`install.packages('ade4')`

28,028

1.7-8

GPL (>= 2)

August 9th, 2017

abouheif.eg

Phylogenies and quantitative traits from Abouheif

acacia

Spatial pattern analysis in plant communities

ade4-internal

Internal ade4 functions

ade4-package

The ade4 package

RV.rtest

Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).

RVdist.randtest

Tests of randomization on the correlation between two distance matrices (in R).

add.scatter

Add graphics to an existing plot

Deprecated functions

Deprecated functions in ade4

EH

Amount of Evolutionary History

PI2newick

Import data files from Phylogenetic Independance 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 microsatellites loci

avijons

Bird species distribution

bca.rlq

Between-Class RLQ analysis

bca

Between-Class Analysis

butterfly

Genetics-Ecology-Environment Triple

bwca.dpcoa

Between- and within-class double principal coordinate analysis

ardeche

Fauna Table with double (row and column) partitioning

area.plot

Graphical Display of Areas

banque

Table of Factors

baran95

African Estuary Fishes

arrival

Arrivals at an intensive care unit

as.taxo

Taxonomy

atlas

Small Ecological Dataset

atya

Genetic variability of Cacadors

bicenter.wt

Double Weighted Centring

bordeaux

Wine Tasting

chazeb

Charolais-Zebus

chevaine

Enzymatic polymorphism in Leuciscus cephalus

chatcat

Qualitative Weighted Variables

chats

Pair of Variables

coleo

Table of Fuzzy Biological Traits

corkdist

Tests of randomization between distances applied to 'kdist' objetcs

corvus

Corvus morphology

dist.quant

Computation of Distance Matrices on Quantitative Variables

divc

Rao's diversity coefficient also called quadratic entropy

apqe

Apportionment of Quadratic Entropy

aravo

Distribution of Alpine plants in Aravo (Valloire, France)

aviurba

Ecological Tables Triplet

bacteria

Genomes of 43 Bacteria

dotcircle

Representation of n values on a circle

doubs

Pair of Ecological Tables

dudi.pco

Principal Coordinates Analysis

dunedata

Dune Meadow Data

cailliez

Transformation to make Euclidean a distance matrix

capitales

Road Distances

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

casitas

Enzymatic polymorphism in Mus musculus

bsetal97

Ecological and Biological Traits

buech

Buech basin

chickenk

Veterinary epidemiological study to assess the risk factors for losses in broiler chickens

clementines

Fruit Production

combine.4thcorner

Functions to combine and adjust the outputs 3-table methods

dist.binary

Computation of Distance Matrices for Binary Data

dist.dudi

Computation of the Distance Matrix from a Statistical Triplet

dudi.dec

Decentred Correspondence Analysis

foucart

K-tables Correspondence Analysis with the same rows and the same columns

fourthcorner

Functions to compute the fourth-corner statistic

humDNAm

human mitochondrial DNA restriction data

deug

Exam marks for some students

disc

Rao's dissimilarity coefficient

dist.genet

Genetic distances from gene frequencies

dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis

elec88

Electoral Data

escopage

K-tables of wine-tasting

euro123

Triangular Data

avimedi

Fauna Table for Constrained Ordinations

bca.coinertia

Between-class coinertia analysis

bf88

Cubic Ecological Data

carni19

Phylogeny and quantative trait of carnivora

costatis

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

costatis.randtest

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

discrimin

Linear Discriminant Analysis (descriptive statistic)

discrimin.coa

Discriminant Correspondence Analysis

divcmax

Maximal value of Rao's diversity coefficient also called
quadratic entropy

dotchart.phylog

Representation of many quantitative variables in front of a phylogenetic tree

ecg

Electrocardiogram data

carni70

Phylogeny and quantitative traits of carnivora

cnc2003

Frequenting movie theaters in France in 2003

coinertia

Coinertia Analysis

dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph

dist.ktab

Mixed-variables coefficient of distance

dudi.acm

Multiple Correspondence Analysis

dudi.coa

Correspondence Analysis

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

dudi.mix

Ordination of Tables mixing quantitative variables and factors

friday87

Faunistic K-tables

ichtyo

Point sampling of fish community

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

ktab.data.frame

Creation of K-tables from a data frame

fruits

Pair of Tables

inertia.dudi

Decomposition of inertia (i.e. contributions) in multivariate methods

irishdata

Geary's Irish Data

kdist

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

ecomor

Ecomorphological Convergence

genet

A class of data: tables of populations and alleles

ggtortoises

Microsatellites of Galapagos tortoises populations

is.euclid

Is a Distance Matrix Euclidean?

kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis

fission

Fission pattern and heritable morphological traits

granulo

Granulometric Curves

gridrowcol

Complete regular grid analysis

kdisteuclid

a way to obtain Euclidean distance matrices

ktab.list.df

Creating a K-tables from a list of data frames.

maples

Phylogeny and quantitative traits of flowers

mariages

Correspondence Analysis Table

meau

Ecological Data : sites-variables, sites-species, where and when

dist.prop

Computation of Distance Matrices of Percentage Data

dpcoa

Double principal coordinate analysis

dudi

Duality Diagram

dudi.nsc

Non symmetric correspondence analysis

julliot

Seed dispersal

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

ktab.within

Process to go from a Within Analysis to a K-tables

kdist2ktab

Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')

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 ecological tables

lingoes

Transformation of a Distance Matrix for becoming Euclidean

lizards

Phylogeny and quantitative traits of lizards

mjrochet

Phylogeny and quantitative traits of teleos fishes

mld

Multi Level Decomposition of unidimensional data

multiblock

Display and summarize multiblock objects

dudi.pca

Principal Component Analysis

fuzzygenet

Reading a table of genetic data (diploid individuals)

gearymoran

Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation

meaudret

Ecological Data : sites-variables, sites-species, where and when

multispati.randtest

Multivariate spatial autocorrelation test (in C)

multispati.rtest

Multivariate spatial autocorrelation test

orisaved

Maximal or minimal amount of originality saved under optimal conditions

lascaux

Genetic/Environment and types of variables

macroloire

Assemblages of Macroinvertebrates in the Loire River (France)

mafragh

Phyto-Ecological Survey

mcoa

Multiple CO-inertia Analysis

mdpcoa

Multiple Double Principal Coordinate Analysis

mollusc

Faunistic Communities and Sampling Experiment

monde84

Global State of the World in 1984

oribatid

Oribatid mite

originality

Originality of a species

palm

Phylogenetic and quantitative traits of amazonian palm trees

pap

Taxonomy and quantitative traits of carnivora

procuste.rtest

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).

hdpg

Genetic Variation In Human Populations

housetasks

Contingency Table

jv73

K-tables Multi-Regions

kcponds

Ponds in a nature reserve

multispati

Multivariate spatial analysis

nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm

njplot

Phylogeny and trait of bacteria

orthogram

Orthonormal decomposition of variance

pta

Partial Triadic Analysis of a K-tables

randboot

Bootstrap simulations

randboot.multiblock

Bootstraped simulations for multiblock methods

krandtest

Class of the Permutation Tests (in C).

ktab

the class of objects 'ktab' (K-tables)

macaca

Landmarks

macon

Wine Tasting

orthobasis

Orthonormal basis for orthonormal transform

pcoscaled

Simplified Analysis in Principal Coordinates

pcw

Distribution of of tropical trees along the Panama canal

procuste

Simple Procruste Rotation between two sets of points

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

kplot.statis

Multiple Graphs of a STATIS Analysis

mantel.randtest

Mantel test (correlation between two distance matrices (in C).)

mantel.rtest

Mantel test (correlation between two distance matrices (in R).)

mfa

Multiple Factorial Analysis

microsatt

Genetic Relationships between cattle breeds with microsatellites

neig

Neighbourhood Graphs

mbpcaiv

Multiblock principal component analysis with instrumental variables

mbpls

Multiblock partial least squares

morphosport

Athletes' Morphology

mstree

Minimal Spanning Tree

procuste.randtest

Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).

quasieuclid

Transformation of a distance matrice to a Euclidean one

randEH

Nee and May's random process

ours

A table of Qualitative Variables

piosphere

Plant traits response to grazing

between

Between-Class Analysis

randtest

Class of the Permutation Tests (in C).

rankrock

Ordination Table

reconst

Reconstitution of Data from a Duality Diagram

s.hist

Display of a scatterplot and its two marginal histograms

s.image

Graph of a variable using image and contour

rlq

RLQ analysis

rpjdl

Avifauna and Vegetation

s.chull

Plot of the factorial maps with polygons of contour by level of a factor

s.class

Plot of factorial maps with representation of point classes

scalewt

Compute or scale data using (weighted) means, variances and
covariances (possibly for the levels of a factor)

scatterutil

Graphical utility functions

sco.boxplot

Representation of the link between a variable and a set of qualitative variables

sepan

Separated Analyses in a K-tables

skulls

Morphometric Evolution

suprow

Projections of Supplementary Rows

santacatalina

Indirect Ordination

sarcelles

Array of Recapture of Rings

scatter.dudi

Plot of the Factorial Maps

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

scatter

Graphical representation of the outputs of a multivariate analysis

sco.match

1D plot of a pair of numeric scores with labels

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

supcol

Projections of Supplementary Columns

supdist

Projection of additional items in a PCO analysis

newick.eg

Phylogenetic trees in Newick format

olympic

Olympic Decathlon

optimEH

Nee and May's optimizing process

randtest.amova

Permutation tests on an analysis of molecular variance (in C).

rhizobium

Genetic structure of two nitrogen fixing bacteria influenced
by geographical isolation and host specialization

rhone

Physico-Chemistry Data

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

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

triangle.plot

Triangular Plotting

trichometeo

Pair of Ecological Data

s.kde2d

Scatter Plot with Kernel Density Estimate

s.label

Scatter Plot

s.match.class

Scatterplot of two sets of coordinates and a partionning into classes

s.multinom

Graph of frequency profiles (useful for instance in genetic)

tithonia

Phylogeny and quantitative traits of flowers

tortues

Morphological Study of the Painted Turtle

wca.rlq

Within-Class RLQ analysis

westafrica

Freshwater fish zoogeography in west Africa

woangers

Plant assemblages in woodlands of the conurbation of Angers (France)

worksurv

French Worker Survey (1970)

yanomama

Distance Matrices

zealand

Road distances in New-Zealand

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 distributions on a numeric score

score.coa

Reciprocal scaling after a correspondence analysis

score.mix

Graphs to Analyse a factor in a Mixed Analysis

newick2phylog

Create phylogeny

niche

Method to Analyse a pair of tables : Environmental and Faunistic Data

pcaiv

Principal component analysis with respect to instrumental variables

perthi02

Contingency Table with a partition in Molecular Biology

phylog

Phylogeny

plot.phylog

Plot phylogenies

within

Within-Class Analysis

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

presid2002

Results of the French presidential elections of 2002

procella

Phylogeny and quantitative traits of birds

randtest.between

Monte-Carlo Test on the between-groups inertia percentage (in C).

randtest.coinertia

Monte-Carlo test on a Co-inertia analysis (in C).

randtest.pcaiv

Monte-Carlo Test on the percentage of explained (i.e.
constrained) inertia

randxval

Two-fold cross-validation

statico

STATIS and Co-Inertia : Analysis of a series of paired ecological tables

statico.krandtest

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

table.cont

Plot of Contingency Tables

table.dist

Graph Display for Distance Matrices

variance.phylog

The phylogenetic ANOVA

varipart

Partition of the variation of a response multivariate table by 2 explanatory tables

wca

Within-Class Analysis

randtest.discrimin

Monte-Carlo Test on a Discriminant Analysis (in C).

randtest.dpcoa

Permutation test for double principal coordinate analysis (DPCoA)

rtest

Class of the Permutation Tests (in R).

rtest.between

Monte-Carlo Test on the between-groups inertia percentage (in R).

s.corcircle

Plot of the factorial maps of a correlation circle

rtest.discrimin

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

s.arrow

Plot of the factorial maps for the projection of a vector basis

s.traject

Trajectory Plot

s.value

Representation of a value in a graph

sco.gauss

Relationships between one score and qualitative variables

sco.label

1D plot of a numeric score with labels

withincoinertia

Within-class coinertia analysis

score.pca

Graphs to Analyse a factor in PCA

seconde

Students and Subjects

statis

STATIS, a method for analysing K-tables

steppe

Transect in the Vegetation

s.distri

Plot of a frequency distribution

s.logo

Representation of an object in a graph by a picture

s.match

Plot of Paired Coordinates

scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis

scatter.coa

Plot of the factorial maps for a correspondence analysis

score

Graphs for One Dimension

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

testdim.multiblock

Selection of the number of dimension by two-fold cross-validation for multiblock methods

tintoodiel

Tinto and Odiel estuary geochemistry

ungulates

Phylogeny and quantitative traits of ungulates.

uniquewt.df

Elimination of Duplicated Rows in a Array

vegtf

Vegetation in Trois-Fontaines

veuvage

Example for Centring in PCA

syndicats

Two Questions asked on a Sample of 1000 Respondents

t3012

Average temperatures of 30 French cities

taxo.eg

Examples of taxonomy

testdim

Function to perform a test of dimensionality

toxicity

Homogeneous Table

triangle.class

Triangular Representation and Groups of points

withinpca

Normed within principal component analysis

witwit.coa

Internal Correspondence Analysis