ade4 v1.7-15
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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>.
Functions in ade4
| Name | Description | |
| Deprecated functions | Deprecated functions in ade4 | |
| acacia | Spatial pattern analysis in plant communities | |
| area.plot | Graphical Display of Areas | |
| ade4-internal | Internal ade4 functions | |
| arrival | Arrivals at an intensive care unit | |
| add.scatter | Add graphics to an existing plot | |
| as.taxo | Taxonomy | |
| atlas | Small Ecological Dataset | |
| atya | Genetic variability of Cacadors | |
| ade4-package | The ade4 package | |
| adegraphicsLoaded | Utility function to test if the package adegraphics is loaded | |
| aminoacyl | Codon usage | |
| avijons | Bird species distribution | |
| amova | Analysis of molecular variance | |
| RVdist.randtest | Tests of randomization on the correlation between two distance matrices (in R). | |
| avimedi | Fauna Table for Constrained Ordinations | |
| aviurba | Ecological Tables Triplet | |
| buech | Buech basin | |
| bacteria | Genomes of 43 Bacteria | |
| RV.rtest | Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R). | |
| bordeaux | Wine Tasting | |
| banque | Table of Factors | |
| PI2newick | Import data files from Phylogenetic Independance Package | |
| bsetal97 | Ecological and Biological Traits | |
| carni19 | Phylogeny and quantative trait of carnivora | |
| capitales | Road Distances | |
| butterfly | Genetics-Ecology-Environment Triple | |
| carniherbi49 | Taxonomy, phylogenies and quantitative traits of carnivora and herbivora | |
| corvus | Corvus morphology | |
| costatis | STATIS and Co-Inertia : Analysis of a series of paired ecological tables | |
| carni70 | Phylogeny and quantitative traits of carnivora | |
| divcmax | Maximal value of Rao's diversity coefficient also called quadratic entropy | |
| apis108 | Allelic frequencies in ten honeybees populations at eight microsatellites loci | |
| divc | Rao's diversity coefficient also called quadratic entropy | |
| chazeb | Charolais-Zebus | |
| abouheif.eg | Phylogenies and quantitative traits from Abouheif | |
| dudi | Duality Diagram | |
| apqe | Apportionment of Quadratic Entropy | |
| chevaine | Enzymatic polymorphism in Leuciscus cephalus | |
| aravo | Distribution of Alpine plants in Aravo (Valloire, France) | |
| chats | Pair of Variables | |
| ardeche | Fauna Table with double (row and column) partitioning | |
| deug | Exam marks for some students | |
| disc | Rao's dissimilarity coefficient | |
| chickenk | Veterinary epidemiological study to assess the risk factors for losses in broiler chickens | |
| dudi.mix | Ordination of Tables mixing quantitative variables and factors | |
| costatis.randtest | Monte-Carlo test on a Costatis analysis (in C). | |
| baran95 | African Estuary Fishes | |
| dist.dudi | Computation of the Distance Matrix from a Statistical Triplet | |
| dist.binary | Computation of Distance Matrices for Binary Data | |
| fourthcorner | Functions to compute the fourth-corner statistic | |
| dudi.acm | Multiple Correspondence Analysis | |
| dudi.nsc | Non symmetric correspondence analysis | |
| dagnelie.test | Dagnelie multinormality test | |
| bca | Between-Class Analysis | |
| irishdata | Geary's Irish Data | |
| friday87 | Faunistic K-tables | |
| dudi.dec | Decentred Correspondence Analysis | |
| euro123 | Triangular Data | |
| escopage | K-tables of wine-tasting | |
| dudi.coa | Correspondence Analysis | |
| krandtest | Class of the Permutation Tests (in C). | |
| is.euclid | Is a Distance Matrix Euclidean? | |
| discrimin | Linear Discriminant Analysis (descriptive statistic) | |
| ggtortoises | Microsatellites of Galapagos tortoises populations | |
| bf88 | Cubic Ecological Data | |
| kplot.statis | Multiple Graphs of a STATIS Analysis | |
| bicenter.wt | Double Weighted Centring | |
| kplot.pta | Multiple Graphs for a Partial Triadic Analysis | |
| kplot.sepan | Multiple Graphs for Separated Analyses in a K-tables | |
| ktab.data.frame | Creation of K-tables from a data frame | |
| kcponds | Ponds in a nature reserve | |
| kdist | the class of objects 'kdist' (K distance matrices) | |
| mantel.rtest | Mantel test (correlation between two distance matrices (in R).) | |
| ktab | the class of objects 'ktab' (K-tables) | |
| casitas | Enzymatic polymorphism in Mus musculus | |
| maples | Phylogeny and quantitative traits of flowers | |
| granulo | Granulometric Curves | |
| monde84 | Global State of the World in 1984 | |
| lizards | Phylogeny and quantitative traits of lizards | |
| discrimin.coa | Discriminant Correspondence Analysis | |
| morphosport | Athletes' Morphology | |
| between | Between-Class Analysis | |
| multispati | Multivariate spatial analysis | |
| originality | Originality of a species | |
| multispati.randtest | Multivariate spatial autocorrelation test (in C) | |
| piosphere | Plant traits response to grazing | |
| dudi.fca | Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis | |
| bca.rlq | Between-Class RLQ analysis | |
| combine.4thcorner | Functions to combine and adjust the outputs 3-table methods | |
| corkdist | Tests of randomization between distances applied to 'kdist' objetcs | |
| dist.ktab | Mixed-variables coefficient of distance | |
| oribatid | Oribatid mite | |
| dist.neig | Computation of the Distance Matrix associated to a Neighbouring Graph | |
| doubs | Pair of Ecological Tables | |
| dpcoa | Double principal coordinate analysis | |
| macaca | Landmarks | |
| bca.coinertia | Between-class coinertia analysis | |
| mcoa | Multiple CO-inertia Analysis | |
| dunedata | Dune Meadow Data | |
| mbpls | Multiblock partial least squares | |
| dudi.pca | Principal Component Analysis | |
| chatcat | Qualitative Weighted Variables | |
| dudi.hillsmith | Ordination of Tables mixing quantitative variables and factors | |
| dudi.pco | Principal Coordinates Analysis | |
| randboot | Bootstrap simulations | |
| rhizobium | Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization | |
| bwca.dpcoa | Between- and within-class double principal coordinate analysis | |
| hdpg | Genetic Variation In Human Populations | |
| s.hist | Display of a scatterplot and its two marginal histograms | |
| s.distri | Plot of a frequency distribution | |
| cailliez | Transformation to make Euclidean a distance matrix | |
| gridrowcol | Complete regular grid analysis | |
| reconst | Reconstitution of Data from a Duality Diagram | |
| s.match | Plot of Paired Coordinates | |
| foucart | K-tables Correspondence Analysis with the same rows and the same columns | |
| fission | Fission pattern and heritable morphological traits | |
| jv73 | K-tables Multi-Regions | |
| mdpcoa | Multiple Double Principal Coordinate Analysis | |
| julliot | Seed dispersal | |
| cnc2003 | Frequenting movie theaters in France in 2003 | |
| quasieuclid | Transformation of a distance matrice to a Euclidean one | |
| kplot.mfa | Multiple Graphs for a Multiple Factorial Analysis | |
| meau | Ecological Data : sites-variables, sites-species, where and when | |
| clementines | Fruit Production | |
| ecg | Electrocardiogram data | |
| coleo | Table of Fuzzy Biological Traits | |
| s.match.class | Scatterplot of two sets of coordinates and a partionning into classes | |
| kplot.mcoa | Multiple Graphs for a Multiple Co-inertia Analysis | |
| ktab.match2ktabs | STATIS and Co-Inertia : Analysis of a series of paired ecological tables | |
| mafragh | Phyto-Ecological Survey | |
| coinertia | Coinertia Analysis | |
| dist.prop | Computation of Distance Matrices of Percentage Data | |
| dotchart.phylog | Representation of many quantitative variables in front of a phylogenetic tree | |
| dist.quant | Computation of Distance Matrices on Quantitative Variables | |
| kdist2ktab | Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab') | |
| ichtyo | Point sampling of fish community | |
| newick.eg | Phylogenetic trees in Newick format | |
| dotcircle | Representation of n values on a circle | |
| inertia.dudi | Decomposition of inertia (i.e. contributions) in multivariate methods | |
| mantel.randtest | Mantel test (correlation between two distance matrices (in C).) | |
| ecomor | Ecomorphological Convergence | |
| ktab.within | Process to go from a Within Analysis to a K-tables | |
| orthobasis | Orthonormal basis for orthonormal transform | |
| scatter | Graphical representation of the outputs of a multivariate analysis | |
| scatter.acm | Plot of the factorial maps in a Multiple Correspondence Analysis | |
| newick2phylog | Create phylogeny | |
| lascaux | Genetic/Environment and types of variables | |
| kdisteuclid | a way to obtain Euclidean distance matrices | |
| ours | A table of Qualitative Variables | |
| elec88 | Electoral Data | |
| plot.phylog | Plot phylogenies | |
| fruits | Pair of Tables | |
| multiblock | Display and summarize multiblock objects | |
| score.acm | Graphs to study one factor in a Multiple Correspondence Analysis | |
| gearymoran | Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation | |
| statis | STATIS, a method for analysing K-tables | |
| mld | Multi Level Decomposition of unidimensional data | |
| mollusc | Faunistic Communities and Sampling Experiment | |
| mstree | Minimal Spanning Tree | |
| 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 | |
| score.coa | Reciprocal scaling after a correspondence analysis | |
| within | Within-Class Analysis | |
| pcaiv | Principal component analysis with respect to instrumental variables | |
| statico.krandtest | Monte-Carlo test on a Statico analysis (in C). | |
| randtest.amova | Permutation tests on an analysis of molecular variance (in C). | |
| macon | Wine Tasting | |
| tintoodiel | Tinto and Odiel estuary geochemistry | |
| testdim.multiblock | Selection of the number of dimension by two-fold cross-validation for multiblock methods | |
| niche | Method to Analyse a pair of tables : Environmental and Faunistic Data | |
| macroloire | Assemblages of Macroinvertebrates in the Loire River (France) | |
| nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm | |
| mjrochet | Phylogeny and quantitative traits of teleos fishes | |
| presid2002 | Results of the French presidential elections of 2002 | |
| wca.coinertia | Within-class coinertia analysis | |
| procella | Phylogeny and quantitative traits of birds | |
| lingoes | Transformation of a Distance Matrix for becoming Euclidean | |
| pcaivortho | Principal Component Analysis with respect to orthogonal instrumental variables | |
| housetasks | Contingency Table | |
| microsatt | Genetic Relationships between cattle breeds with microsatellites | |
| wca | Within-Class Analysis | |
| randtest.between | Monte-Carlo Test on the between-groups inertia percentage (in C). | |
| woangers | Plant assemblages in woodlands of the conurbation of Angers (France) | |
| rtest.discrimin | Monte-Carlo Test on a Discriminant Analysis (in R). | |
| kplot.foucart | Multiple Graphs for the Foucart's Correspondence Analysis | |
| kplot | Generic Function for Multiple Graphs in a K-tables Analysis | |
| randtest.discrimin | Monte-Carlo Test on a Discriminant Analysis (in C). | |
| njplot | Phylogeny and trait of bacteria | |
| humDNAm | human mitochondrial DNA restriction data | |
| procuste.randtest | Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C). | |
| rtest.between | Monte-Carlo Test on the between-groups inertia percentage (in R). | |
| s.value | Representation of a value in a graph | |
| rankrock | Ordination Table | |
| procuste | Simple Procruste Rotation between two sets of points | |
| santacatalina | Indirect Ordination | |
| sarcelles | Array of Recapture of Rings | |
| randxval | Two-fold cross-validation | |
| ktab.list.df | Creating a K-tables from a list of data frames. | |
| randtest.coinertia | Monte-Carlo test on a Co-inertia analysis (in C). | |
| ktab.list.dudi | Creation of a K-tables from a list of duality diagrams | |
| rpjdl | Avifauna and Vegetation | |
| sco.label | 1D plot of a numeric score with labels | |
| scalewt | Compute or scale data using (weighted) means, variances and covariances (possibly for the levels of a factor) | |
| sco.match | 1D plot of a pair of numeric scores with labels | |
| statico | STATIS and Co-Inertia : Analysis of a series of paired ecological tables | |
| t3012 | Average temperatures of 30 French cities | |
| skulls | Morphometric Evolution | |
| syndicats | Two Questions asked on a Sample of 1000 Respondents | |
| trichometeo | Pair of Ecological Data | |
| rtest | Class of the Permutation Tests (in R). | |
| s.multinom | Graph of frequency profiles (useful for instance in genetic) | |
| mariages | Correspondence Analysis Table | |
| meaudret | Ecological Data : sites-variables, sites-species, where and when | |
| wca.rlq | Within-Class RLQ analysis | |
| randboot.multiblock | Bootstraped simulations for multiblock methods | |
| olympic | Olympic Decathlon | |
| mbpcaiv | Multiblock principal component analysis with instrumental variables | |
| triangle.plot | Triangular Plotting | |
| pcoscaled | Simplified Analysis in Principal Coordinates | |
| pcw | Distribution of of tropical trees along the Panama canal | |
| worksurv | French Worker Survey (1970) | |
| s.traject | Trajectory Plot | |
| rhone | Physico-Chemistry Data | |
| multispati.rtest | Multivariate spatial autocorrelation test | |
| mfa | Multiple Factorial Analysis | |
| randtest | Class of the Permutation Tests (in C). | |
| rlq | RLQ analysis | |
| scatter.coa | Plot of the factorial maps for a correspondence analysis | |
| westafrica | Freshwater fish zoogeography in west Africa | |
| score.pca | Graphs to Analyse a factor in PCA | |
| scatter.dudi | Plot of the Factorial Maps | |
| s.class | Plot of factorial maps with representation of point classes | |
| palm | Phylogenetic and quantitative traits of amazonian palm trees | |
| s.corcircle | Plot of the factorial maps of a correlation circle | |
| neig | Neighbourhood Graphs | |
| pap | Taxonomy and quantitative traits of carnivora | |
| table.phylog | Plot arrays in front of a phylogenetic tree | |
| steppe | Transect in the Vegetation | |
| supcol | Projections of Supplementary Columns | |
| table.paint | Plot of the arrays by grey levels | |
| perthi02 | Contingency Table with a partition in Molecular Biology | |
| score.mix | Graphs to Analyse a factor in a Mixed Analysis | |
| s.label | Scatter Plot | |
| withinpca | Normed within principal component analysis | |
| pta | Partial Triadic Analysis of a K-tables | |
| s.logo | Representation of an object in a graph by a picture | |
| ungulates | Phylogeny and quantitative traits of ungulates. | |
| toxicity | Homogeneous Table | |
| randtest.dpcoa | Permutation test for double principal coordinate analysis (DPCoA) | |
| phylog | Phylogeny | |
| triangle.class | Triangular Representation and Groups of points | |
| procuste.rtest | Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R). | |
| witwit.coa | Internal Correspondence Analysis | |
| uniquewt.df | Elimination of Duplicated Rows in a Array | |
| sco.quant | Graph to Analyse the Relation between a Score and Quantitative Variables | |
| sco.boxplot | Representation of the link between a variable and a set of qualitative variables | |
| zealand | Road distances in New-Zealand | |
| yanomama | Distance Matrices | |
| randtest.pcaiv | Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia | |
| sco.class | 1D plot of a numeric score and a factor with labels | |
| score | Graphs for One Dimension | |
| s.arrow | Plot of the factorial maps for the projection of a vector basis | |
| supdist | Projection of additional items in a PCO analysis | |
| s.chull | Plot of the factorial maps with polygons of contour by level of a factor | |
| s.image | Graph of a variable using image and contour | |
| suprow | Projections of Supplementary Rows | |
| s.kde2d | Scatter Plot with Kernel Density Estimate | |
| veuvage | Example for Centring in PCA | |
| testdim | Function to perform a test of dimensionality | |
| tarentaise | Mountain Avifauna | |
| vegtf | Vegetation in Trois-Fontaines | |
| table.value | Plot of the Arrays | |
| scatter.fca | Plot of the factorial maps for a fuzzy correspondence analysis | |
| taxo.eg | Examples of taxonomy | |
| scatterutil | Graphical utility functions | |
| sco.gauss | Relationships between one score and qualitative variables | |
| sco.distri | Representation by mean- standard deviation of a set of weight distributions on a numeric score | |
| seconde | Students and Subjects | |
| table.cont | Plot of Contingency Tables | |
| sepan | Separated Analyses in a K-tables | |
| tithonia | Phylogeny and quantitative traits of flowers | |
| table.dist | Graph Display for Distance Matrices | |
| varipart | Partition of the variation of a response multivariate table by 2 explanatory tables | |
| variance.phylog | The phylogenetic ANOVA | |
| tortues | Morphological Study of the Painted Turtle | |
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Details
| Date | 2020-02-13 |
| License | GPL (>= 2) |
| URL | http://pbil.univ-lyon1.fr/ADE-4 |
| BugReports | https://github.com/sdray/ade4/issues |
| Encoding | UTF-8 |
| NeedsCompilation | yes |
| Packaged | 2020-02-13 09:06:03 UTC; stephane |
| Repository | CRAN |
| Date/Publication | 2020-02-13 11:50:07 UTC |
| suggests | ade4TkGUI , adegraphics , adephylo , ape , CircStats , deldir , lattice , spdep , splancs , waveslim |
| imports | graphics , grDevices , MASS , methods , pixmap , sp , stats , utils |
| depends | R (>= 2.10) |
| Contributors | AnneBatrice Dufour, Jean Thioulouse, Stéphane Dray |
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