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PI2newick Import data files from Phylogenetic
Independance 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).
abouheif.eg Phylogenies and quantitative traits from
Abouheif
acacia Spatial pattern analysis in plant communities
add.scatter Add graphics to an existing plot
ade4-deprecated Deprecated functions in ade4
ade4-package The ade4 package
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
aravo Distribution of Alpine plants in Aravo
(Valloire, France)
ardeche Fauna Table with double (row and column)
partitioning
area.plot Graphical Display of Areas
arrival Arrivals at an intensive care unit
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
bacteria Genomes of 43 Bacteria
banque Table of Factors
baran95 African Estuary Fishes
bca Between-Class Analysis
bca.coinertia Between-class coinertia analysis
bca.rlq Between-Class RLQ analysis
bf88 Cubic Ecological Data
bicenter.wt Double Weighted Centring
bordeaux Wine Tasting
bsetal97 Ecological and Biological Traits
buech Buech basin
butterfly Genetics-Ecology-Environment Triple
bwca.dpcoa Between- and within-class double principal
coordinate analysis
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
chatcat Qualitative Weighted Variables
chats Pair of Variables
chazeb Charolais-Zebus
chevaine Enzymatic polymorphism in Leuciscus cephalus
chickenk Veterinary epidemiological study to assess the
risk factors for losses in broiler chickens
clementines Fruit Production
cnc2003 Frequenting movie theaters in France in 2003
coinertia Coinertia Analysis
coleo Table of Fuzzy Biological Traits
combine.4thcorner Functions to combine and adjust the outputs
3-table methods
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
costatis.randtest Monte-Carlo test on a Costatis analysis (in C).
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
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.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
ecg Electrocardiogram data
ecomor Ecomorphological Convergence
elec88 Electoral Data
escopage K-tables of wine-tasting
euro123 Triangular Data
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
friday87 Faunistic K-tables
fruits Pair of Tables
fuzzygenet Reading a table of genetic data (diploid
individuals)
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
hdpg Genetic Variation In Human Populations
housetasks Contingency Table
humDNAm human mitochondrial DNA restriction data
ichtyo Point sampling of fish community
inertia.dudi Decomposition of inertia (i.e. contributions)
in multivariate methods
irishdata Geary's Irish Data
is.euclid Is a Distance Matrix Euclidean?
julliot Seed dispersal
jv73 K-tables Multi-Regions
kcponds Ponds in a nature reserve
kdist the class of objects 'kdist' (K distance
matrices)
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.statis Multiple Graphs of a STATIS 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.within Process to go from a Within Analysis to a
K-tables
lascaux Genetic/Environment and types of variables
lingoes Transformation of a Distance Matrix for
becoming Euclidean
lizards Phylogeny and quantitative traits of lizards
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).)
maples Phylogeny and quantitative traits of flowers
mariages Correspondence Analysis Table
mbpcaiv Multiblock principal component analysis with
instrumental variables
mbpls Multiblock partial least squares
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
neig Neighbourhood Graphs
newick.eg Phylogenetic trees in Newick format
newick2phylog Create phylogeny
niche 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
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
orthogram Orthonormal decomposition of variance
ours A table of Qualitative Variables
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
pcw Distribution of of tropical trees along the
Panama canal
perthi02 Contingency Table with a partition in Molecular
Biology
phylog Phylogeny
piosphere Plant traits response to grazing
plot.phylog Plot phylogenies
presid2002 Results of the French presidential elections of
2002
print.within Within-Class 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
quasieuclid Transformation of a distance matrice to a
Euclidean one
randEH Nee and May's random process
randboot Bootstrap simulations
randboot.multiblock Bootstraped simulations for multiblock methods
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.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)
randtest.pcaiv Monte-Carlo Test on the percentage of explained
(i.e. constrained) inertia
randxval Two-fold cross-validation
rankrock Ordination Table
reconst Reconstitution of Data from a Duality Diagram
rhizobium Genetic structure of two nitrogen fixing
bacteria influenced by geographical isolation
and host specialization
rhone Physico-Chemistry Data
rlq RLQ analysis
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).
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 Compute or scale data using (weighted) means,
variances and covariances (possibly for the
levels of a factor)
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
scatterutil 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
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
statico.krandtest Monte-Carlo test on a Statico analysis (in C).
statis STATIS, a method for analysing K-tables
steppe Transect in the Vegetation
summary.between Between-Class Analysis
summary.multiblock Display and summarize multiblock objects
supcol Projections of Supplementary Columns
suprow 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
t3012 Average temperatures of 30 French cities
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.value Plot of the Arrays
tarentaise Mountain Avifauna
taxo.eg Examples of taxonomy
testdim Function to perform a test of dimensionality
testdim.multiblock Selection of the number of dimension by
two-fold cross-validation for multiblock
methods
tintoodiel Tinto and Odiel estuary geochemistry
tithonia Phylogeny and quantitative traits of flowers
tortues Morphological Study of the Painted Turtle
toxicity Homogeneous Table
triangle.class Triangular Representation and Groups of points
triangle.plot Triangular Plotting
trichometeo Pair of Ecological Data
ungulates Phylogeny and quantitative traits of ungulates.
uniquewt.df Elimination of Duplicated Rows in a Array
variance.phylog The phylogenetic ANOVA
vegtf Vegetation in Trois-Fontaines
veuvage Example for Centring in PCA
wca Within-Class Analysis
wca.rlq Within-Class RLQ analysis
westafrica Freshwater fish zoogeography in west Africa
withincoinertia Within-class coinertia analysis
withinpca Normed within principal component analysis
witwit.coa Internal Correspondence Analysis
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
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