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

abouheif.eg | Phylogenies and quantitative traits from Abouheif |

acacia | Spatial pattern analysis in plant communities |

add.scatter | Add graphics to an existing plot |

ade4-deprecated | Deprecated functions in ade4 |

ade4-internal | Internal ade4 functions |

ade4.package | The ade4 package |

adegraphicsLoaded | Utility function to test if the package adegraphics is loaded |

aminoacyl | Codon usage |

amova | Analysis of molecular variance |

apis108 | Allelic frequencies in ten honeybees populations at eight... |

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 |

arrival | Arrivals at an intensive care unit |

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 |

bacteria | Genomes of 43 Bacteria |

banque | Table of Factors |

baran95 | African Estuary Fishes |

bca | Between-Class Analysis |

bca.coinertia | Between-class coinertia analysis |

bca.rlq | Between-Class RLQ analysis |

bf88 | Cubic Ecological Data |

bicenter.wt | Double Weighted Centring |

bordeaux | Wine Tasting |

bsetal97 | Ecological and Biological Traits |

buech | Buech basin |

butterfly | Genetics-Ecology-Environment Triple |

bwca.dpcoa | Between- and within-class double principal coordinate... |

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... |

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... |

clementines | Fruit Production |

cnc2003 | Frequenting movie theaters in France in 2003 |

coinertia | Coinertia Analysis |

coleo | Table of Fuzzy Biological Traits |

combine.4thcorner | Functions to combine and adjust the outputs 3-table methods |

corkdist | Tests of randomization between distances applied to 'kdist'... |

corvus | Corvus morphology |

costatis | STATIS and Co-Inertia : Analysis of a series of paired... |

costatis.randtest | Monte-Carlo test on a Costatis analysis (in C). |

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... |

dist.prop | Computation of Distance Matrices of Percentage Data |

dist.quant | Computation of Distance Matrices on Quantitative Variables |

divc | Rao's diversity coefficient also called quadratic entropy |

divcmax | Maximal value of Rao's diversity coefficient also called... |

dotchart.phylog | Representation of many quantitative variables in front of a... |

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... |

dudi.hillsmith | Ordination of Tables mixing quantitative variables and... |

dudi.mix | Ordination of Tables mixing quantitative variables and... |

dudi.nsc | Non symmetric correspondence analysis |

dudi.pca | Principal Component Analysis |

dudi.pco | Principal Coordinates Analysis |

dunedata | Dune Meadow Data |

ecg | Electrocardiogram data |

ecomor | Ecomorphological Convergence |

elec88 | Electoral Data |

escopage | K-tables of wine-tasting |

euro123 | Triangular Data |

fission | Fission pattern and heritable morphological traits |

foucart | K-tables Correspondence Analysis with the same rows and the... |

fourthcorner | Functions to compute the fourth-corner statistic |

friday87 | Faunistic K-tables |

fruits | Pair of Tables |

gearymoran | Moran's I and Geary'c randomization tests for spatial and... |

ggtortoises | Microsatellites of Galapagos tortoises populations |

granulo | Granulometric Curves |

gridrowcol | Complete regular grid analysis |

hdpg | Genetic Variation In Human Populations |

houmousr | Morphometric data set |

housetasks | Contingency Table |

humDNAm | human mitochondrial DNA restriction data |

ichtyo | Point sampling of fish community |

inertia.dudi | Decomposition of inertia (i.e. contributions) in multivariate... |

irishdata | Geary's Irish Data |

is.euclid | Is a Distance Matrix Euclidean? |

julliot | Seed dispersal |

jv73 | K-tables Multi-Regions |

kcponds | Ponds in a nature reserve |

kdist | the class of objects 'kdist' (K distance matrices) |

kdist2ktab | Transformation of K distance matrices (object 'kdist') into K... |

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 |

krandtest | Class of the Permutation Tests (in C). |

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... |

ktab.within | Process to go from a Within Analysis to a K-tables |

lascaux | Genetic/Environment and types of variables |

lingoes | Transformation of a Distance Matrix for becoming Euclidean |

lizards | Phylogeny and quantitative traits of lizards |

loocv.bca | 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' |

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... |

mantel.rtest | Mantel test (correlation between two distance matrices (in... |

maples | Phylogeny and quantitative traits of flowers |

mariages | Correspondence Analysis Table |

mbpcaiv | Multiblock principal component analysis with instrumental... |

mbpls | Multiblock partial least squares |

mcoa | Multiple CO-inertia Analysis |

mdpcoa | Multiple Double Principal Coordinate Analysis |

meau | Ecological Data : sites-variables, sites-species, where and... |

meaudret | Ecological Data : sites-variables, sites-species, where and... |

mfa | Multiple Factorial Analysis |

microsatt | Genetic Relationships between cattle breeds with... |

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 |

multiblock | Display and summarize multiblock objects |

multispati | Multivariate spatial analysis |

multispati.randtest | Multivariate spatial autocorrelation test (in C) |

multispati.rtest | Multivariate spatial autocorrelation test |

neig | Neighbourhood Graphs |

newick2phylog | Create phylogeny |

newick.eg | Phylogenetic trees in Newick format |

niche | Method to Analyse a pair of tables : Environmental and... |

nipals | Non-linear Iterative Partial Least Squares (NIPALS) algorithm |

njplot | Phylogeny and trait of bacteria |

olympic | Olympic Decathlon |

oribatid | Oribatid mite |

originality | Originality of a species |

orthobasis | Orthonormal basis for orthonormal transform |

ours | A table of Qualitative Variables |

palm | Phylogenetic and quantitative traits of amazonian palm trees |

pap | Taxonomy and quantitative traits of carnivora |

pcaiv | Principal component analysis with respect to instrumental... |

pcaivortho | Principal Component Analysis with respect to orthogonal... |

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 |

PI2newick | Import data files from Phylogenetic Independance Package |

piosphere | Plant traits response to grazing |

plot.between | Between-Class Analysis |

plot.phylog | Plot phylogenies |

plot.within | Within-Class Analysis |

presid2002 | Results of the French presidential elections of 2002 |

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... |

procuste.rtest | Monte-Carlo Test on the sum of the singular values of a... |

pta | Partial Triadic Analysis of a K-tables |

quasieuclid | Transformation of a distance matrice to a Euclidean one |

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... |

randtest.between | Monte-Carlo Test on the between-groups inertia percentage (in... |

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... |

randtest.pcaiv | Monte-Carlo Test on the percentage of explained (i.e.... |

randxval | Two-fold cross-validation |

rankrock | Ordination Table |

reconst | Reconstitution of Data from a Duality Diagram |

rhizobium | Genetic structure of two nitrogen fixing bacteria influenced... |

rhone | Physico-Chemistry Data |

rlq | RLQ analysis |

rpjdl | Avifauna and Vegetation |

rtest | Class of the Permutation Tests (in R). |

rtest.between | Monte-Carlo Test on the between-groups inertia percentage (in... |

rtest.discrimin | Monte-Carlo Test on a Discriminant Analysis (in R). |

RVdist.randtest | Tests of randomization on the correlation between two... |

RVintra.randtest | Monte-Carlo Test on the sum of eigenvalues of a within-class... |

RV.randtest | Monte-Carlo Test on the sum of eigenvalues of a co-inertia... |

RV.rtest | Monte-Carlo Test on the sum of eigenvalues of a co-inertia... |

santacatalina | Indirect Ordination |

sarcelles | Array of Recapture of Rings |

s.arrow | Plot of the factorial maps for the projection of a vector... |

scalewt | Compute or scale data using (weighted) means, variances and... |

scatter | Graphical representation of the outputs of a multivariate... |

scatter.acm | Plot of the factorial maps in a Multiple Correspondence... |

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... |

scatterutil | Graphical utility functions |

s.chull | Plot of the factorial maps with polygons of contour by level... |

s.class | Plot of factorial maps with representation of point classes |

sco.boxplot | Representation of the link between a variable and a set of... |

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... |

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... |

s.corcircle | Plot of the factorial maps of a correlation circle |

score | Graphs for One Dimension |

score.acm | Graphs to study one factor in a Multiple Correspondence... |

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 |

s.distri | Plot of a frequency distribution |

seconde | Students and Subjects |

sepan | Separated Analyses in a K-tables |

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 |

skulls | Morphometric Evolution |

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... |

s.multinom | Graph of frequency profiles (useful for instance in genetic) |

statico | STATIS and Co-Inertia : Analysis of a series of paired... |

statico.krandtest | Monte-Carlo test on a Statico analysis (in C). |

statis | STATIS, a method for analysing K-tables |

steppe | Transect in the Vegetation |

s.traject | Trajectory Plot |

supcol | Projections of Supplementary Columns |

supdist | Projection of additional items in a PCO analysis |

suprow | Projections of Supplementary Rows |

suprow.pta | Projections of Supplementary Rows for a Partial Triadic... |

s.value | Representation of a value in a graph |

symbols.phylog | Representation of a quantitative variable in front of a... |

syndicats | Two Questions asked on a Sample of 1000 Respondents |

t3012 | Average temperatures of 30 French cities |

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.value | Plot of the Arrays |

tarentaise | Mountain Avifauna |

taxo.eg | Examples of taxonomy |

testdim | Function to perform a test of dimensionality |

testdim.multiblock | Selection of the number of dimension by two-fold... |

tintoodiel | Tinto and Odiel estuary geochemistry |

tithonia | Phylogeny and quantitative traits of flowers |

tortues | Morphological Study of the Painted Turtle |

toxicity | Homogeneous Table |

triangle.class | Triangular Representation and Groups of points |

triangle.plot | Triangular Plotting |

trichometeo | Pair of Ecological Data |

ungulates | Phylogeny and quantitative traits of ungulates. |

uniquewt.df | Elimination of Duplicated Rows in a Array |

variance.phylog | The phylogenetic ANOVA |

varipart | Partition of the variation of a response multivariate table... |

vegtf | Vegetation in Trois-Fontaines |

veuvage | Example for Centring in PCA |

wca | Within-Class Analysis |

wca.coinertia | Within-class coinertia 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 |

woangers | Plant assemblages in woodlands of the conurbation of Angers... |

worksurv | French Worker Survey (1970) |

yanomama | Distance Matrices |

zealand | Road distances in New-Zealand |

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