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ade4 (version 1.3-3)
Analysis of Environmental Data : Exploratory and Euclidean methods in Environmental sciences
Description
Multivariate data analysis and graphical display.
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Install
install.packages('ade4')
Monthly Downloads
39,762
Version
1.3-3
License
GPL version 2 or newer
Homepage
http://pbil.univ-lyon1.fr/ADE-4
Maintainer
Jean Thioulouse
Last Published
November 21st, 2004
Functions in ade4 (1.3-3)
Search functions
score.pca
Graphs to Analyse a factor in PCA
santacatalina
Indirect Ordination
toxicity
Homogeneous Table
supcol
Projections of Supplementary Columns
scatter.dudi
Plot of the Factorial Maps
table.dist
Graph Display for Distance Matrices
yanomama
Distance Matrices
score.mix
Graphs to Analyse a factor in a Mixed Analysis
syndicats
Two Questions asked on a Sample of 1000 Respondents
uniquewt.df
Elimination of Duplicated Rows in a Array
ungulates
Phylogeny and quantitative traits of ungulates.
table.phylog
Plot arrays in front of a phylogenetic tree
variance.phylog
The phylogenetic ANOVA
t3012
Average temperatures of 30 French cities
triangle.plot
Triangular Plotting
score.coa
Graphs to analyse a factor in a correspondence analysis
tortues
Morphological Study of the Painted Turtle
seconde
Students and Subjects
scatter.coa
Plot of the factorial maps for a correspondence analysis
sco.boxplot
Representation of the link between a variable and a set of qualitative variables
score.acm
Graphs to study one factor in a Multiple Correspondence Analysis
score
Graphs for One Dimension
worksurv
French Worker Survey (1970)
sco.quant
Graph to Analyse the Relation between a Score and Quantitative Variables
zealand
Road distances in New-Zealand
within
Within Analyses
table.paint
Plot of the arrays by grey levels
scatter.acm
Plot of the factorial maps in multiple correspondence analysis
suprow
Projections of Supplementary Rows
statis
STATIS, a method for analysing K-tables
symbols.phylog
Representation of a quantitative variable in front of a phylogenetic tree
tarentaise
Mountain Avifauna
tintoodiel
Tinto and Odiel estuary geochemistry
table.cont
Plot of Contingency Tables
table.value
Plot of the Arrays
trichometeo
Pair of Ecological Data
triangle.class
Triangular Representation and Groups of points
westafrica
Freshwater fish zoogeography in west Africa
as.taxo
Taxonomy
casitas
Enzymatic polymorphism in Mus musculus
atya
Genetic variability of Cacadors
corkdist
Tests of randomization between distances applied to 'kdist' objetcs
coleo
Table of Fuzzy Biological Traits
bsetal97
Ecological and Biological Traits
kdist
the class of objects 'kdist' (K distance matrices)
abouheif.eg
Phylogenies and quantitative traits from Abouheif
multispati
Multivariate spatial analysis
rtest
Class of the Permutation Tests (in R).
s.arrow
Plot of the factorial maps for the projection of a vector basis
friday87
Faunistic K-tables
capitales
Road Distances
palm
Phylogenetic and quantitative traits of amazonian palm trees
mcoa
Multiple CO-inertia Analysis
atlas
Small Ecological Dataset
arrival
Arrivals at an intensive care unit
ktab.match2ktabs
STATIS and Co-Inertia : Analysis of a series of paired ecological tables
euro123
Triangular Data
orthobasis
Orthonormal basis for orthonormal transform
randtest
Class of the Permutation Tests (in C).
bicenter.wt
Double Weighted Centring
genet
A class of data: tables of populations and alleles
niche
Method to Analyse a pair of tables : Environmental and Faunistic Data
granulo
Granulometric Curves
s.traject
Trajectory Plot
avijons
Bird species distribution
inertia.dudi
Statistics of inertia in a one-table analysis
chazeb
Charolais-Zebus
pap
Taxonomy and quantitative traits of carnivora
dudi.acm
Multiple Correspondence Analysis
PI2newick
Import data files from Phylogenetic Independance Package
between
Between-Class Analysis
cnc2003
Frequenting movie theaters in France in 2003
ardeche
Fauna Table with double (row and column) partitioning
rpjdl
Avifauna and Vegetation
area.plot
Graphical Display of Areas
avimedi
Fauna Table for Constrained Ordinations
carni19
Phylogeny and quantative trait of carnivora
dudi.dec
Decentred Correspondence Analysis
mstree
Minimal Spanning Tree
dist.prop
Computation of Distance Matrices of Percentage Data
corvus
Corvus morphology
dudi.fca
Fuzzy Correspondence Analysis
dist.binary
Computation of Distance Matrices for Binary Data
tithonia
Phylogeny and quantitative traits of flowers
olympic
Olympic Decathlon
kdisteuclid
a way to obtain Euclidean distance matrices
phylog
Phylogeny
procella
Phylogeny and quantitative traits of birds
perthi02
Contingency Table with a partition in Molecular Biology
julliot
Seed dispersal
s.chull
Plot of the factorial maps with polygons of contour by level of a factor
bacteria
Genomes of 43 Bacteria
s.match
Plot of Paired Coordinates
ecomor
Ecomorphological Convergence
njplot
Phylogeny and trait of bacteria
macon
Wine Tasting
mantel.rtest
Mantel test (correlation between two distance matrices (in R).)
orthogram
Orthonormal decomposition of variance
housetasks
Contingency Table
dudi.nsc
Non symmetric correspondence analysis
ours
A table of Qualitative Variables
s.distri
Plot of a frequency distribution
ecg
Electrocardiogram data
ade4toR
Format Change Utility
dist.quant
Computation of Distance Matrices on Quantitative Variables
s.hist
Display of a scatterplot and its two marginal histograms
elec88
Electoral Data
is.euclid
Is a Distance Matrix Euclidean ?
kplot.foucart
Multiple Graphs for the Foucart's Correspondence Analysis
s.corcircle
Plot of the factorial maps of a correlation circle
jv73
K-tables Multi-Regions
sarcelles
Array of Recapture of Rings
dpcoa
Double principal coordinate analysis
kplot.mfa
Multiple Graphs for a Multiple Factorial Analysis
fuzzygenet
Reading a table of genetic data (diploid individuals)
lizards
Phylogeny and quantitative traits of lizards
coinertia
Coinertia Analysis
s.value
Representation of a value in a graph
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
aviurba
Ecological Tables Triplet
s.kde2d
Scatter Plot with Kernel Density Estimate
kplot.pta
Multiple Graphs for a Partial Triadic Analysis
dist.neig
Computation of the Distance Matrix associated to a Neighbouring Graph
mafragh
Phyto-Ecological Survey
RV.rtest
Monte-Carlo Test on the sum of eigenvalues of a co-inertia analysis (in R).
procuste.rtest
Monte-Carlo Test on the sum of the singular values of a procustean rotation (in R).
quasieuclid
Transformation of a distance matrice to a Euclidean one
dudi.pca
Principal Component Analysis
clementines
Fruit Production
dudi.pco
Principal Coordinates Analysis
dudi.coa
Correspondence Analysis
rlq
RLQ analysis
randtest.amova
Permutation tests on an analysis of molecular variance (in C).
irishdata
Geary's Irish Data
foucart
K-tables Correspondence Analysis with the same rows and the same columns
rhone
Physico-Chemistry Data
procuste
Simple Procruste Rotation between two sets of points
ichtyo
Point sampling of fish community
s.label
Scatter Plot
procuste.randtest
Monte-Carlo Test on the sum of the singular values of a procustean rotation (in C).
chevaine
Enzymatic polymorphism in Leuciscus cephalus
s.image
Graph of a variable using image and contour
rtest.discrimin
Monte-Carlo Test on a Discriminant Analysis (in R).
rtest.between
Monte-Carlo Test on the between-groups inertia percentage (in R).
plot.phylog
Plot phylogenies
randtest.discrimin
Monte-Carlo Test on a Discriminant Analysis (in C).
newick2phylog
Create phylogeny
pcoscaled
Simplified Analysis in Principal Coordinates
kplot.statis
Multiple Graphs of a STATIS Analysis
microsatt
Genetic Relationships between cattle breeds with microsatellites
acacia
Spatial pattern analysis in plant communities
pcaiv
Principal component analysis with respect to instrumental variables
discrimin
Linear Discriminant Analysis (descriptive statistic)
dist.dudi
Computation of the Distance Matrix of a Statistical Triplet
mantel.randtest
Mantel test (correlation between two distance matrices (in C).)
bf88
Cubic Ecological Data
gridrowcol
Complete regular grid analysis
morphosport
Athletes' Morphology
escopage
K-tables of wine-tasting
maples
Phylogeny and quantitative traits of flowers
randtest.coinertia
Monte-Carlo test on a coinertia analysis (in C).
divcmax
Maximal value of Rao's diversity coefficient also called quadratic entropy
pta
Partial Triadic Analysis of a K-tables
cca
Canonical Correspondence Analysis
oribatid
Oribatid mite
kplot.sepan
Multiple Graphs for Separated Analyses in a K-tables
mollusc
Faunistic Communities and Sampling Experiment
s.class
Plot of factorial maps with representation of point classes
mld
Multi Level Decomposition of unidimensional data
deug
Exam marks for some students
ktab.list.df
Creating a K-tables from a list of data frames.
ktab.data.frame
Creation of K-tables from a data frame
witwit.coa
Internal Correspondence Analysis
mariages
Correspondence Analysis Table
chatcat
Qualitative Weighted Variables
bordeaux
Wine Tasting
monde84
Global State of the World in 1984
doubs
Pair of Ecological Tables
dotcircle
Representation of n values on a circle
fruits
Pair of Tables
meau
Ecological Data : sites-variables, sites-species, where and when
dist.genet
Genetic distances from gene frequencies
gearymoran
Moran's I and Geary'c randomization tests for spatial and phylogenetic autocorrelation
veuvage
Example for Centring in PCA
sco.distri
Representation by mean- standard deviation of a set of weight distributions on a numeric score
dudi.hillsmith
Ordination of Tables mixing quantitative variables and factors
lascaux
Genetic/Environment and types of variables
kdist2ktab
Transformation of K distance matrices (object 'kdist') into K Euclidean representations (object 'ktab')
mfa
Multiple Factorial Analysis
meaudret
Ecological Data : sites-variables, sites-species, where and when
multispati.rtest
Multivariate spatial autocorrelation test
carni70
Phylogeny and quantitative traits of carnivora
amova
Analysis of molecular variance
chats
Pair of Variables
buech
Buech basin
baran95
African Estuary Fishes
multispati.randtest
Multivariate spatial autocorrelation test (in C)
macaca
Landmarks
kplot.mcoa
Multiple Graphs for a Multiple Co-inertia Analysis
butterfly
Genetics-Ecology-Environment Triple
scatter
Scatter Plot
apis108
Allelic frequencies in ten honeybees populations at eight microsatellites loci
RVdist.randtest
Tests of randomization on the correlation between two distance matrices (in R).
newick.eg
Phylogenetic trees in Newick format
pcaivortho
Principal Component Analysis with respect to orthogonal instrumental variables
rankrock
Ordination Table
scatter.fca
Plot of the factorial maps for a fuzzy correspondence analysis
skulls
Morphometric Evolution
within.pca
Normed within Principal Component Analysis
humDNAm
human mitochondrial DNA restriction data
randtest.between
Monte-Carlo Test on the between-groups inertia percentage (in C).
neig
Neighbourhood Graphs
carniherbi49
Taxonomy, phylogenies and quantitative traits of carnivora and herbivora
krandtest
Class of the Permutation Tests (in C).
kcponds
Ponds in a nature reserve
ktab.within
Process to go from a Within Analysis to a K-tables
randtest-internal
Internal Permutation Tests functions (in C).
ktab
the class of objects 'ktab' (K-tables)
presid2002
Results of the French presidential elections of 2002
fission
Fission pattern and heritable morphological traits
mjrochet
Phylogeny and quantitative traits of teleos fishes
dudi.mix
Ordination of Tables mixing quantitative variables and factors
divc
Rao's diversity coefficient also called quadratic entropy
discrimin.coa
Discriminant Correspondence Analysis
disc
Rao's dissimilarity coefficient
cailliez
Transformation to make Euclidean a distance matrix
lingoes
Transformation of a Distance Matrix for becoming Euclidean
banque
Table of Factors
reconst
Reconstitution of Data from a Duality Diagram
aminoacyl
Codon usage
sepan
Separated Analyses in a K-tables
taxo.eg
Examples of taxonomy
scalewt
Centring and Scaling a Matrix of Any Weighting
dudi
Duality Diagram
steppe
Transect in the Vegetation
dunedata
Dune Meadow Data