ade4 v1.7-15

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

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) <doi:10.18637/jss.v022.i04>.

Functions in ade4

Name Description
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
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Date 2020-02-13
License GPL (>= 2)
URL http://pbil.univ-lyon1.fr/ADE-4
BugReports https://github.com/sdray/ade4/issues
Encoding UTF-8
NeedsCompilation yes
Packaged 2020-02-13 09:06:03 UTC; stephane
Repository CRAN
Date/Publication 2020-02-13 11:50:07 UTC

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