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


[Up] [Top]

Documentation for package ‘ade4’ version 1.5-2

Help Pages

A B C D E F G H I J K L M N O P Q R S T U V W Y Z misc

ade4-package The ade4 package

-- A --

abouheif.eg Phylogenies and quantitative traits from Abouheif
acacia Spatial pattern analysis in plant communities
acm.burt Multiple Correspondence Analysis
acm.disjonctif Multiple Correspondence Analysis
add.position.triangle Triangular Plotting
add.scatter Add graphics to an existing plot
add.scatter.eig Add graphics to an existing plot
ade4 The ade4 package
ade4-deprecated Deprecated functions in ade4
ade4toR Format Change Utility
aminoacyl Codon usage
amova Analysis of molecular variance
apis108 Allelic frequencies in ten honeybees populations at eight microsatellites loci
apqe Apportionment of Quadratic Entropy
ardeche Fauna Table with double (row and column) partitioning
area.plot Graphical Display of Areas
area.util.class Graphical Display of Areas
area.util.contour Graphical Display of Areas
area.util.xy Graphical Display of Areas
area2link Graphical Display of Areas
area2poly Graphical Display of Areas
arrival Arrivals at an intensive care unit
as.data.frame.kdist the class of objects 'kdist' (K distance matrices)
as.dudi Duality Diagram
as.krandtest Class of the Permutation Tests (in C).
as.randtest Class of the Permutation Tests (in C).
as.rtest Class of the Permutation Tests (in R).
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

-- B --

bacteria Genomes of 43 Bacteria
banque Table of Factors
baran95 African Estuary Fishes
bca Between-Class Analysis
bca.coinertia Between-class coinertia analysis
bca.dudi Between-Class Analysis
bca.rlq Between-Class RLQ analysis
between Between-Class Analysis
betweencoinertia Between-class coinertia analysis
bf88 Cubic Ecological Data
bicenter.wt Double Weighted Centring
biplot.dudi Graphical representation of the outputs of a multivariate analysis
bordeaux Wine Tasting
boxplot.acm Multiple Correspondence Analysis
bsetal97 Ecological and Biological Traits
buech Buech basin
butterfly Genetics-Ecology-Environment Triple

-- C --

c.kdist the class of objects 'kdist' (K distance matrices)
c.ktab the class of objects 'ktab' (K-tables)
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 and herbivora
casitas Enzymatic polymorphism in Mus musculus
cca Canonical Correspondence Analysis
char2genet A class of data: tables of populations and alleles
chatcat Qualitative Weighted Variables
chats Pair of Variables
chazeb Charolais-Zebus
chevaine Enzymatic polymorphism in Leuciscus cephalus
clementines Fruit Production
cnc2003 Frequenting movie theaters in France in 2003
coinertia Coinertia Analysis
col.names the class of objects 'ktab' (K-tables)
col.names.ktab the class of objects 'ktab' (K-tables)
col.names<- the class of objects 'ktab' (K-tables)
col.names<-.ktab the class of objects 'ktab' (K-tables)
coleo Table of Fuzzy Biological Traits
combine.4thcorner Functions to compute the fourth-corner statistic
corkdist Tests of randomization between distances applied to 'kdist' objetcs
corvus Corvus morphology
costatis STATIS and Co-Inertia : Analysis of a series of paired ecological tables
count2genet A class of data: tables of populations and alleles

-- D --

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.genet Genetic distances from gene frequencies
dist.ktab Mixed-variables coefficient of distance
dist.neig Computation of the Distance Matrix associated to a Neighbouring Graph
dist.prop Computation of Distance Matrices of Percentage Data
dist.quant Computation of Distance Matrices on Quantitative Variables
dist.taxo Taxonomy
divc Rao's diversity coefficient also called quadratic entropy
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
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 Analysis
dudi.fpca Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
dudi.hillsmith Ordination of Tables mixing quantitative variables and factors
dudi.mix Ordination of Tables mixing quantitative variables and factors
dudi.nsc Non symmetric correspondence analysis
dudi.pca Principal Component Analysis
dudi.pco Principal Coordinates Analysis
dunedata Dune Meadow Data

-- E --

ecg Electrocardiogram data
ecomor Ecomorphological Convergence
EH Amount of Evolutionary History
elec88 Electoral Data
enum.phylog Plot phylogenies
escopage K-tables of wine-tasting
euro123 Triangular Data

-- F --

fission Fission pattern and heritable morphological traits
foucart K-tables Correspondence Analysis with the same rows and the same columns
fourthcorner Functions to compute the fourth-corner statistic
fourthcorner2 Functions to compute the fourth-corner statistic
freq2genet A class of data: tables of populations and alleles
friday87 Faunistic K-tables
fruits Pair of Tables
fuzzygenet Reading a table of genetic data (diploid individuals)

-- G --

gearymoran Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation
genet A class of data: tables of populations and alleles
ggtortoises Microsatellites of Galapagos tortoises populations
granulo Granulometric Curves
gridrowcol Complete regular grid analysis

-- H --

haar2level Multi Level Decomposition of unidimensional data
hclust2phylog Create phylogeny
hdpg Genetic Variation In Human Populations
housetasks Contingency Table
humDNAm human mitochondrial DNA restriction data

-- I --

ichtyo Point sampling of fish community
inertia.dudi Statistics of inertia in a one-table analysis
irishdata Geary's Irish Data
is.dudi Duality Diagram
is.euclid Is a Distance Matrix Euclidean ?
is.ktab the class of objects 'ktab' (K-tables)

-- J --

julliot Seed dispersal
jv73 K-tables Multi-Regions

-- K --

kcponds Ponds in a nature reserve
kdist the class of objects 'kdist' (K distance matrices)
kdist.cor Mixed-variables coefficient of distance
kdist2ktab Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')
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.sepan.coa Multiple Graphs for Separated Analyses in a K-tables
kplot.statis Multiple Graphs of a STATIS Analysis
kplotX.mdpcoa Multiple Double Principal Coordinate 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 ecological tables
ktab.util.addfactor<- the class of objects 'ktab' (K-tables)
ktab.util.names the class of objects 'ktab' (K-tables)
ktab.within Process to go from a Within Analysis to a K-tables

-- L --

lascaux Genetic/Environment and types of variables
ldist.ktab Mixed-variables coefficient of distance
lingoes Transformation of a Distance Matrix for becoming Euclidean
lizards Phylogeny and quantitative traits of lizards

-- M --

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 C).)
mantel.rtest Mantel test (correlation between two distance matrices (in R).)
mantelkdist Tests of randomization between distances applied to 'kdist' objetcs
maples Phylogeny and quantitative traits of flowers
mariages Correspondence Analysis Table
mcoa Multiple CO-inertia Analysis
mdpcoa Multiple Double Principal Coordinate Analysis
meau Ecological Data : sites-variables, sites-species, where and when
meaudret Ecological Data : sites-variables, sites-species, where and when
mfa Multiple Factorial Analysis
microsatt Genetic Relationships between cattle breeds with microsatellites
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
multispati Multivariate spatial analysis
multispati.randtest Multivariate spatial autocorrelation test (in C)
multispati.rtest Multivariate spatial autocorrelation test

-- N --

nb2neig Neighbourhood Graphs
neig Neighbourhood Graphs
neig.util.GtoL Neighbourhood Graphs
neig.util.LtoG Neighbourhood Graphs
neig2mat Neighbourhood Graphs
neig2nb Neighbourhood Graphs
newick.eg Phylogenetic trees in Newick format
newick2phylog Create phylogeny
newick2phylog.addtools Create phylogeny
niche Method to Analyse a pair of tables : Environmental and Faunistic Data
niche.param Method to Analyse a pair of tables : Environmental and Faunistic Data
nipals Non-linear Iterative Partial Least Squares (NIPALS) algorithm
njplot Phylogeny and trait of bacteria

-- O --

olympic Olympic Decathlon
optimEH Nee and May's optimizing process
oribatid Oribatid mite
originality Originality of a species
orisaved Maximal or minimal amount of originality saved under optimal conditions
orthobasis Orthonormal basis for orthonormal transform
orthobasis.circ Orthonormal basis for orthonormal transform
orthobasis.haar Orthonormal basis for orthonormal transform
orthobasis.line Orthonormal basis for orthonormal transform
orthobasis.listw Orthonormal basis for orthonormal transform
orthobasis.mat Orthonormal basis for orthonormal transform
orthobasis.neig Orthonormal basis for orthonormal transform
orthogram Orthonormal decomposition of variance
orthogram-deprecated Orthonormal decomposition of variance
ours A table of Qualitative Variables

-- P --

palm Phylogenetic and quantitative traits of amazonian palm trees
pap Taxonomy and quantitative traits of carnivora
pcaiv Principal component analysis with respect to instrumental variables
pcaivortho Principal Component Analysis with respect to orthogonal instrumental variables
pcoscaled Simplified Analysis in Principal Coordinates
perthi02 Contingency Table with a partition in Molecular Biology
phylog Phylogeny
phylog.extract Phylogeny
phylog.permut Phylogeny
PI2newick Import data files from Phylogenetic Independance Package
piosphere Plant traits response to grazing
plot.4thcorner Functions to compute the fourth-corner statistic
plot.betcoi Between-Class Analysis
plot.betrlq Between-Class RLQ analysis
plot.between Between-Class Analysis
plot.coinertia Coinertia Analysis
plot.corkdist Tests of randomization between distances applied to 'kdist' objetcs
plot.discrimin Linear Discriminant Analysis (descriptive statistic)
plot.dpcoa Double principal coordinate analysis
plot.foucart K-tables Correspondence Analysis with the same rows and the same columns
plot.krandtest Class of the Permutation Tests (in C).
plot.mcoa Multiple CO-inertia Analysis
plot.mfa Multiple Factorial Analysis
plot.multispati Multivariate spatial analysis
plot.niche Method to Analyse a pair of tables : Environmental and Faunistic Data
plot.pcaiv Principal component analysis with respect to instrumental variables
plot.phylog Plot phylogenies
plot.procuste Simple Procruste Rotation between two sets of points
plot.pta Partial Triadic Analysis of a K-tables
plot.randtest Class of the Permutation Tests (in C).
plot.rlq RLQ analysis
plot.rtest Class of the Permutation Tests (in R).
plot.sepan Separated Analyses in a K-tables
plot.statis STATIS, a method for analysing K-tables
plot.witcoi Within-Class Analysis
plot.within Within-Class Analysis
plot.witrlq Within-Class RLQ analysis
poly2area Graphical Display of Areas
prep.binary Mixed-variables coefficient of distance
prep.circular Mixed-variables coefficient of distance
prep.fuzzy Mixed-variables coefficient of distance
prep.fuzzy.var Fuzzy Correspondence Analysis and Fuzzy Principal Components Analysis
prep.mdpcoa Multiple Double Principal Coordinate Analysis
presid2002 Results of the French presidential elections of 2002
print.4thcorner Functions to compute the fourth-corner statistic
print.amova Analysis of molecular variance
print.apqe Apportionment of Quadratic Entropy
print.betcoi Between-Class Analysis
print.betrlq Between-Class RLQ analysis
print.between Between-Class Analysis
print.coinertia Coinertia Analysis
print.corkdist Tests of randomization between distances applied to 'kdist' objetcs
print.discrimin Linear Discriminant Analysis (descriptive statistic)
print.dpcoa Double principal coordinate analysis
print.dudi Duality Diagram
print.foucart K-tables Correspondence Analysis with the same rows and the same columns
print.kdist the class of objects 'kdist' (K distance matrices)
print.krandtest Class of the Permutation Tests (in C).
print.ktab the class of objects 'ktab' (K-tables)
print.mcoa Multiple CO-inertia Analysis
print.mfa Multiple Factorial Analysis
print.multispati Multivariate spatial analysis
print.neig Neighbourhood Graphs
print.niche Method to Analyse a pair of tables : Environmental and Faunistic Data
print.nipals Non-linear Iterative Partial Least Squares (NIPALS) algorithm
print.orthobasis Orthonormal basis for orthonormal transform
print.pcaiv Principal component analysis with respect to instrumental variables
print.phylog Phylogeny
print.procuste Simple Procruste Rotation between two sets of points
print.pta Partial Triadic Analysis of a K-tables
print.randtest Class of the Permutation Tests (in C).
print.rlq RLQ analysis
print.rtest Class of the Permutation Tests (in R).
print.sepan Separated Analyses in a K-tables
print.statis STATIS, a method for analysing K-tables
print.witcoi Within-Class Analysis
print.within Within-Class Analysis
print.witrlq Within-Class RLQ analysis
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 procustean rotation (in C).
procuste.rtest Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).
pta Partial Triadic Analysis of a K-tables

-- Q --

quasieuclid Transformation of a distance matrice to a Euclidean one

-- R --

radial.phylog Plot phylogenies
randEH Nee and May's random process
randtest Class of the Permutation Tests (in C).
randtest.amova Permutation tests on an analysis of molecular variance (in C).
randtest.between Monte-Carlo Test on the between-groups inertia percentage (in C).
randtest.cca Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia
randtest.coinertia Monte-Carlo test on a Co-inertia analysis (in C).
randtest.discrimin Monte-Carlo Test on a Discriminant Analysis (in C).
randtest.pcaiv Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia
randtest.pcaivortho Monte-Carlo Test on the percentage of explained (i.e. constrained) inertia
randtest.rlq RLQ analysis
rankrock Ordination Table
reciprocal.coa Reciprocal scaling after a correspondence analysis
reconst Reconstitution of Data from a Duality Diagram
reconst.coa Reconstitution of Data from a Duality Diagram
reconst.pca Reconstitution of Data from a Duality Diagram
redo.dudi Duality Diagram
rhizobium Genetic structure of two nitrogen fixing bacteria influenced by geographical isolation and host specialization
rhone Physico-Chemistry Data
rlq RLQ analysis
row.names.ktab the class of objects 'ktab' (K-tables)
row.names<-.ktab the class of objects 'ktab' (K-tables)
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).
rtest.discrimin Monte-Carlo Test on a Discriminant Analysis (in R).
rtest.niche Method to Analyse a pair of tables : Environmental and Faunistic Data
Rtoade4 Format Change Utility
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).
RVkdist Tests of randomization between distances applied to 'kdist' objetcs

-- S --

s.arrow Plot of the factorial maps for the projection of a vector basis
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
s.corcircle Plot of the factorial maps of a correlation circle
s.distri Plot of a frequency distribution
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
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 classes
s.multinom Graph of frequency profiles (useful for instance in genetic)
s.traject Trajectory Plot
s.value Representation of a value in a graph
santacatalina Indirect Ordination
sarcelles Array of Recapture of Rings
scalewt Centring and Scaling a Matrix of Any Weighting
scatter Graphical representation of the outputs of a multivariate analysis
scatter.acm Plot of the factorial maps in a Multiple Correspondence Analysis
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 analysis
scatter.nipals Non-linear Iterative Partial Least Squares (NIPALS) algorithm
scatter.pco Principal Coordinates Analysis
scatterutil.base Graphical utility functions
scatterutil.chull Graphical utility functions
scatterutil.convrot90 Graphical utility functions
scatterutil.eigen Graphical utility functions
scatterutil.ellipse Graphical utility functions
scatterutil.eti Graphical utility functions
scatterutil.eti.circ Graphical utility functions
scatterutil.grid Graphical utility functions
scatterutil.legend.bw.square Graphical utility functions
scatterutil.legend.square.grey Graphical utility functions
scatterutil.legendgris Graphical utility functions
scatterutil.logo Representation of an object in a graph by a picture
scatterutil.scaling Graphical utility functions
scatterutil.sco Graphical utility functions
scatterutil.star Graphical utility functions
scatterutil.sub Graphical utility functions
sco.boxplot Representation of the link between a variable and a set of qualitative variables
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
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
score Graphs for One Dimension
score.acm Graphs to study one factor in a Multiple Correspondence Analysis
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
scores.neig Neighbourhood Graphs
scoreutil.base Graphs for One Dimension
screeplot.dudi Graphical representation of the outputs of a multivariate analysis
seconde Students and Subjects
sepan Separated Analyses in a K-tables
skulls Morphometric Evolution
statico STATIS and Co-Inertia : Analysis of a series of paired ecological tables
statis STATIS, a method for analysing K-tables
steppe Transect in the Vegetation
summary.4thcorner Functions to compute the fourth-corner statistic
summary.coinertia Coinertia Analysis
summary.corkdist Tests of randomization between distances applied to 'kdist' objetcs
summary.dist Is a Distance Matrix Euclidean ?
summary.dudi Duality Diagram
summary.mcoa Multiple CO-inertia Analysis
summary.mfa Multiple Factorial Analysis
summary.multispati Multivariate spatial analysis
summary.neig Neighbourhood Graphs
summary.pcaiv Principal component analysis with respect to instrumental variables
summary.pcaivortho Principal Component Analysis with respect to orthogonal instrumental variables
summary.rlq RLQ analysis
summary.sepan Separated Analyses in a K-tables
summary.witwit Internal Correspondence Analysis
supcol Projections of Supplementary Columns
supcol.coa Projections of Supplementary Columns
supcol.default Projections of Supplementary Columns
suprow Projections of Supplementary Rows
suprow.coa Projections of Supplementary Rows
suprow.default Projections of Supplementary Rows
suprow.pca Projections of Supplementary Rows
symbols.phylog Representation of a quantitative variable in front of a phylogenetic tree
syndicats Two Questions asked on a Sample of 1000 Respondents

-- T --

t.dudi Duality Diagram
t.ktab the class of objects 'ktab' (K-tables)
t3012 Average temperatures of 30 French cities
tab.names the class of objects 'ktab' (K-tables)
tab.names.ktab the class of objects 'ktab' (K-tables)
tab.names<- the class of objects 'ktab' (K-tables)
tab.names<-.ktab the class of objects 'ktab' (K-tables)
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.prepare Plot of the Arrays
table.value Plot of the Arrays
tarentaise Mountain Avifauna
taxo.eg Examples of taxonomy
taxo2phylog Create phylogeny
testdim Function to perform a test of dimensionality
testdim.pca Function to perform a test of dimensionality
tintoodiel Tinto and Odiel estuary geochemistry
tithonia Phylogeny and quantitative traits of flowers
tortues Morphological Study of the Painted Turtle
toxicity Homogeneous Table
triangle.biplot Triangular Plotting
triangle.class Triangular Representation and Groups of points
triangle.param Triangular Plotting
triangle.plot Triangular Plotting
triangle.posipoint Triangular Plotting
trichometeo Pair of Ecological Data

-- U --

ungulates Phylogeny and quantitative traits of ungulates.
uniquewt.df Elimination of Duplicated Rows in a Array

-- V --

variance.phylog The phylogenetic ANOVA
vegtf Vegetation in Trois-Fontaines
veuvage Example for Centring in PCA

-- W --

wca Within-Class Analysis
wca.coinertia Within-class coinertia analysis
wca.dudi Within-Class Analysis
wca.rlq Within-Class RLQ analysis
westafrica Freshwater fish zoogeography in west Africa
within Within-Class Analysis
withincoinertia Within-class coinertia analysis
withinpca Normed within principal component analysis
witwit.coa Internal Correspondence Analysis
witwitsepan Internal Correspondence Analysis
woangers Plant assemblages in woodlands of the conurbation of Angers (France)
worksurv French Worker Survey (1970)

-- Y --

yanomama Distance Matrices

-- Z --

zealand Road distances in New-Zealand

-- misc --

[.kdist the class of objects 'kdist' (K distance matrices)
[.ktab the class of objects 'ktab' (K-tables)