plot.pta | Partial Triadic Analysis of a K-tables
plot.randtest | Class of the Permutation Tests (in C).
plot.rlq | RLQ analysis
plot.sepan | Separated Analyses in a K-tables
plot.statis | STATIS, a method for analysing K-tables
plot.witcoi | Within-Class Analysis
plot.within | Within-Class Analysis
plot.witrlq | Within-Class RLQ analysis
poly2area | Graphical Display of Areas
predict.dudi | Projections of Supplementary Rows
prep.binary | Mixed-variables coefficient of distance
prep.circular | Mixed-variables coefficient of distance
prep.fuzzy | Mixed-variables coefficient of distance
prep.fuzzy.var | Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
prep.mdpcoa | Multiple Double Principal Coordinate Analysis
presid2002 | Results of the French presidential elections of 2002
print.4thcorner | Functions to compute the fourth-corner statistic
print.amova | Analysis of molecular variance
print.apqe | Apportionment of Quadratic Entropy
print.bcaloocv | Leave-one-out cross-validation for a 'bca'
print.betcoi | Between-Class Analysis
print.betdpcoa | Between- and within-class double principal coordinate analysis
print.betrlq | Between-Class RLQ analysis
print.between | Between-Class Analysis
print.coinertia | Coinertia Analysis
print.corkdist | Tests of randomization between distances applied to 'kdist' objetcs
print.discloocv | Leave-one-out cross-validation for a 'discrimin' analysis
print.discrimin | Linear Discriminant Analysis (descriptive statistic)
print.dpcoa | Double principal coordinate analysis
print.dudi | Duality Diagram
print.foucart | K-tables Correspondence Analysis with the same rows and the same columns
print.inertia | Decomposition of inertia (i.e. contributions) in multivariate methods
print.kdist | the class of objects 'kdist' (K distance matrices)
print.krandboot | Bootstrap simulations
print.krandtest | Class of the Permutation Tests (in C).
print.krandxval | Two-fold cross-validation
print.ktab | the class of objects 'ktab' (K-tables)
print.mcoa | Multiple CO-inertia Analysis
print.mfa | Multiple Factorial Analysis
print.multiblock | Display and summarize multiblock objects
print.neig | Neighbourhood Graphs
print.niche | Method to Analyse a pair of tables : Environmental and Faunistic Data
print.nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm
print.orthobasis | Orthonormal basis for orthonormal transform
print.pcaiv | Principal component analysis with respect to instrumental variables
print.phylog | Phylogeny
print.procuste | Simple Procruste Rotation between two sets of points
print.pta | Partial Triadic Analysis of a K-tables
print.randboot | Bootstrap simulations
print.randtest | Class of the Permutation Tests (in C).
print.randxval | Two-fold cross-validation
print.rlq | RLQ analysis
print.sepan | Separated Analyses in a K-tables
print.statis | STATIS, a method for analysing K-tables
print.varipart | Partition of the variation of a response multivariate table by 2 explanatory tables
print.witcoi | Within-Class Analysis
print.witdpcoa | Between- and within-class double principal coordinate analysis
print.within | Within-Class Analysis
print.witrlq | Within-Class RLQ analysis
procella | Phylogeny and quantitative traits of birds
procuste | Simple Procruste Rotation between two sets of points
procuste.randtest | Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).
procuste.rtest | Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).
pta | Partial Triadic Analysis of a K-tables

## -- Q --

quasieuclid | Transformation of a distance matrice to a Euclidean one

## -- R --

radial.phylog | Plot phylogenies
randboot | Bootstrap simulations
randboot.multiblock | Bootstraped simulations for multiblock methods
randtest | Class of the Permutation Tests (in C).
randtest.amova | Permutation tests on an analysis of molecular variance (in C).
randtest.between | Monte-Carlo Test on the between-groups inertia percentage (in C).
randtest.betwit | Between- and within-class double principal coordinate analysis
randtest.coinertia | Monte-Carlo test on a Co-inertia analysis (in C).
randtest.discrimin | Monte-Carlo Test on a Discriminant Analysis (in C).
randtest.dpcoa | Permutation test for double principal coordinate analysis (DPCoA)
randtest.pcaiv | Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia
randtest.pcaivortho | Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia
randtest.procuste | Simple Procruste Rotation between two sets of points
randtest.rlq | RLQ analysis
randxval | Two-fold cross-validation
rankrock | Ordination Table
reciprocal.coa | Reciprocal scaling after a correspondence analysis
reconst | Reconstitution of Data from a Duality Diagram
reconst.coa | Reconstitution of Data from a Duality Diagram
reconst.pca | Reconstitution of Data from a Duality Diagram
redo.dudi | Duality Diagram
rhizobium | Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization
rhone | Physico-Chemistry Data
rlq | RLQ analysis
row.names.ktab | the class of objects 'ktab' (K-tables)
row.names<-.ktab | the class of objects 'ktab' (K-tables)
rpjdl | Avifauna and Vegetation
rtest | Class of the Permutation Tests (in R).
rtest.between | Monte-Carlo Test on the between-groups inertia percentage (in R).
rtest.discrimin | Monte-Carlo Test on a Discriminant Analysis (in R).
rtest.niche | Method to Analyse a pair of tables : Environmental and Faunistic Data
RV.randtest | Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in C++ with Rcpp).
RV.rtest | Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).
RVdist.randtest | Tests of randomization on the correlation between two distance matrices (in R).
RVintra.randtest | Monte-Carlo Test on the sum of eigenvalues of a within-class co-inertia analysis (in C++ with Rcpp).
RVkdist | Tests of randomization between distances applied to 'kdist' objetcs

## -- S --

s.arrow | Plot of the factorial maps for the projection of a vector basis
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.corcircle | Plot of the factorial maps of a correlation circle
s.distri | Plot of a frequency distribution
s.hist | Display of a scatterplot and its two marginal histograms
s.image | Graph of a variable using image and contour
s.kde2d | Scatter Plot with Kernel Density Estimate
s.label | Scatter Plot
s.logo | Representation of an object in a graph by a picture
s.match | Plot of Paired Coordinates
s.match.class | Scatterplot of two sets of coordinates and a partionning into classes
s.multinom | Graph of frequency profiles (useful for instance in genetic)
s.traject | Trajectory Plot
s.value | Representation of a value in a graph
santacatalina | Indirect Ordination
sarcelles | Array of Recapture of Rings
scalefacwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
scalewt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
scatter | Graphical representation of the outputs of a multivariate analysis
scatter.acm | Plot of the factorial maps in a Multiple Correspondence Analysis
scatter.coa | Plot of the factorial maps for a correspondence analysis
scatter.dudi | Plot of the Factorial Maps
scatter.fca | Plot of the factorial maps for a fuzzy correspondence analysis
scatter.nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm
scatter.pco | Principal Coordinates Analysis
scatterutil | Graphical utility functions
scatterutil.base | Graphical utility functions
scatterutil.chull | Graphical utility functions
scatterutil.convrot90 | Graphical utility functions
scatterutil.eigen | Graphical utility functions
scatterutil.ellipse | Graphical utility functions
scatterutil.eti | Graphical utility functions
scatterutil.eti.circ | Graphical utility functions
scatterutil.grid | Graphical utility functions
scatterutil.legend.bw.square | Graphical utility functions
scatterutil.legend.square.grey | Graphical utility functions
scatterutil.legendgris | Graphical utility functions
scatterutil.logo | Representation of an object in a graph by a picture
scatterutil.scaling | Graphical utility functions
scatterutil.sco | Graphical utility functions
scatterutil.star | Graphical utility functions
scatterutil.sub | Graphical utility functions
sco.boxplot | Representation of the link between a variable and a set of qualitative variables
sco.class | 1D plot of a numeric score and a factor with labels
sco.distri | Representation by mean- standard deviation of a set of weight distributions on a numeric score
sco.gauss | Relationships between one score and qualitative variables
sco.label | 1D plot of a numeric score with labels
sco.match | 1D plot of a pair of numeric scores with labels
sco.quant | Graph to Analyse the Relation between a Score and Quantitative Variables
score | Graphs for One Dimension
score.acm | Graphs to study one factor in a Multiple Correspondence Analysis
score.coa | Reciprocal scaling after a correspondence analysis
score.mix | Graphs to Analyse a factor in a Mixed Analysis
score.pca | Graphs to Analyse a factor in PCA
scores.neig | Neighbourhood Graphs
scoreutil.base | Graphs for One Dimension
screeplot.dudi | Graphical representation of the outputs of a multivariate analysis
seconde | Students and Subjects
sepan | Separated Analyses in a K-tables
skulls | Morphometric Evolution
statico | STATIS and Co-Inertia : Analysis of a series of paired ecological tables
statico.krandtest | Monte-Carlo test on a Statico analysis (in C).
statis | STATIS, a method for analysing K-tables
steppe | Transect in the Vegetation
summary.4thcorner | Functions to compute the fourth-corner statistic
summary.between | Between-Class Analysis
summary.betwit | Between- and within-class double principal coordinate analysis
summary.coinertia | Coinertia Analysis
summary.corkdist | Tests of randomization between distances applied to 'kdist' objetcs
summary.dist | Is a Distance Matrix Euclidean?
summary.dpcoa | Double principal coordinate analysis
summary.dudi | Duality Diagram
summary.inertia | Decomposition of inertia (i.e. contributions) in multivariate methods
summary.mcoa | Multiple CO-inertia Analysis
summary.mfa | Multiple Factorial Analysis
summary.multiblock | Display and summarize multiblock objects
summary.neig | Neighbourhood Graphs
summary.orthobasis | Orthonormal basis for orthonormal transform
summary.pcaiv | Principal component analysis with respect to instrumental variables
summary.pcaivortho | Principal Component Analysis with respect to orthogonal instrumental variables
summary.rlq | RLQ analysis
summary.sepan | Separated Analyses in a K-tables
summary.within | Within-Class Analysis
summary.witwit | Internal Correspondence Analysis
supcol | Projections of Supplementary Columns
supcol.coa | Projections of Supplementary Columns
supcol.dudi | Projections of Supplementary Columns
supdist | Projection of additional items in a PCO analysis
suprow | Projections of Supplementary Rows
suprow.acm | Projections of Supplementary Rows
suprow.coa | Projections of Supplementary Rows
suprow.dudi | Projections of Supplementary Rows
suprow.fca | Projections of Supplementary Rows
suprow.mix | Projections of Supplementary Rows
suprow.pca | Projections of Supplementary Rows
suprow.pta | Projections of Supplementary Rows for a Partial Triadic Analysis of K-tables
symbols.phylog | Representation of a quantitative variable in front of a phylogenetic tree
syndicats | Two Questions asked on a Sample of 1000 Respondents

## -- T --

t.dudi | Duality Diagram
t.ktab | the class of objects 'ktab' (K-tables)
t3012 | Average temperatures of 30 French cities
tab.names | the class of objects 'ktab' (K-tables)
tab.names.ktab | the class of objects 'ktab' (K-tables)
tab.names<- | the class of objects 'ktab' (K-tables)
tab.names<-.ktab | the class of objects 'ktab' (K-tables)
table.cont | Plot of Contingency Tables
table.dist | Graph Display for Distance Matrices
table.paint | Plot of the arrays by grey levels
table.phylog | Plot arrays in front of a phylogenetic tree
table.prepare | Plot of the Arrays
table.value | Plot of the Arrays
tarentaise | Mountain Avifauna
taxo.eg | Examples of taxonomy
taxo2phylog | Create phylogeny
testdim | Function to perform a test of dimensionality
testdim.multiblock | Selection of the number of dimension by two-fold cross-validation for multiblock methods
testdim.pca | Function to perform a test of dimensionality
tintoodiel | Tinto and Odiel estuary geochemistry
tithonia | Phylogeny and quantitative traits of flowers
tortues | Morphological Study of the Painted Turtle
toxicity | Homogeneous Table
triangle.biplot | Triangular Plotting
triangle.class | Triangular Representation and Groups of points
triangle.param | Triangular Plotting
triangle.plot | Triangular Plotting
triangle.posipoint | Triangular Plotting
trichometeo | Pair of Ecological Data

## -- U --

ungulates | Phylogeny and quantitative traits of ungulates.
uniquewt.df | Elimination of Duplicated Rows in a Array

## -- V --

varfacwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
variance.phylog | The phylogenetic ANOVA
varipart | Partition of the variation of a response multivariate table by 2 explanatory tables
varwt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor)
vegtf | Vegetation in Trois-Fontaines
veuvage | Example for Centring in PCA

## -- W --

wca | Within-Class Analysis
wca.coinertia | Within-class coinertia analysis
wca.dpcoa | Between- and within-class double principal coordinate analysis
wca.dudi | Within-Class Analysis
wca.rlq | Within-Class RLQ analysis
westafrica | Freshwater fish zoogeography in west Africa
withinpca | Normed within principal component analysis
witwit.coa | Internal Correspondence Analysis
witwitsepan | Internal Correspondence Analysis
woangers | Plant assemblages in woodlands of the conurbation of Angers (France)
worksurv | French Worker Survey (1970)

## -- Y --

yanomama | Distance Matrices

## -- Z --

zealand | Road distances in New-Zealand

## -- misc --

[.dudi | Duality Diagram
[.kdist | the class of objects 'kdist' (K distance matrices)
[.krandtest | Class of the Permutation Tests (in C).
[.ktab | the class of objects 'ktab' (K-tables)
[[.krandtest | Class of the Permutation Tests (in C).