_pkgdown.yml

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
  - dpcaiv
  - dvaripart
  - 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