Maintainer: | William Gearty, Brian O'Meara, Jacob Berv, Gustavo A. Ballen, Diniz Ferreira, Hilmar Lapp, Lars Schmitz, Martin R. Smith, Nathan S. Upham, Jonathan A. Nations |
Contact: | willgearty at gmail.com |
Version: | 2024-01-30 |
URL: | https://CRAN.R-project.org/view=Phylogenetics |
Source: | https://github.com/cran-task-views/Phylogenetics/ |
Contributions: | Suggestions and improvements for this task view are very welcome and can be made through issues or pull requests on GitHub or via e-mail to the maintainer address. For further details see the Contributing guide. |
Citation: | William Gearty, Brian O'Meara, Jacob Berv, Gustavo A. Ballen, Diniz Ferreira, Hilmar Lapp, Lars Schmitz, Martin R. Smith, Nathan S. Upham, Jonathan A. Nations (2024). CRAN Task View: Phylogenetics. Version 2024-01-30. URL https://CRAN.R-project.org/view=Phylogenetics. |
Installation: | The packages from this task view can be installed automatically using the ctv package. For example, ctv::install.views("Phylogenetics", coreOnly = TRUE) installs all the core packages or ctv::update.views("Phylogenetics") installs all packages that are not yet installed and up-to-date. See the CRAN Task View Initiative for more details. |
The history of life unfolds within a phylogenetic context, and phylogenetic trees (often shortened to “trees”) are developed to represent this evolutionary history. Comparative phylogenetic methods are statistical approaches for analyzing historical patterns along such phylogenetic trees. This task view describes R packages that (i) facilitate the handling, manipulation and analysis of phylogenetic trees; (ii) implement comparative phylogenetic methods; (iii) apply phylogenetic methods to specific disciplines. This is an active research area and much of the information is subject to change. Many important packages are not on CRAN: either they were formerly on CRAN and were later archived (for example, if they failed to incorporate necessary changes as R is updated) or they are developed elsewhere and are not yet available on CRAN. Such packages may be found on GitHub, R-Forge, Bioconductor, or authors’ websites. At least ten packages start as phy* in this domain, including two pairs of similarly named packages (phytools and phylotools, phylobase and phybase); users are encouraged to read and distinguish carefully between package names.
If you have any questions, feel free to reach out to the task view maintainers or the maintainers of specific packages. Questions may also be directed to the R-SIG-Phylo mailing-list after subscription.
ape implements the S3 phylo class which is commonly used to store phylogenetic trees in R. It is commonly used for reading, writing, and visualizing trees in the Newick/Phylip and NEXUS formats. It also has many functions for manipulating trees (e.g., rooting trees, dropping tips, randomly resolving polytomies), inferring trees (e.g., neighbour joining, bio-nj, and fast ME methods), and performing phylogenetic comparative analyses (e.g., reconstructing discrete and continuous characters, fitting basic models of trait evolution and diversification). It can also be used to generate random trees, pull in data from GenBank, and create lineage through time and correlogram plots.
phylobase implements the S4 phylo4 class which combines phylogenetic trees and comparative data. While not used as commonly as the S3 phylo class, this new class is gaining traction among newer packages that implement phylogenetic comparative methods (e.g., adephylo and phylosignal).
geiger implements a large suite of model fitting approaches for analyses of trait evolution and diversification. It is most commonly used to fit and compare various models of discrete and continuous trait evolution (e.g., Brownian motion, Ornstein-Uhlenbeck, Pagel’s transforms, and models with trends). It also is commonly used to simulate phylogenies and the evolution of discrete and continuous characters. It also has several auxiliary functions that are often used by other packages.
phytools has a constantly increasing range of functions for performing phylogenetic comparative analyses and visualizing (e.g., projecting into a morphospace), manipulating (e.g., branch length scaling and transformations, adding tips, finding subtrees), reading or writing, and even inferring phylogenetic trees and comparative data.
Packages within the task view fall within one or more of the following task categories:
"simmap"
trees with an encoded discrete character."simmap"
object by various methods, convert a tree with a mapped character into a simple "phylo"
object with unbranching nodes or a root edge into a single unbranching node, and other things.diversitree:::plot2.phylo()
).See the Epidemiology task view for details about packages useful for epidemiology, including phylogenetic epidemiology.
Core: | ape, geiger, phylobase, phytools. |
Regular: | adephylo, adiv, apex, aphid, aphylo, babette, BAMMtools, beastier, beautier, betapart, BoSSA, brms, CALANGO, caper, castor, Claddis, convevol, CRABS, DAMOCLES, DDD, deeptime, dendextend, dispRity, distory, diversitree, entropart, epm, evobiR, EvoPhylo, FossilSim, geomorph, ggmuller, ggplot2, GUniFrac, hisse, HMPTrees, idendr0, ips, markophylo, MCMCglmm, metafor, motmot, MPSEM, mvMORPH, nLTT, ouch, OUwie, paleobuddy, paleotree, paleoTS, PBD, PCPS, phangorn, phyclust, phyext2, phylocanvas, phyloclim, PHYLOGR, phylogram, phylolm, phyloregion, phylosignal, phylotate, phylotools, phyloTop, phyreg, picante, pmc, Quartet, RevGadgets, Revticulate, rncl, RNeXML, Rogue, rotl, RPANDA, Rphylopars, RRPP, secsse, SigTree, strap, surface, SYNCSA, taxize, tbea, TBRDist, TESS, tidytree, tracerer, treebalance, treebase, treedater, TreeDist, TreeSearch, TreeSim, treespace, treestats, TreeTools, vegan, windex. |
Archived: | metacoder. |