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ade4 (version 1.7-6)

Analysis of Ecological 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

1.7-6

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

March 23rd, 2017

Functions in ade4 (1.7-6)

randtest.between

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

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

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

Class of the Permutation Tests (in C).
mafragh

Phyto-Ecological Survey
macroloire

Assemblages of Macroinvertebrates in the Loire River (France)
pcaivortho

Principal Component Analysis with respect to orthogonal instrumental variables
carniherbi49

Taxonomy, phylogenies and quantitative traits of carnivora and herbivora
dist.prop

Computation of Distance Matrices of Percentage Data
cnc2003

Frequenting movie theaters in France in 2003
coinertia

Coinertia Analysis
deug

Exam marks for some students
disc

Rao's dissimilarity coefficient
friday87

Faunistic K-tables
irishdata

Geary's Irish Data
kdisteuclid

a way to obtain Euclidean distance matrices
kplot

Generic Function for Multiple Graphs in a K-tables Analysis
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
mbpls

Multiblock partial least squares
multispati.rtest

Multivariate spatial autocorrelation test
optimEH

Nee and May's optimizing process
mbpcaiv

Multiblock principal component analysis with instrumental variables
olympic

Olympic Decathlon
orthogram

Orthonormal decomposition of variance
ours

A table of Qualitative Variables
piosphere

Plant traits response to grazing
between

Between-Class Analysis
randboot

Bootstrap simulations
rlq

RLQ analysis
randboot.multiblock

Bootstraped simulations for multiblock methods
multispati.randtest

Multivariate spatial autocorrelation test (in C)
rpjdl

Avifauna and Vegetation
rtest

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

Monte-Carlo Test on the between-groups inertia percentage (in R).
s.kde2d

Scatter Plot with Kernel Density Estimate
s.label

Scatter Plot
scatter.dudi

Plot of the Factorial Maps
scatter.fca

Plot of the factorial maps for a fuzzy correspondence 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
t3012

Average temperatures of 30 French cities
suprow

Projections of Supplementary Rows
table.cont

Plot of Contingency Tables
triangle.class

Triangular Representation and Groups of points
triangle.plot

Triangular Plotting
woangers

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

French Worker Survey (1970)
baran95

African Estuary Fishes
inertia.dudi

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

Enzymatic polymorphism in Mus musculus
ade4-internal

Internal ade4 functions
aminoacyl

Codon usage
amova

Analysis of molecular variance
fruits

Pair of Tables
bca.coinertia

Between-class coinertia analysis
bca

Between-Class Analysis
bca.rlq

Between-Class RLQ analysis
acacia

Spatial pattern analysis in plant communities
aravo

Distribution of Alpine plants in Aravo (Valloire, France)
dist.binary

Computation of Distance Matrices for Binary Data
abouheif.eg

Phylogenies and quantitative traits from Abouheif
ardeche

Fauna Table with double (row and column) partitioning
as.taxo

Taxonomy
atlas

Small Ecological Dataset
bf88

Cubic Ecological Data
dist.dudi

Computation of the Distance Matrix from a Statistical Triplet
bicenter.wt

Double Weighted Centring
dpcoa

Double principal coordinate analysis
dudi

Duality Diagram
dudi.hillsmith

Ordination of Tables mixing quantitative variables and factors
humDNAm

human mitochondrial DNA restriction data
ichtyo

Point sampling of fish community
granulo

Granulometric Curves
gridrowcol

Complete regular grid analysis
kplot.foucart

Multiple Graphs for the Foucart's Correspondence Analysis
kplot.mcoa

Multiple Graphs for a Multiple Co-inertia Analysis
kplot.sepan

Multiple Graphs for Separated Analyses in a K-tables
kplot.statis

Multiple Graphs of a STATIS Analysis
ktab.within

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

Genetic/Environment and types of variables
hdpg

Genetic Variation In Human Populations
plot.phylog

Plot phylogenies
housetasks

Contingency Table
dudi.dec

Decentred Correspondence Analysis
EH

Amount of Evolutionary History
PI2newick

Import data files from Phylogenetic Independance Package
ade4-package

The ade4 package
add.scatter

Add graphics to an existing plot
Deprecated functions

Deprecated functions in ade4
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).
apis108

Allelic frequencies in ten honeybees populations at eight microsatellites loci
apqe

Apportionment of Quadratic Entropy
area.plot

Graphical Display of Areas
arrival

Arrivals at an intensive care unit
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
bordeaux

Wine Tasting
bsetal97

Ecological and Biological Traits
chazeb

Charolais-Zebus
chevaine

Enzymatic polymorphism in Leuciscus cephalus
corkdist

Tests of randomization between distances applied to 'kdist' objetcs
corvus

Corvus morphology
carni70

Phylogeny and quantitative traits of carnivora
coleo

Table of Fuzzy Biological Traits
combine.4thcorner

Functions to combine and adjust the outputs 3-table methods
capitales

Road Distances
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).
dudi.fca

Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
elec88

Electoral Data
escopage

K-tables of wine-tasting
genet

A class of data: tables of populations and alleles
ggtortoises

Microsatellites of Galapagos tortoises populations
discrimin

Linear Discriminant Analysis (descriptive statistic)
discrimin.coa

Discriminant Correspondence Analysis
dudi.acm

Multiple Correspondence Analysis
dudi.coa

Correspondence Analysis
buech

Buech basin
butterfly

Genetics-Ecology-Environment Triple
kdist2ktab

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

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

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

Canonical Correspondence Analysis
ade4toR

Format Change Utility
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
dist.neig

Computation of the Distance Matrix associated to a Neighbouring Graph
dist.quant

Computation of Distance Matrices on Quantitative Variables
divc

Rao's diversity coefficient also called quadratic entropy
adegraphicsLoaded

Utility function to test if the package adegraphics is loaded
multiblock

Display and summarize multiblock objects
multispati

Multivariate spatial analysis
neig

Neighbourhood Graphs
newick.eg

Phylogenetic trees in Newick format
dudi.pco

Principal Coordinates Analysis
dunedata

Dune Meadow Data
fuzzygenet

Reading a table of genetic data (diploid individuals)
gearymoran

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

Is a Distance Matrix Euclidean?
julliot

Seed dispersal
bwca.dpcoa

Between- and within-class double principal coordinate analysis
cailliez

Transformation to make Euclidean a distance matrix
ktab

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

Phylogenetic and quantitative traits of amazonian palm trees
pap

Taxonomy and quantitative traits of carnivora
perthi02

Contingency Table with a partition in Molecular Biology
phylog

Phylogeny
mcoa

Multiple CO-inertia Analysis
mdpcoa

Multiple Double Principal Coordinate Analysis
newick2phylog

Create phylogeny
niche

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

Maximal or minimal amount of originality saved under optimal conditions
orthobasis

Orthonormal basis for orthonormal transform
within

Within-Class Analysis
dudi.nsc

Non symmetric correspondence analysis
dudi.pca

Principal Component Analysis
euro123

Triangular Data
fission

Fission pattern and heritable morphological traits
ecomor

Ecomorphological Convergence
fourthcorner

Functions to compute the fourth-corner statistic
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 (DPCoA)
macaca

Landmarks
macon

Wine Tasting
mfa

Multiple Factorial Analysis
ktab.data.frame

Creation of K-tables from a data frame
ktab.list.df

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

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

Two-fold cross-validation
s.hist

Display of a scatterplot and its two marginal histograms
santacatalina

Indirect Ordination
sarcelles

Array of Recapture of Rings
microsatt

Genetic Relationships between cattle breeds with microsatellites
mollusc

Faunistic Communities and Sampling Experiment
monde84

Global State of the World in 1984
oribatid

Oribatid mite
originality

Originality of a species
pcaiv

Principal component analysis with respect to instrumental variables
maples

Phylogeny and quantitative traits of flowers
mariages

Correspondence Analysis Table
mjrochet

Phylogeny and quantitative traits of teleos fishes
mld

Multi Level Decomposition of unidimensional data
scatterutil

Graphical utility functions
sco.boxplot

Representation of the link between a variable and a set of qualitative variables
randtest.amova

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

Qualitative Weighted Variables
chats

Pair of Variables
chickenk

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

Class of the Permutation Tests (in C).
s.image

Graph of a variable using image and contour
s.traject

Trajectory Plot
s.value

Representation of a value in a graph
scalewt

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

Fruit Production
dist.genet

Genetic distances from gene frequencies
dist.ktab

Mixed-variables coefficient of distance
dotcircle

Representation of n values on a circle
scatter

Graphical representation of the outputs of a multivariate analysis
score

Graphs for One Dimension
score.acm

Graphs to study one factor in a Multiple Correspondence Analysis
sepan

Separated Analyses in a K-tables
s.corcircle

Plot of the factorial maps of a correlation circle
s.distri

Plot of a frequency distribution
score.coa

Reciprocal scaling after a correspondence analysis
score.mix

Graphs to Analyse a factor in a Mixed Analysis
statico

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

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

Function to perform a test of dimensionality
doubs

Pair of Ecological Tables
dudi.mix

Ordination of Tables mixing quantitative variables and factors
procuste

Simple Procruste Rotation between two sets of points
procuste.randtest

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

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

Morphometric Evolution
tarentaise

Mountain Avifauna
taxo.eg

Examples of taxonomy
tintoodiel

Tinto and Odiel estuary geochemistry
statis

STATIS, a method for analysing K-tables
steppe

Transect in the Vegetation
tortues

Morphological Study of the Painted Turtle
tithonia

Phylogeny and quantitative traits of flowers
withinpca

Normed within principal component analysis
witwit.coa

Internal Correspondence Analysis
pta

Partial Triadic Analysis of a K-tables
rhizobium

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

Physico-Chemistry Data
rtest.discrimin

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

Homogeneous Table
wca.rlq

Within-Class RLQ analysis
westafrica

Freshwater fish zoogeography in west Africa
s.arrow

Plot of the factorial maps for the projection of a vector basis
s.logo

Representation of an object in a graph by a picture
s.match

Plot of Paired Coordinates
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
sco.gauss

Relationships between one score and qualitative variables
sco.label

1D plot of a numeric score with labels
testdim.multiblock

Selection of the number of dimension by two-fold cross-validation for multiblock methods
jv73

K-tables Multi-Regions
kplot.mfa

Multiple Graphs for a Multiple Factorial Analysis
kplot.pta

Multiple Graphs for a Partial Triadic Analysis
kcponds

Ponds in a nature reserve
mantel.randtest

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

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

Graph Display for Distance Matrices
table.paint

Plot of the arrays by grey levels
uniquewt.df

Elimination of Duplicated Rows in a Array
morphosport

Athletes' Morphology
mstree

Minimal Spanning Tree
nipals

Non-linear Iterative Partial Least Squares (NIPALS) algorithm
njplot

Phylogeny and trait of bacteria
pcoscaled

Simplified Analysis in Principal Coordinates
pcw

Distribution of of tropical trees along the Panama canal
presid2002

Results of the French presidential elections of 2002
procella

Phylogeny and quantitative traits of birds
quasieuclid

Transformation of a distance matrice to a Euclidean one
randEH

Nee and May's random process
rankrock

Ordination Table
reconst

Reconstitution of Data from a Duality Diagram
s.chull

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

The phylogenetic ANOVA
vegtf

Vegetation in Trois-Fontaines
veuvage

Example for Centring in PCA
s.class

Plot of factorial maps with representation of point classes
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)
scatter.acm

Plot of the factorial maps in a Multiple Correspondence Analysis
scatter.coa

Plot of the factorial maps for a correspondence analysis
score.pca

Graphs to Analyse a factor in PCA
seconde

Students and Subjects
symbols.phylog

Representation of a quantitative variable in front of a phylogenetic tree
syndicats

Two Questions asked on a Sample of 1000 Respondents
table.phylog

Plot arrays in front of a phylogenetic tree
table.value

Plot of the Arrays
trichometeo

Pair of Ecological Data
ungulates

Phylogeny and quantitative traits of ungulates.
wca

Within-Class Analysis
withincoinertia

Within-class coinertia analysis
yanomama

Distance Matrices
zealand

Road distances in New-Zealand