adephylo: adephylo: exploratory analyses for the phylogenetic comparative method.

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Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa.

Author
Thibaut Jombart <t.jombart@imperial.ac.uk>, Stephane Dray <stephane.dray@univ-lyon1.fr>, Anders Ellern Bilgrau <abilgrau@math.aau.dk>
Date of publication
2015-02-21 12:44:06
Maintainer
Thibaut Jombart <t.jombart@imperial.ac.uk>
License
GPL (>=2)
Version
1.1-7

View on R-Forge

Man pages

abouheif
Abouheif's test based on Moran's I
adephylo.package
The adephylo package
bullseye
Fan-like phylogeny with possible representation of traits on...
carni19
Phylogeny and quantative trait of carnivora
carni70
Phylogeny and quantitative traits of carnivora
dibas
DIstance-Based Assignment
distRoot
Compute the distance of tips to the root
distTips
Compute some phylogenetic distance between tips
listDD
List direct descendants for all nodes of a tree
listTips
List tips descendings from all nodes of a tree
lizards
Phylogeny and quantitative traits of lizards
maples
Phylogeny and quantitative traits of flowers
miscUtils
Low-level auxiliary functions for adephylo
mjrochet
Phylogeny and quantitative traits of teleos fishes
moranIdx
Computes Moran's index for a variable
orthobasis
Computes Moran's eigenvectors from a tree or a phylogenetic...
orthogram
Orthonormal decomposition of variance
palm
Phylogenetic and quantitative traits of amazonian palm trees
ppca
Phylogenetic principal component analysis
procella
Phylogeny and quantitative traits of birds
proxTips
Compute some phylogenetic proximities between tips
sp.tips
Find the shortest path between tips of a tree
table.phylo4d
Graphical display of phylogeny and traits
tithonia
Phylogeny and quantitative traits of flowers
treePart
Define partitions of tips according from a tree
ungulates
Phylogeny and quantitative traits of ungulates.

Files in this package

adephylo/ChangeLog
adephylo/DESCRIPTION
adephylo/NAMESPACE
adephylo/R
adephylo/R/abouheif.R
adephylo/R/bullseye.R
adephylo/R/dibas.R
adephylo/R/distances.R
adephylo/R/moran.R
adephylo/R/orthobasis.R
adephylo/R/orthogram.R
adephylo/R/partition.R
adephylo/R/ppca.R
adephylo/R/proximities.R
adephylo/R/table.phylo4d.R
adephylo/R/utils.R
adephylo/R/zzz.R
adephylo/TODO
adephylo/build
adephylo/build/vignette.rds
adephylo/data
adephylo/data/carni19.RData
adephylo/data/carni70.RData
adephylo/data/lizards.RData
adephylo/data/maples.RData
adephylo/data/mjrochet.RData
adephylo/data/palm.RData
adephylo/data/procella.RData
adephylo/data/tithonia.RData
adephylo/data/ungulates.RData
adephylo/inst
adephylo/inst/CITATION
adephylo/inst/doc
adephylo/inst/doc/adephylo.R
adephylo/inst/doc/adephylo.Rnw
adephylo/inst/doc/adephylo.pdf
adephylo/man
adephylo/man/abouheif.Rd
adephylo/man/adephylo.package.Rd
adephylo/man/bullseye.Rd
adephylo/man/carni19.Rd
adephylo/man/carni70.Rd
adephylo/man/dibas.Rd
adephylo/man/distRoot.Rd
adephylo/man/distTips.Rd
adephylo/man/listDD.Rd
adephylo/man/listTips.Rd
adephylo/man/lizards.Rd
adephylo/man/maples.Rd
adephylo/man/miscUtils.Rd
adephylo/man/mjrochet.Rd
adephylo/man/moranIdx.Rd
adephylo/man/orthobasis.Rd
adephylo/man/orthogram.Rd
adephylo/man/palm.Rd
adephylo/man/ppca.Rd
adephylo/man/procella.Rd
adephylo/man/proxTips.Rd
adephylo/man/sp.tips.Rd
adephylo/man/table.phylo4d.Rd
adephylo/man/tithonia.Rd
adephylo/man/treePart.Rd
adephylo/man/ungulates.Rd
adephylo/src
adephylo/src/adesub.c
adephylo/src/adesub.h
adephylo/src/distPhylo.c
adephylo/src/misc.c
adephylo/src/phylog.c
adephylo/src/sptips.c
adephylo/src/sptips.h
adephylo/vignettes
adephylo/vignettes/adephylo.Rnw
adephylo/vignettes/figs
adephylo/vignettes/figs/adephylo-012.pdf
adephylo/vignettes/figs/adephylo-012.png
adephylo/vignettes/figs/adephylo-016.pdf
adephylo/vignettes/figs/adephylo-017.pdf
adephylo/vignettes/figs/adephylo-017.png
adephylo/vignettes/figs/adephylo-018.pdf
adephylo/vignettes/figs/adephylo-aboutest.pdf
adephylo/vignettes/figs/adephylo-figFourBas.pdf
adephylo/vignettes/figs/adephylo-lm1.pdf
adephylo/vignettes/figs/adephylo-loadings.pdf
adephylo/vignettes/figs/adephylo-orthobas1.pdf
adephylo/vignettes/figs/adephylo-pca1.pdf
adephylo/vignettes/figs/adephylo-pca2.pdf
adephylo/vignettes/figs/adephylo-phylo4d.pdf
adephylo/vignettes/figs/adephylo-phylo4d.png
adephylo/vignettes/figs/adephylo-resid.pdf
adephylo/vignettes/figs/adephylo-treePart.pdf
adephylo/vignettes/figs/adephylo-treePart.png