# 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 | |

No Results! |

## Last month downloads

## 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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