ade4: Analysis of Ecological Data : Exploratory and Euclidean Methods in Environmental Sciences

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Multivariate data analysis and graphical display.

Author
Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Date of publication
2016-03-01 17:07:34
Maintainer
Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
License
GPL (>= 2)
Version
1.7-4
URLs

View on CRAN

Man pages

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-internal
Internal ade4 functions
ade4.package
The ade4 package
ade4toR
Format Change Utility
adegraphicsLoaded
Utility function to test if the package adegraphics is loaded
aminoacyl
Codon usage
amova
Analysis of molecular variance
apis108
Allelic frequencies in ten honeybees populations at eight...
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.rlq
Between-Class RLQ analysis
between
Between-Class Analysis
betweencoinertia
Between-class coinertia 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...
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...
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...
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'...
corvus
Corvus morphology
costatis
STATIS and Co-Inertia : Analysis of a series of paired...
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...
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...
dotchart.phylog
Representation of many quantitative variables in front of a...
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...
dudi.hillsmith
Ordination of Tables mixing quantitative variables and...
dudi.mix
Ordination of Tables mixing quantitative variables and...
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
EH
Amount of Evolutionary History
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...
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...
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
Statistics of inertia in a one-table analysis
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...
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...
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...
mantel.rtest
Mantel test (correlation between two distance matrices (in...
maples
Phylogeny and quantitative traits of flowers
mariages
Correspondence Analysis Table
mbpcaiv
Multiblock principal component analysis with instrumental...
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...
meaudret
Ecological Data : sites-variables, sites-species, where and...
mfa
Multiple Factorial Analysis
microsatt
Genetic Relationships between cattle breeds with...
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
multiblock
Display and summarize multiblock objects
multispati
Multivariate spatial analysis
multispati.randtest
Multivariate spatial autocorrelation test (in C)
multispati.rtest
Multivariate spatial autocorrelation test
neig
Neighbourhood Graphs
newick2phylog
Create phylogeny
newick.eg
Phylogenetic trees in Newick format
niche
Method to Analyse a pair of tables : Environmental and...
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...
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...
pcaivortho
Principal Component Analysis with respect to orthogonal...
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
PI2newick
Import data files from Phylogenetic Independance Package
piosphere
Plant traits response to grazing
plot.between
Between-Class Analysis
plot.phylog
Plot phylogenies
plot.within
Within-Class Analysis
presid2002
Results of the French presidential elections of 2002
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...
procuste.rtest
Monte-Carlo Test on the sum of the singular values of a...
pta
Partial Triadic Analysis of a K-tables
quasieuclid
Transformation of a distance matrice to a Euclidean one
randboot
Bootstrap simulations
randboot.multiblock
Bootstraped simulations for multiblock methods
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...
randtest.between
Monte-Carlo Test on the between-groups inertia percentage (in...
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...
randtest.pcaiv
Monte-Carlo Test on the percentage of explained (i.e....
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...
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...
rtest.discrimin
Monte-Carlo Test on a Discriminant Analysis (in R).
RVdist.randtest
Tests of randomization on the correlation between two...
RV.rtest
Monte-Carlo Test on the sum of eigenvalues of a co-inertia...
santacatalina
Indirect Ordination
sarcelles
Array of Recapture of Rings
s.arrow
Plot of the factorial maps for the projection of a vector...
scalewt
Compute or scale data using (weighted) means, variances and...
scatter
Graphical representation of the outputs of a multivariate...
scatter.acm
Plot of the factorial maps in a Multiple Correspondence...
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...
scatterutil
Graphical utility functions
s.chull
Plot of the factorial maps with polygons of contour by level...
s.class
Plot of factorial maps with representation of point classes
sco.boxplot
Representation of the link between a variable and a set of...
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...
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...
s.corcircle
Plot of the factorial maps of a correlation circle
score
Graphs for One Dimension
score.acm
Graphs to study one factor in a Multiple Correspondence...
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
s.distri
Plot of a frequency distribution
seconde
Students and Subjects
sepan
Separated Analyses in a K-tables
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
skulls
Morphometric Evolution
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...
s.multinom
Graph of frequency profiles (useful for instance in genetic)
statico
STATIS and Co-Inertia : Analysis of a series of paired...
statico.krandtest
Monte-Carlo test on a Statico analysis (in C).
statis
STATIS, a method for analysing K-tables
steppe
Transect in the Vegetation
s.traject
Trajectory Plot
supcol
Projections of Supplementary Columns
suprow
Projections of Supplementary Rows
s.value
Representation of a value in a graph
symbols.phylog
Representation of a quantitative variable in front of a...
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...
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.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
woangers
Plant assemblages in woodlands of the conurbation of Angers...
worksurv
French Worker Survey (1970)
yanomama
Distance Matrices
zealand
Road distances in New-Zealand

Files in this package

ade4
ade4/inst
ade4/inst/pictures
ade4/inst/pictures/ireland.pnm
ade4/inst/pictures/tintoodiel.pnm
ade4/inst/pictures/avijonsvil.pnm
ade4/inst/pictures/sarcelles.pnm
ade4/inst/pictures/paris.pnm
ade4/inst/pictures/avijonsrou.pnm
ade4/inst/pictures/butterfly.pnm
ade4/inst/pictures/atyadigi.pnm
ade4/inst/pictures/atyacarto.pnm
ade4/inst/pictures/avijonsveg.pnm
ade4/inst/pictures/fatala.pnm
ade4/inst/pictures/capitales.pnm
ade4/inst/pictures/france_sm00.pnm
ade4/inst/pictures/avijonseau.pnm
ade4/inst/CITATION
ade4/src
ade4/src/Makevars
ade4/src/adesub.h
ade4/src/divsub.h
ade4/src/divsub.c
ade4/src/fourthcorner.c
ade4/src/phylog.c
ade4/src/tests.c
ade4/src/testrlq.c
ade4/src/testdim.c
ade4/src/testamova.c
ade4/src/adesub.c
ade4/NAMESPACE
ade4/data
ade4/data/baran95.rda
ade4/data/mafragh.rda
ade4/data/buech.rda
ade4/data/taxo.eg.rda
ade4/data/lascaux.rda
ade4/data/acacia.rda
ade4/data/westafrica.rda
ade4/data/meaudret.rda
ade4/data/corvus.rda
ade4/data/macroloire.rda
ade4/data/bacteria.rda
ade4/data/aminoacyl.rda
ade4/data/macaca.rda
ade4/data/fruits.rda
ade4/data/bsetal97.rda
ade4/data/bf88.rda
ade4/data/chats.rda
ade4/data/abouheif.eg.rda
ade4/data/deug.rda
ade4/data/piosphere.rda
ade4/data/chazeb.rda
ade4/data/clementines.rda
ade4/data/seconde.rda
ade4/data/perthi02.rda
ade4/data/fission.rda
ade4/data/elec88.rda
ade4/data/ecg.rda
ade4/data/chatcat.rda
ade4/data/yanomama.rda
ade4/data/escopage.rda
ade4/data/mollusc.rda
ade4/data/ungulates.rda
ade4/data/ecomor.rda
ade4/data/carniherbi49.rda
ade4/data/julliot.rda
ade4/data/humDNAm.rda
ade4/data/veuvage.rda
ade4/data/aravo.rda
ade4/data/kcponds.rda
ade4/data/avimedi.rda
ade4/data/banque.rda
ade4/data/tithonia.rda
ade4/data/syndicats.rda
ade4/data/tintoodiel.rda
ade4/data/avijons.rda
ade4/data/trichometeo.rda
ade4/data/meau.rda
ade4/data/dunedata.rda
ade4/data/atya.rda
ade4/data/capitales.rda
ade4/data/rpjdl.rda
ade4/data/chevaine.rda
ade4/data/woangers.rda
ade4/data/pcw.rda
ade4/data/monde84.rda
ade4/data/lizards.rda
ade4/data/ardeche.rda
ade4/data/vegtf.rda
ade4/data/irishdata.rda
ade4/data/t3012.rda
ade4/data/microsatt.rda
ade4/data/oribatid.rda
ade4/data/casitas.rda
ade4/data/rhizobium.rda
ade4/data/hdpg.rda
ade4/data/friday87.rda
ade4/data/olympic.rda
ade4/data/palm.rda
ade4/data/maples.rda
ade4/data/sarcelles.rda
ade4/data/ours.rda
ade4/data/mariages.rda
ade4/data/apis108.rda
ade4/data/ggtortoises.rda
ade4/data/ichtyo.rda
ade4/data/presid2002.rda
ade4/data/macon.rda
ade4/data/datalist
ade4/data/mjrochet.rda
ade4/data/tortues.rda
ade4/data/chickenk.rda
ade4/data/zealand.rda
ade4/data/carni19.rda
ade4/data/steppe.rda
ade4/data/tarentaise.rda
ade4/data/bordeaux.rda
ade4/data/euro123.rda
ade4/data/arrival.rda
ade4/data/coleo.rda
ade4/data/granulo.rda
ade4/data/jv73.rda
ade4/data/rhone.rda
ade4/data/santacatalina.rda
ade4/data/cnc2003.rda
ade4/data/newick.eg.rda
ade4/data/worksurv.rda
ade4/data/toxicity.rda
ade4/data/doubs.rda
ade4/data/carni70.rda
ade4/data/pap.rda
ade4/data/housetasks.rda
ade4/data/aviurba.rda
ade4/data/njplot.rda
ade4/data/procella.rda
ade4/data/atlas.rda
ade4/data/morphosport.rda
ade4/data/rankrock.rda
ade4/data/butterfly.rda
ade4/data/skulls.rda
ade4/R
ade4/R/ade4toR.R
ade4/R/multiblock.R
ade4/R/randxval.R
ade4/R/s.chull.R
ade4/R/dist.quant.R
ade4/R/sco.gauss.R
ade4/R/sco.match.R
ade4/R/s.distri.R
ade4/R/randEH.R
ade4/R/randtest.dpcoa.R
ade4/R/score.coa.R
ade4/R/s.logo.R
ade4/R/rlq.R
ade4/R/uniquewt.df.R
ade4/R/dudi.R
ade4/R/dudi.pca.R
ade4/R/dudi.fca.R
ade4/R/foucart.R
ade4/R/dudi.mix.R
ade4/R/sepan.R
ade4/R/dist.ktab.R
ade4/R/randtest.between.R
ade4/R/mcoa.R
ade4/R/krandboot.R
ade4/R/s.traject.R
ade4/R/divcmax.R
ade4/R/lingoes.R
ade4/R/orthobasis.R
ade4/R/score.acm.R
ade4/R/witwit.R
ade4/R/fourthcorner2.R
ade4/R/RV.rtest.R
ade4/R/s.label.R
ade4/R/dist.dudi.R
ade4/R/witwitsepan.R
ade4/R/sco.class.R
ade4/R/s.corcircle.R
ade4/R/kdist2ktab.R
ade4/R/fourthcorner.R
ade4/R/add.scatter.R
ade4/R/kplot.R
ade4/R/orthogram.R
ade4/R/dotchart.phylog.R
ade4/R/amova.R
ade4/R/supcol.R
ade4/R/betweencoinertia.R
ade4/R/ktab.within.R
ade4/R/s.value.R
ade4/R/sco.boxplot.R
ade4/R/pcoscaled.R
ade4/R/randtest.coinertia.R
ade4/R/procuste.R
ade4/R/rtest.between.R
ade4/R/pta.R
ade4/R/kplot.mfa.R
ade4/R/nipals.R
ade4/R/gearymoran.R
ade4/R/randboot.R
ade4/R/optimEH.R
ade4/R/fourthcorner.rlq.R
ade4/R/s.hist.R
ade4/R/quasieuclid.R
ade4/R/score.R
ade4/R/s.multinom.R
ade4/R/scatter.acm.R
ade4/R/within.R
ade4/R/gridrowcol.R
ade4/R/table.paint.R
ade4/R/bca.rlq.R
ade4/R/mbpls.R
ade4/R/table.value.R
ade4/R/scalewt.R
ade4/R/niche.R
ade4/R/utilities.R
ade4/R/area.plot.R
ade4/R/table.phylog.R
ade4/R/ktab.R
ade4/R/withincoinertia.R
ade4/R/multispati.randtest.R
ade4/R/mdpcoa.R
ade4/R/s.arrow.R
ade4/R/randtest.amova.R
ade4/R/disc.R
ade4/R/table.dist.R
ade4/R/randtest.rlq.R
ade4/R/neig.R
ade4/R/dudi.hillsmith.R
ade4/R/dudi.acm.R
ade4/R/symbols.phylog.R
ade4/R/dudi.dec.R
ade4/R/mstree.R
ade4/R/wca.rlq.R
ade4/R/score.pca.R
ade4/R/RVdist.randtest.R
ade4/R/randtest.cca.R
ade4/R/sco.distri.R
ade4/R/rtest.R
ade4/R/sco.label.R
ade4/R/bicenter.wt.R
ade4/R/originality.R
ade4/R/procuste.rtest.R
ade4/R/orisaved.R
ade4/R/p.adjust.4thcorner.R
ade4/R/dudi.nsc.R
ade4/R/cca.R
ade4/R/mantel.randtest.R
ade4/R/randtest.pcaivortho.R
ade4/R/mantel.rtest.R
ade4/R/krandxval.R
ade4/R/dotcircle.R
ade4/R/costatis.R
ade4/R/ktab.match2ktabs.R
ade4/R/is.euclid.R
ade4/R/rtest.discrimin.R
ade4/R/PI2newick.R
ade4/R/kdisteuclid.R
ade4/R/pcaivortho.R
ade4/R/plot.4thcorner.R
ade4/R/krandtest.R
ade4/R/randtest.R
ade4/R/scatter.coa.R
ade4/R/pcaiv.R
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