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ade4 (version 1.2-2)

Analysis of Environmental Data : Exploratory and Euclidean methods in Environmental sciences

Description

Multivariate data analysis and graphical display.

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Version

Install

install.packages('ade4')

Monthly Downloads

51,023

Version

1.2-2

License

GPL version 2 or newer

Homepage

http://pbil.univ-lyon1.fr/ADE-4

Maintainer

Jean Thioulouse

Last Published

February 14th, 2025

Functions in ade4 (1.2-2)

dudi.dec

Decentred Correspondence Analysis

cailliez

Transformation to make Euclidean a distance matrix

ardeche

Fauna Table with double (row and column) partitioning

bicenter.wt

Double Weighted Centring

euro123

Triangular Data

aviurba

Ecological Tables Triplet

PI2newick

Import data files from Phylogenetic Independance Package

banque

Table of Factors

disc

Rao's dissimilarity coefficient

bacteria

Genomes of 43 Bacteria

dist.quant

Computation of Distance Matrices on Quantitative Variables

avijons

Bird species distribution

avimedi

Fauna Table for Constrained Ordinations

dudi.acm

Multiple Correspondence Analysis

cca

Canonical Correspondence Analysis

chevaine

Enzymatic polymorphism in Leuciscus cephalus

macon

Wine Tasting

amova

Analysis of molecular variance

friday87

Faunistic K-tables

ichtyo

Point sampling of fish community

corvus

Corvus morphology

coleo

Table of Fuzzy Biological Traits

Computation of the Distance Matrix associated to a Neighbouring Graph

dist.genet

Genetic distances from gene frequencies

clementines

Fruit Production

lingoes

Transformation of a Distance Matrix for becoming Euclidean

ktab.match2ktabs

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

area.plot

Graphical Display of Areas

apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci

dudi.pco

Principal Coordinates Analysis

scatter.coa

Plot of the factorial maps for a correspondence analysis

oribatid

Oribatid mite

dudi.nsc

Non symmetric correspondence analysis

kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis

escopage

K-tables of wine-tasting

ecg

Electrocardiogram data

gearymoran

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

dudi.fca

Fuzzy Correspondence Analysis

bordeaux

Wine Tasting

randtest.coinertia

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

Multiple CO-inertia Analysis

deug

Exam marks for some students

randtest.amova

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

mantel.randtest

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

housetasks

Contingency Table

dist.dudi

Computation of the Distance Matrix of a Statistical Triplet

baran95

African Estuary Fishes

ktab.within

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

s.label

Scatter Plot

RV.rtest

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

lizards

Phylogeny and quantitative traits of lizards

jv73

K-tables Multi-Regions

dudi.mix

Ordination of Tables mixing quantitative variables and factors

fission

Fission pattern and heritable morphological traits

carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora

humDNAm

human mitochondrial DNA restriction data

atlas

Small Ecological Dataset

carni19

Phylogeny and quantative trait of carnivora

RVdist.randtest

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

abouheif.eg

Phylogenies and quantitative traits from Abouheif

arrival

Arrivals at an intensive care unit

scalewt

Centring and Scaling a Matrix of Any Weighting

elec88

Electoral Data

ade4toR

Format Change Utility

macaca

Landmarks

score

Graphs for One Dimension

Representation by mean- standard deviation of a set of weight distributions on a numeric score

casitas

Enzymatic polymorphism in Mus musculus

inertia.dudi

Statistics of inertia in a one-table analysis

chatcat

Qualitative Weighted Variables

kdist

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

discrimin.coa

Discriminant Correspondence Analysis

genet

A class of data: tables of populations and alleles

kdist2ktab

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

kcponds

Ponds in a nature reserve

pcaiv

Principal component analysis with respect to instrumental variables

microsatt

Genetic Relationships between cattle breeds with microsatellites

atya

Genetic variability of Cacadors

multispati.randtest

Multivariate spatial autocorrelation test (in C)

monde84

Global State of the World in 1984

dist.prop

Computation of Distance Matrices of Percentage Data

dudi.pca

Principal Component Analysis

fruits

Pair of Tables

gridrowcol

Complete regular grid analysis

Multiple Graphs for a Multiple Co-inertia Analysis

doubs

Pair of Ecological Tables

chazeb

Charolais-Zebus

newick.eg

Phylogenetic trees in Newick format

ecomor

Ecomorphological Convergence

between

Between-Class Analysis

acacia

Spatial pattern analysis in plant communities

veuvage

Example for Centring in PCA

mantel.rtest

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

plot.phylog

Plot phylogenies

meau

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

multispati.rtest

Multivariate spatial autocorrelation test

kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis

supcol

Projections of Supplementary Columns

newick2phylog

Create phylogeny

maples

Phylogeny and quantitative traits of flowers

scatter.fca

Plot of the factorial maps for a fuzzy correspondence analysis

table.cont

Plot of Contingency Tables

skulls

Morphometric Evolution

score.acm

Graphs to study one factor in a Multiple Correspondence Analysis

ours

A table of Qualitative Variables

krandtest

Class of the Permutation Tests (in C).

trichometeo

Pair of Ecological Data

pcoscaled

Simplified Analysis in Principal Coordinates

perthi02

Contingency Table with a partition in Molecular Biology

mjrochet

Phylogeny and quantitative traits of teleos fishes

reconst

Reconstitution of Data from a Duality Diagram

rtest.between

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

discrimin

Linear Discriminant Analysis (descriptive statistic)

rpjdl

Avifauna and Vegetation

scatter.dudi

Plot of the Factorial Maps

pta

Partial Triadic Analysis of a K-tables

s.distri

Plot of a frequency distribution

table.value

Plot of the Arrays

sco.quant

Graph to Analyse the Relation between a Score and Quantitative Variables

pap

Taxonomy and quantitative traits of carnivora

neig

Neighbourhood Graphs

tithonia

Phylogeny and quantitative traits of flowers

procuste.rtest

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

procuste

Simple Procruste Rotation between two sets of points

dudi

Duality Diagram

randtest.discrimin

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

santacatalina

Indirect Ordination

quasieuclid

Transformation of a distance matrice to a Euclidean one

s.corcircle

Plot of the factorial maps of a correlation circle

mstree

Minimal Spanning Tree

procella

Phylogeny and quantitative traits of birds

ktab.list.dudi

Creation of a K-tables from a list of duality diagrams

kplot

Generic Function for Multiple Graphs in a K-tables Analysis

rlq

RLQ analysis

randtest.between

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

suprow

Projections of Supplementary Rows

orthobasis

Orthonormal basis for orthonormal transform

bf88

Cubic Ecological Data

dpcoa

Double principal coordinate analysis

kdisteuclid

a way to obtain Euclidean distance matrices

procuste.randtest

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

syndicats

Two Questions asked on a Sample of 1000 Respondents

ungulates

Phylogeny and quantitative traits of ungulates.

zealand

Road distances in New-Zealand

mafragh

Phyto-Ecological Survey

mariages

Correspondence Analysis Table

rankrock

Ordination Table

njplot

Phylogeny and trait of bacteria

meaudret

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

score.mix

Graphs to Analyse a factor in a Mixed Analysis

mld

Multi Level Decomposition of unidimensional data

s.class

Plot of factorial maps with representation of point classes

kplot.statis

Multiple Graphs of a STATIS Analysis

score.pca

Graphs to Analyse a factor in PCA

multispati

Multivariate spatial analysis

t3012

Average temperatures of 30 French cities

statis

STATIS, a method for analysing K-tables

sepan

Separated Analyses in a K-tables

randtest

Class of the Permutation Tests (in C).

tarentaise

Mountain Avifauna

tortues

Morphological Study of the Painted Turtle

randtest-internal

Internal Permutation Tests functions (in C).

table.paint

Plot of the arrays by grey levels

s.chull

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

Elimination of Duplicated Rows in a Array

sarcelles

Array of Recapture of Rings

palm

Phylogenetic and quantitative traits of amazonian palm trees

symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree

score.coa

Graphs to analyse a factor in a correspondence analysis

s.traject

Trajectory Plot

s.hist

Display of a scatterplot and its two marginal histograms

seconde

Students and Subjects

s.image

Graph of a variable using image and contour

table.dist

Graph Display for Distance Matrices

phylog

Phylogeny

tintoodiel

Tinto and Odiel estuary geochemistry

rtest

Class of the Permutation Tests (in R).

within.pca

Normed within Principal Component Analysis

scatter.acm

Plot of the factorial maps in multiple correspondence analysis

variance.phylog

The phylogenetic ANOVA

westafrica

Freshwater fish zoogeography in west Africa

witwit.coa

Internal Correspondence Analysis

worksurv

French Worker Survey (1970)

butterfly

Genetics-Ecology-Environment Triple

bsetal97

Ecological and Biological Traits

carni70

Phylogeny and quantitative traits of carnivora

kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables

ktab.list.df

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

lascaux

Genetic/Environment and types of variables

mollusc

Faunistic Communities and Sampling Experiment

Rao's diversity coefficient also called quadratic entropy

ktab

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

mfa

Multiple Factorial Analysis

niche

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

rhone

Physico-Chemistry Data

s.match

Plot of Paired Coordinates

sco.boxplot

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

ktab.data.frame

Creation of K-tables from a data frame

orthogram

Orthonormal decomposition of variance

as.taxo

Taxonomy

dist.binary

Computation of Distance Matrices for Binary Data

foucart

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

is.euclid

Is a Distance Matrix Euclidean ?

corkdist

Tests of randomization on the correlation between distances applied to 'kdist' objetcs

kplot.pta

Multiple Graphs for a Partial Triadic Analysis

rtest.discrimin

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

dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors

pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables

dudi.coa

Correspondence Analysis

dotcircle

Representation of n values on a circle

s.value

Representation of a value in a graph

toxicity

Homogeneous Table

s.arrow

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

table.phylog

Plot arrays in front of a phylogenetic tree

steppe

Transect in the Vegetation

dunedata

Dune Meadow Data