/
_pkgdown.yml
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/
_pkgdown.yml
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url: ~
destination : docs
template:
bootstrap: 5
bootswatch: yeti
navbar:
title: "ade4"
left:
- text: "New to ade4?"
menu:
- text: "Installation"
href: articles/install.html
- text: "Getting started"
href: articles/get_started.html
- text: "Vignettes"
href: vignettes.html
menu:
- text: "Graphical representation of multivariate data"
href: https://cran.r-project.org/web/packages/adegraphics/vignettes/adegraphics.html
- text: "Environmental variables structures"
href: articles/ChapEnvVarStruct.html
- text: "Species structures"
href: articles/ChapSpeciesStruct.html
- text: "Taking into account groups of sites"
href: articles/ChapBetGr.html
- text: "Description of species-environment relationships"
href: articles/Chap2tables.html
- text: "Analysing Changes in Structures"
href: articles/ChapKtables.html
- text: "Analysing Changes in Co-structures"
href: articles/Chap2Ktables.html
- text: "Related packages"
href: articles/related.html
- text: "News"
href: news/index.html
- text: "Reference"
href: reference/index.html
- text: "Ressources"
menu:
- text: "ade4shiny"
href: https://lbbe-shiny.univ-lyon1.fr/ade4shiny/
- text: "FAQ"
href: articles/faq.html
- text: "adelist"
href: "https://listes.univ-lyon1.fr/sympa/info/adelist"
- text: "ade4 book"
href: articles/book.html
- text: "Papers"
href: articles/papers.html
right:
- text: "LBBE"
icon: fa-leaf
href: https://lbbe-web.univ-lyon1.fr/en
- icon: fa-github
href: https://github.com/adeverse/ade4
reference:
- title: One-table analysis
desc: These functions are designed for the analysis of a single table.
- subtitle: Methods
desc: Functions to run the analysis
contents:
- dudi.acm
- dudi.coa
- dudi.dec
- dudi.fca
- dudi.fpca
- dudi.hillsmith
- dudi.mix
- dudi.nsc
- dudi.pca
- dudi.pco
- pcoscaled
- nipals
- subtitle: Graphics
desc: Functions to display the results of the analysis
contents:
- reciprocal.coa
- scatter
- scatter.acm
- scatter.coa
- scatter.dudi
- scatter.fca
- score
- score.acm
- score.mix
- score.pca
- title: Two-table analysis
desc: These functions are designed for the analysis of a pair of tables.
- subtitle: Methods
desc: Functions to run the analysis
contents:
- coinertia
- pcaiv
- pcaivortho
- procuste
- niche
- niche.param
- varipart
- subtitle: Tests
desc: Functions to evaluate the significance of observed structures
contents:
- procuste.randtest
- procuste.rtest
- randtest.coinertia
- randtest.pcaiv
- RV.randtest
- RV.rtest
- RVintra.randtest
- title: Three-table methods
desc: 3-tables methods.
contents:
- combine.4thcorner
- combine.randtest.rlq
- fourthcorner.rlq
- rlq
- fourthcorner
- fourthcorner2
- p.adjust.4thcorner
- title: Analysis including categorical variables (`factor`)
desc: These functions allows to consider a partition of individuals to focus on or remove differences between groups.
- subtitle: Methods
contents:
- bca
- bca.coinertia
- bca.rlq
- bwca.dpcoa
- discrimin
- discrimin.coa
- wca
- wca.coinertia
- wca.rlq
- withinpca
- witwit.coa
- witwitsepan
- subtitle: Additional tools
contents:
- loocv.between
- loocv.discrimin
- randtest.between
- randtest.discrimin
- rtest.between
- rtest.discrimin
- title: Management of `dudi` objects
desc: These functions provides functionalities to manage objects of the class `dudi` (they can be used on the outputs od several methods to analyze one or two tables for instance).
contents:
- as.dudi
- biplot.dudi
- dist.dudi
- inertia
- inertia.dudi
- is.dudi
- loocv
- reconst
- redo.dudi
- supcol
- suprow
- testdim
- title: K-table analysis
desc: Functions designed to manage and analyze data structured in several tables (a.k.a. multitable analysis)
- subtitle: Methods
desc: Functions to run the analysis
contents:
- costatis
- foucart
- mdpcoa
- mbpls
- mbpcaiv
- mcoa
- mfa
- pta
- sepan
- statico
- statis
- subtitle: Graphics
desc: Functions to display the results of the analysis
contents:
- kplot
- kplot.foucart
- kplot.mcoa
- kplot.mfa
- kplot.pta
- kplotsepan.coa
- kplot.statis
- kplotX.mdpcoa
- multiblock
- subtitle: Utilities
desc: Functions to manage objects of class `ktab`
contents:
- col.names
- is.ktab
- ktab.data.frame
- ktab.list.df
- ktab.list.dudi
- ktab.match2ktabs
- ktab.within
- prep.mdpcoa
- tab.names
- suprow.pta
- subtitle: Tests
desc: Functions to evaluate the significance of observed structures
contents:
- costatis.randtest
- randboot.multiblock
- testdim.multiblock
- statico.krandtest
- title: Distance methods
contents:
- cailliez
- dist.binary
- dist.dudi
- dist.ktab
- dist.neig
- dist.prop
- dist.quant
- dist.taxo
- dudi.pco
- kdist
- kdist.cor
- kdist2ktab
- kdisteuclid
- ldist.ktab
- mantel.randtest
- mantel.rtest
- mantelkdist
- prep.binary
- prep.circular
- prep.fuzzy
- quasieuclid
- RVdist.randtest
- RVkdist
- supdist
- table.dist
- as.taxo
- is.euclid
- lingoes
- mstree
- pcoscaled
- title: Graphics
desc: Functions to draw graphics. See functions of the package `adegraphics` for a more flexible implementation based on `lattice`.
- subtitle: 1D plot
contents:
- sco.boxplot
- sco.class
- sco.distri
- sco.gauss
- sco.quant
- sco.label
- sco.match
- subtitle: 2D plot
contents:
- s.arrow
- s.chull
- s.class
- s.corcircle
- s.distri
- s.hist
- s.image
- s.kde2d
- s.label
- s.logo
- s.match
- s.match.class
- s.multinom
- s.traject
- s.value
- subtitle: Other types of plot
contents:
- dotcircle
- table.cont
- table.dist
- table.paint
- table.value
- triangle.biplot
- triangle.class
- triangle.plot
- subtitle: Utilities
desc: These functions are mainly designed for internal use.
contents:
- add.scatter
- add.scatter.eig
- scatterutil.base
- scatterutil.chull
- scatterutil.convrot90
- scatterutil.eigen
- scatterutil.ellipse
- scatterutil.eti
- scatterutil.eti.circ
- scatterutil.grid
- scatterutil.legend.bw.square
- scatterutil.legend.square.grey
- scatterutil.legendgris
- scatterutil.logo
- scatterutil.scaling
- scatterutil.sco
- scatterutil.star
- scatterutil.sub
- subtitle: Diversity
desc: Functions focusing on the measurment of diversity. See also the package `adiv` for more functionalities.
contents:
- amova
- apqe
- disc
- divc
- divcmax
- dpcoa
- originality
- randtest.dpcoa
- randtest.amova
- subtitle: Spatial
desc: Functions focusing on the analysis of spatial data. See also the package `adespatial` for more functionalities.
contents:
- gridrowcol
- haar2level
- mld
- mstree
- is.orthobasis
- orthobasis.circ
- orthobasis.haar
- orthobasis.line
- orthobasis.mat
- orthobasis.neig
- nb2neig
- neig
- neig2mat
- neig2nb
- scores.neig
- title: Phylogenetic methods
desc: These functions allows to manage phylogenetic data. See functions of the package `adephylo` for a more flexible implementation based on `ape` and `phylobase`.
contents:
- dotchart.phylog
- enum.phylog
- gearymoran
- hclust2phylog
- newick2phylog
- phylog.extract
- phylog.permut
- radial.phylog
- symbols.phylog
- table.phylog
- taxo2phylog
- variance.phylog
- PI2newick
- symbols.phylog
- title: Tests
desc: Utilities functions to manage results of randomization procedures.
contents:
- as.krandboot
- as.krandtest
- as.krandxval
- as.randboot
- as.randtest
- as.randxval
- randboot
- randtest
- rtest
- title: Misc
contents:
- ade4-package
- acm.burt
- acm.disjonctif
- adegraphicsLoaded
- bicenter.wt
- covwt
- covfacwt
- dagnelie.test
- meanfacwt
- scalewt
- scalefacwt
- uniquewt.df
- title: internal
contents:
- ade4-internal
- prep.fuzzy.var
- area.plot
- area2link
- area2poly
- poly2area
- title: Datasets
desc: Datasets available in ade4. You can access them by typing `r data(dataset)`.
contents:
- abouheif.eg
- acacia
- aminoacyl
- apis108
- aravo
- ardeche
- arrival
- atlas
- atya
- avijons
- avimedi
- aviurba
- bacteria
- banque
- baran95
- bf88
- bordeaux
- bsetal97
- buech
- butterfly
- capitales
- carni19
- carni70
- carniherbi49
- casitas
- chatcat
- chats
- chazeb
- chevaine
- chickenk
- clementines
- cnc2003
- coleo
- corvus
- deug
- doubs
- dunedata
- ecg
- ecomor
- elec88
- escopage
- euro123
- fission
- friday87
- fruits
- ggtortoises
- granulo
- hdpg
- houmousr
- housetasks
- humDNAm
- ichtyo
- irishdata
- julliot
- jv73
- kcponds
- lascaux
- lizards
- macaca
- macon
- macroloire
- mafragh
- maples
- mariages
- meau
- meaudret
- microsatt
- mjrochet
- mollusc
- monde84
- morphosport
- newick.eg
- njplot
- olympic
- oribatid
- ours
- palm
- pap
- pcw
- perthi02
- piosphere
- presid2002
- procella
- rankrock
- rhizobium
- rhone
- rpjdl
- santacatalina
- sarcelles
- seconde
- skulls
- steppe
- syndicats
- t3012
- tarentaise
- taxo.eg
- tintoodiel
- tithonia
- tortues
- toxicity
- trichometeo
- ungulates
- vegtf
- veuvage
- westafrica
- woangers
- worksurv
- yanomama
- zealand
- title: Deprecated
contents:
- '`Deprecated functions`'
- between
- within