Package: adephylo 1.1-17

Aurélie Siberchicot

adephylo: Exploratory Analyses for the Phylogenetic Comparative Method

Multivariate tools to analyze comparative data, i.e. a phylogeny and some traits measured for each taxa. The package contains functions to represent comparative data, compute phylogenetic proximities, perform multivariate analysis with phylogenetic constraints and test for the presence of phylogenetic autocorrelation. The package is described in Jombart et al (2010) <doi:10.1093/bioinformatics/btq292>.

Authors:Stéphane Dray [aut], Thibaut Jombart [aut], Anders Ellern Bilgrau [ctb], Aurélie Siberchicot [ctb, cre]

adephylo_1.1-17.tar.gz
adephylo_1.1-17.zip(r-4.5)adephylo_1.1-17.zip(r-4.4)adephylo_1.1-17.zip(r-4.3)
adephylo_1.1-17.tgz(r-4.5-arm64)adephylo_1.1-17.tgz(r-4.4-x86_64)adephylo_1.1-17.tgz(r-4.4-arm64)adephylo_1.1-17.tgz(r-4.3-x86_64)adephylo_1.1-17.tgz(r-4.3-arm64)
adephylo_1.1-17.tar.gz(r-4.5-noble)adephylo_1.1-17.tar.gz(r-4.4-noble)
adephylo_1.1-17.tgz(r-4.4-emscripten)adephylo_1.1-17.tgz(r-4.3-emscripten)
adephylo.pdf |adephylo.html
adephylo/json (API)

# Install 'adephylo' in R:
install.packages('adephylo', repos = c('https://phylotastic.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/adeverse/adephylo/issues

Datasets:
  • carni19 - Phylogeny and quantative trait of carnivora
  • carni70 - Phylogeny and quantitative traits of carnivora
  • lizards - Phylogeny and quantitative traits of lizards
  • maples - Phylogeny and quantitative traits of flowers
  • mjrochet - Phylogeny and quantitative traits of teleos fishes
  • palm - Phylogenetic and quantitative traits of amazonian palm trees
  • procella - Phylogeny and quantitative traits of birds
  • tithonia - Phylogeny and quantitative traits of flowers
  • ungulates - Phylogeny and quantitative traits of ungulates.

On CRAN:adephylo-1.1-16(2023-10-06)

8.66 score 9 stars 4 packages 312 scripts 4.5k downloads 42 mentions 16 exports 88 dependencies

Last updated 19 days agofrom:a8e9574337. Checks:10 OK. Indexed: no.

TargetResultLatest binary
Doc / VignettesOKJan 29 2025
R-4.5-win-x86_64OKJan 29 2025
R-4.5-mac-aarch64OKJan 29 2025
R-4.5-linux-x86_64OKJan 29 2025
R-4.4-win-x86_64OKJan 29 2025
R-4.4-mac-x86_64OKJan 29 2025
R-4.4-mac-aarch64OKJan 29 2025
R-4.3-win-x86_64OKJan 29 2025
R-4.3-mac-x86_64OKJan 29 2025
R-4.3-mac-aarch64OKJan 29 2025

Exports:.tipToRootabouheif.moranbullseyedistRootdistTipslistDDlistTipsme.phylomoran.idxorthobasis.phyloorthogramppcaproxTipssp.tipstable.phylo4dtreePart

Dependencies:ade4adegenetapeaskpassbase64encbootbslibcachemcliclustercolorspacecommonmarkcpp11crayoncurldigestdplyrfansifarverfastmapfontawesomefsgenericsggplot2gluegtablehmshtmltoolshttpuvhttrigraphisobandjquerylibjsonlitelabelinglaterlatticelifecyclemagrittrMASSMatrixmemoisemgcvmimemunsellnlmeopensslpermutephylobasepillarpixmappkgconfigplyrprettyunitsprogresspromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloreshape2rlangrnclRNeXMLsassscalessegmentedseqinrshinysourcetoolsspstringistringrsystibbletidyrtidyselectutf8uuidvctrsveganviridisLitewithrXMLxml2xtable

adephylo: exploratory analyses for the phylogenetic comparative method

Rendered fromadephylo.Rnwusingutils::Sweaveon Jan 29 2025.

Last update: 2023-10-03
Started: 2015-08-25

Citation

To cite the adephylo package:

Jombart T., Dray S. (2008). adephylo: exploratory analyses for the phylogenetic comparative method.

Corresponding BibTeX entry:

  @Article{,
    title = {adephylo: exploratory analyses for the phylogenetic
      comparative method.},
    journal = {Bioinformatics},
    year = {2010},
    author = {Thibaut Jombart and St\'ephane Dray},
    volume = {26},
    pages = {1907-1909},
    doi = {10.1093/bioinformatics/btq292},
  }

Readme and manuals

adephylo

Exploratory Analyses for the Phylogenetic Comparative Method


Please note! Since January 2024, this repository has belonged to the adeverse organization. To avoid confusion, we strongly recommend updating any existing local clones to point to the new repository URL. You can do this by using git remote on the command line:

git remote set-url origin git@github.com:adeverse/adephylo.git

or

git remote set-url origin https://github.com/adeverse/adephylo.git


Installing adephylo adephylo

To install the development version from github:

library(devtools)
install_github("adeverse/adephylo")

The stable version can be installed from CRAN using:

install.packages("adephylo")

Once installed, the package can be loaded using:

library("adephylo")

Development team

Authors/developers

adephylo is developed by:

Maintainer

Help Manual

Help pageTopics
Low-level auxiliary functions for adephylo.tipToRoot
Abouheif's test based on Moran's Iabouheif.moran
Fan-like phylogeny with possible representation of traits on tipsbullseye
Phylogeny and quantative trait of carnivoracarni19
Phylogeny and quantitative traits of carnivoracarni70
Compute the distance of tips to the rootdistRoot
Compute some phylogenetic distance between tipsdistTips
List direct descendants for all nodes of a treelistDD
List tips descendings from all nodes of a treelistTips
Phylogeny and quantitative traits of lizardslizards
Phylogeny and quantitative traits of flowersmaples
Phylogeny and quantitative traits of teleos fishesmjrochet
Computes Moran's index for a variablemoran.idx
Computes Moran's eigenvectors from a tree or a phylogenetic proximity matrixme.phylo orthobasis.phylo
Orthonormal decomposition of varianceorthogram
Phylogenetic and quantitative traits of amazonian palm treespalm
Phylogenetic principal component analysisplot.ppca ppca print.ppca scatter.ppca screeplot.ppca summary.ppca
Phylogeny and quantitative traits of birdsprocella
Compute some phylogenetic proximities between tipsproxTips
Find the shortest path between tips of a treesp.tips
Graphical display of phylogeny and traitstable.phylo4d
Phylogeny and quantitative traits of flowerstithonia
Define partitions of tips according from a treetreePart
Phylogeny and quantitative traits of ungulates.ungulates