| 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 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 |
| Multivariate spatial analysis | multispati plot.multispati print.multispati summary.multispati |
| Multivariate spatial autocorrelation test (in C) | multispati.randtest |
| Multivariate spatial autocorrelation test | multispati.rtest |
| 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 |
