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

abouheif.egPhylogenies and quantitative traits from Abouheif
acaciaSpatial pattern analysis in plant communities
add.scatterAdd graphics to an existing plot
ade4-deprecatedDeprecated functions in ade4
ade4-internalInternal ade4 functions
ade4.packageThe ade4 package
adegraphicsLoadedUtility function to test if the package adegraphics is loaded
aminoacylCodon usage
amovaAnalysis of molecular variance
apis108Allelic frequencies in ten honeybees populations at eight...
apqeApportionment of Quadratic Entropy
aravoDistribution of Alpine plants in Aravo (Valloire, France)
ardecheFauna Table with double (row and column) partitioning
area.plotGraphical Display of Areas
arrivalArrivals at an intensive care unit
atlasSmall Ecological Dataset
atyaGenetic variability of Cacadors
avijonsBird species distribution
avimediFauna Table for Constrained Ordinations
aviurbaEcological Tables Triplet
bacteriaGenomes of 43 Bacteria
banqueTable of Factors
baran95African Estuary Fishes
bcaBetween-Class Analysis
bca.coinertiaBetween-class coinertia analysis
bca.rlqBetween-Class RLQ analysis
bf88Cubic Ecological Data
bicenter.wtDouble Weighted Centring
bordeauxWine Tasting
bsetal97Ecological and Biological Traits
buechBuech basin
butterflyGenetics-Ecology-Environment Triple
bwca.dpcoaBetween- and within-class double principal coordinate...
cailliezTransformation to make Euclidean a distance matrix
capitalesRoad Distances
carni19Phylogeny and quantative trait of carnivora
carni70Phylogeny and quantitative traits of carnivora
carniherbi49Taxonomy, phylogenies and quantitative traits of carnivora...
casitasEnzymatic polymorphism in Mus musculus
chatcatQualitative Weighted Variables
chatsPair of Variables
chevaineEnzymatic polymorphism in Leuciscus cephalus
chickenkVeterinary epidemiological study to assess the risk factors...
clementinesFruit Production
cnc2003Frequenting movie theaters in France in 2003
coinertiaCoinertia Analysis
coleoTable of Fuzzy Biological Traits
combine.4thcornerFunctions to combine and adjust the outputs 3-table methods
corkdistTests of randomization between distances applied to 'kdist'...
corvusCorvus morphology
costatisSTATIS and Co-Inertia : Analysis of a series of paired...
costatis.randtestMonte-Carlo test on a Costatis analysis (in C).
dagnelie.testDagnelie multinormality test
deugExam marks for some students
discRao's dissimilarity coefficient
discriminLinear Discriminant Analysis (descriptive statistic)
discrimin.coaDiscriminant Correspondence Analysis
dist.binaryComputation of Distance Matrices for Binary Data
dist.dudiComputation of the Distance Matrix from a Statistical Triplet
dist.ktabMixed-variables coefficient of distance
dist.neigComputation of the Distance Matrix associated to a...
dist.propComputation of Distance Matrices of Percentage Data
dist.quantComputation of Distance Matrices on Quantitative Variables
divcRao's diversity coefficient also called quadratic entropy
divcmaxMaximal value of Rao's diversity coefficient also called...
dotchart.phylogRepresentation of many quantitative variables in front of a...
dotcircleRepresentation of n values on a circle
doubsPair of Ecological Tables
dpcoaDouble principal coordinate analysis
dudiDuality Diagram
dudi.acmMultiple Correspondence Analysis
dudi.coaCorrespondence Analysis
dudi.decDecentred Correspondence Analysis
dudi.fcaFuzzy Correspondence Analysis and Fuzzy Principal Components...
dudi.hillsmithOrdination of Tables mixing quantitative variables and...
dudi.mixOrdination of Tables mixing quantitative variables and...
dudi.nscNon symmetric correspondence analysis
dudi.pcaPrincipal Component Analysis
dudi.pcoPrincipal Coordinates Analysis
dunedataDune Meadow Data
ecgElectrocardiogram data
ecomorEcomorphological Convergence
elec88Electoral Data
escopageK-tables of wine-tasting
euro123Triangular Data
fissionFission pattern and heritable morphological traits
foucartK-tables Correspondence Analysis with the same rows and the...
fourthcornerFunctions to compute the fourth-corner statistic
friday87Faunistic K-tables
fruitsPair of Tables
gearymoranMoran's I and Geary'c randomization tests for spatial and...
ggtortoisesMicrosatellites of Galapagos tortoises populations
granuloGranulometric Curves
gridrowcolComplete regular grid analysis
hdpgGenetic Variation In Human Populations
houmousrMorphometric data set
housetasksContingency Table
humDNAmhuman mitochondrial DNA restriction data
ichtyoPoint sampling of fish community
inertia.dudiDecomposition of inertia (i.e. contributions) in multivariate...
irishdataGeary's Irish Data
is.euclidIs a Distance Matrix Euclidean?
julliotSeed dispersal
jv73K-tables Multi-Regions
kcpondsPonds in a nature reserve
kdistthe class of objects 'kdist' (K distance matrices)
kdist2ktabTransformation of K distance matrices (object 'kdist') into K...
kdisteuclida way to obtain Euclidean distance matrices
kplotGeneric Function for Multiple Graphs in a K-tables Analysis
kplot.foucartMultiple Graphs for the Foucart's Correspondence Analysis
kplot.mcoaMultiple Graphs for a Multiple Co-inertia Analysis
kplot.mfaMultiple Graphs for a Multiple Factorial Analysis
kplot.ptaMultiple Graphs for a Partial Triadic Analysis
kplot.sepanMultiple Graphs for Separated Analyses in a K-tables
kplot.statisMultiple Graphs of a STATIS Analysis
krandtestClass of the Permutation Tests (in C).
ktabthe class of objects 'ktab' (K-tables) of K-tables from a data frame
ktab.list.dfCreating a K-tables from a list of data frames.
ktab.list.dudiCreation of a K-tables from a list of duality diagrams
ktab.match2ktabsSTATIS and Co-Inertia : Analysis of a series of paired...
ktab.withinProcess to go from a Within Analysis to a K-tables
lascauxGenetic/Environment and types of variables
lingoesTransformation of a Distance Matrix for becoming Euclidean
lizardsPhylogeny and quantitative traits of lizards
loocv.bcaLeave-one-out cross-validation for a 'bca'
loocv.discriminLeave-one-out cross-validation for a 'discrimin' analysis
loocv.dudiLeave-one-out cross-validation for a 'dudi'
maconWine Tasting
macroloireAssemblages of Macroinvertebrates in the Loire River (France)
mafraghPhyto-Ecological Survey
mantel.randtestMantel test (correlation between two distance matrices (in...
mantel.rtestMantel test (correlation between two distance matrices (in...
maplesPhylogeny and quantitative traits of flowers
mariagesCorrespondence Analysis Table
mbpcaivMultiblock principal component analysis with instrumental...
mbplsMultiblock partial least squares
mcoaMultiple CO-inertia Analysis
mdpcoaMultiple Double Principal Coordinate Analysis
meauEcological Data : sites-variables, sites-species, where and...
meaudretEcological Data : sites-variables, sites-species, where and...
mfaMultiple Factorial Analysis
microsattGenetic Relationships between cattle breeds with...
mjrochetPhylogeny and quantitative traits of teleos fishes
mldMulti Level Decomposition of unidimensional data
molluscFaunistic Communities and Sampling Experiment
monde84Global State of the World in 1984
morphosportAthletes' Morphology
mstreeMinimal Spanning Tree
multiblockDisplay and summarize multiblock objects
multispatiMultivariate spatial analysis
multispati.randtestMultivariate spatial autocorrelation test (in C)
multispati.rtestMultivariate spatial autocorrelation test
neigNeighbourhood Graphs
newick2phylogCreate phylogeny
newick.egPhylogenetic trees in Newick format
nicheMethod to Analyse a pair of tables : Environmental and...
nipalsNon-linear Iterative Partial Least Squares (NIPALS) algorithm
njplotPhylogeny and trait of bacteria
olympicOlympic Decathlon
oribatidOribatid mite
originalityOriginality of a species
orthobasisOrthonormal basis for orthonormal transform
oursA table of Qualitative Variables
palmPhylogenetic and quantitative traits of amazonian palm trees
papTaxonomy and quantitative traits of carnivora
pcaivPrincipal component analysis with respect to instrumental...
pcaivorthoPrincipal Component Analysis with respect to orthogonal...
pcoscaledSimplified Analysis in Principal Coordinates
pcwDistribution of of tropical trees along the Panama canal
perthi02Contingency Table with a partition in Molecular Biology
PI2newickImport data files from Phylogenetic Independance Package
piospherePlant traits response to grazing
plot.betweenBetween-Class Analysis
plot.phylogPlot phylogenies
plot.withinWithin-Class Analysis
presid2002Results of the French presidential elections of 2002
procellaPhylogeny and quantitative traits of birds
procusteSimple Procruste Rotation between two sets of points
procuste.randtestMonte-Carlo Test on the sum of the singular values of a...
procuste.rtestMonte-Carlo Test on the sum of the singular values of a...
ptaPartial Triadic Analysis of a K-tables
quasieuclidTransformation of a distance matrice to a Euclidean one
randbootBootstrap simulations
randboot.multiblockBootstraped simulations for multiblock methods
randtestClass of the Permutation Tests (in C).
randtest.amovaPermutation tests on an analysis of molecular variance (in...
randtest.betweenMonte-Carlo Test on the between-groups inertia percentage (in...
randtest.coinertiaMonte-Carlo test on a Co-inertia analysis (in C).
randtest.discriminMonte-Carlo Test on a Discriminant Analysis (in C).
randtest.dpcoaPermutation test for double principal coordinate analysis...
randtest.pcaivMonte-Carlo Test on the percentage of explained (i.e....
randxvalTwo-fold cross-validation
rankrockOrdination Table
reconstReconstitution of Data from a Duality Diagram
rhizobiumGenetic structure of two nitrogen fixing bacteria influenced...
rhonePhysico-Chemistry Data
rlqRLQ analysis
rpjdlAvifauna and Vegetation
rtestClass of the Permutation Tests (in R).
rtest.betweenMonte-Carlo Test on the between-groups inertia percentage (in...
rtest.discriminMonte-Carlo Test on a Discriminant Analysis (in R).
RVdist.randtestTests of randomization on the correlation between two...
RVintra.randtestMonte-Carlo Test on the sum of eigenvalues of a within-class...
RV.randtestMonte-Carlo Test on the sum of eigenvalues of a co-inertia...
RV.rtestMonte-Carlo Test on the sum of eigenvalues of a co-inertia...
santacatalinaIndirect Ordination
sarcellesArray of Recapture of Rings
s.arrowPlot of the factorial maps for the projection of a vector...
scalewtCompute or scale data using (weighted) means, variances and...
scatterGraphical representation of the outputs of a multivariate...
scatter.acmPlot of the factorial maps in a Multiple Correspondence...
scatter.coaPlot of the factorial maps for a correspondence analysis
scatter.dudiPlot of the Factorial Maps
scatter.fcaPlot of the factorial maps for a fuzzy correspondence...
scatterutilGraphical utility functions
s.chullPlot of the factorial maps with polygons of contour by level...
s.classPlot of factorial maps with representation of point classes
sco.boxplotRepresentation of the link between a variable and a set of...
sco.class1D plot of a numeric score and a factor with labels
sco.distriRepresentation by mean- standard deviation of a set of weight...
sco.gaussRelationships between one score and qualitative variables
sco.label1D plot of a numeric score with labels
sco.match1D plot of a pair of numeric scores with labels
sco.quantGraph to Analyse the Relation between a Score and...
s.corcirclePlot of the factorial maps of a correlation circle
scoreGraphs for One Dimension
score.acmGraphs to study one factor in a Multiple Correspondence...
score.coaReciprocal scaling after a correspondence analysis
score.mixGraphs to Analyse a factor in a Mixed Analysis
score.pcaGraphs to Analyse a factor in PCA
s.distriPlot of a frequency distribution
secondeStudents and Subjects
sepanSeparated Analyses in a K-tables
s.histDisplay of a scatterplot and its two marginal histograms
s.imageGraph of a variable using image and contour
s.kde2dScatter Plot with Kernel Density Estimate
skullsMorphometric Evolution
s.labelScatter Plot
s.logoRepresentation of an object in a graph by a picture
s.matchPlot of Paired Coordinates
s.match.classScatterplot of two sets of coordinates and a partionning into...
s.multinomGraph of frequency profiles (useful for instance in genetic)
staticoSTATIS and Co-Inertia : Analysis of a series of paired...
statico.krandtestMonte-Carlo test on a Statico analysis (in C).
statisSTATIS, a method for analysing K-tables
steppeTransect in the Vegetation
s.trajectTrajectory Plot
supcolProjections of Supplementary Columns
supdistProjection of additional items in a PCO analysis
suprowProjections of Supplementary Rows
suprow.ptaProjections of Supplementary Rows for a Partial Triadic...
s.valueRepresentation of a value in a graph
symbols.phylogRepresentation of a quantitative variable in front of a...
syndicatsTwo Questions asked on a Sample of 1000 Respondents
t3012Average temperatures of 30 French cities
table.contPlot of Contingency Tables
table.distGraph Display for Distance Matrices
table.paintPlot of the arrays by grey levels
table.phylogPlot arrays in front of a phylogenetic tree
table.valuePlot of the Arrays
tarentaiseMountain Avifauna
taxo.egExamples of taxonomy
testdimFunction to perform a test of dimensionality
testdim.multiblockSelection of the number of dimension by two-fold...
tintoodielTinto and Odiel estuary geochemistry
tithoniaPhylogeny and quantitative traits of flowers
tortuesMorphological Study of the Painted Turtle
toxicityHomogeneous Table
triangle.classTriangular Representation and Groups of points
triangle.plotTriangular Plotting
trichometeoPair of Ecological Data
ungulatesPhylogeny and quantitative traits of ungulates.
uniquewt.dfElimination of Duplicated Rows in a Array
variance.phylogThe phylogenetic ANOVA
varipartPartition of the variation of a response multivariate table...
vegtfVegetation in Trois-Fontaines
veuvageExample for Centring in PCA
wcaWithin-Class Analysis
wca.coinertiaWithin-class coinertia analysis
wca.rlqWithin-Class RLQ analysis
westafricaFreshwater fish zoogeography in west Africa
withinpcaNormed within principal component analysis
witwit.coaInternal Correspondence Analysis
woangersPlant assemblages in woodlands of the conurbation of Angers...
worksurvFrench Worker Survey (1970)
yanomamaDistance Matrices
zealandRoad distances in New-Zealand
ade4 documentation built on Feb. 16, 2023, 7:58 p.m.