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ade4 (version 1.7-15)

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

Description

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) .

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Version

Install

install.packages('ade4')

Monthly Downloads

36,743

Version

1.7-15

License

GPL (>= 2)

Maintainer

Aurélie Siberchicot

Last Published

February 13th, 2020

Functions in ade4 (1.7-15)

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