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phytools
Phylogenetic Tools for Comparative Biology (and Other Things)
View on CRAN: Click
here
Download and install phytools package within the R console
Install from CRAN:
install.packages("phytools")
Install from Github:
library("remotes")
install_github("cran/phytools") Install by package version:
library("remotes")
install_version("phytools", "2.3-0") Attach the package and use:
library("phytools")
Maintained by
Liam J. Revell
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2011-08-20
Latest Update: 2024-01-09
Description:
A wide range of methods for phylogenetic analysis - concentrated in phylogenetic comparative biology, but also including numerous techniques for visualizing, analyzing, manipulating, reading or writing, and even inferring phylogenetic trees. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, and simulation of phylogenies and trait data. A broad range of plotting methods for phylogenies and comparative data include (but are not restricted to) methods for mapping trait evolution on trees, for projecting trees into phenotype space or a onto a geographic map, and for visualizing correlated speciation between trees. Lastly, numerous functions are designed for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data. For instance, there are functions for computing consensus phylogenies from a set, for simulating phylogenetic trees and data under a range of models, for randomly or non-randomly attaching species or clades to a tree, as well as for a wide range of other manipulations and analyses that phylogenetic biologists might find useful in their research.
How to cite:
Liam J. Revell (2011). phytools: Phylogenetic Tools for Comparative Biology (and Other Things). R package version 2.3-0, https://cran.r-project.org/web/packages/phytools. Accessed 07 Nov. 2024.
Previous versions and publish date:
0.0-8 (2011-08-20 06:57), 0.1-0 (2011-10-17 07:55), 0.1-2 (2011-11-27 10:14), 0.1-5 (2011-12-18 10:10), 0.1-6 (2012-01-11 08:02), 0.1-7 (2012-02-27 08:35), 0.1-8 (2012-05-02 08:28), 0.1-9 (2012-08-08 23:31), 0.2-0 (2012-09-29 23:10), 0.2-1 (2012-11-13 08:09), 0.2-20 (2013-02-17 14:11), 0.2-30 (2013-03-20 19:14), 0.2-40 (2013-04-08 07:20), 0.2-50 (2013-04-20 23:18), 0.2-70 (2013-05-22 21:44), 0.2-80 (2013-05-31 15:21), 0.2-90 (2013-06-30 01:38), 0.3-10 (2013-07-16 16:08), 0.3-72.1 (2014-03-03 09:44), 0.3-72 (2013-10-25 07:29), 0.3-93 (2014-03-03 22:45), 0.4-05 (2014-05-05 07:16), 0.4-21 (2014-06-28 19:31), 0.4-31 (2014-08-26 22:47), 0.4-45 (2015-02-05 22:04), 0.4-56 (2015-04-29 08:41), 0.4-60 (2015-07-10 20:33), 0.5-00 (2015-09-25 09:02), 0.5-10 (2015-12-10 09:57), 0.5-20 (2016-03-06 23:34), 0.5-38 (2016-06-24 07:30), 0.5-64 (2016-12-05 22:45), 0.6-00 (2017-03-28 23:11), 0.6-20 (2017-07-28 07:53), 0.6-44 (2017-11-12 16:13), 0.6-60 (2018-09-28 06:50), 0.6-99 (2019-06-18 14:50), 0.7-20 (2020-03-19 15:20), 0.7-47 (2020-06-01 23:00), 0.7-70 (2020-09-20 00:20), 0.7-80 (2021-06-03 13:10), 0.7-90 (2021-09-25 22:50), 1.0-1 (2022-01-03 14:50), 1.0-3 (2022-04-05 22:20), 1.2-0 (2022-09-01 19:30), 1.5-1 (2023-02-19 14:20), 1.9-16 (2023-07-14 22:00), 2.0-3 (2023-11-09 23:40), 2.1-1 (2024-01-09 11:00)
Other packages that cited phytools R package
View phytools citation profile
Other R packages that phytools depends,
imports, suggests or enhances
Complete documentation for phytools
Functions, R codes and Examples using
the phytools R package
Some associated functions: Dtest . add.arrow . add.color.bar . add.everywhere . add.random . add.simmap.legend . add.species.to.genus . aic.w . allFurcTrees . anc.Bayes . anc.ML . anc.trend . ancThresh . ancr . anoletree . ansi_phylo . applyBranchLengths . as.Qmatrix . as.multiPhylo . ave.rates . averageTree . bd . bind.tip . bind.tree.simmap . bmPlot . branching.diffusion . brownie.lite . brownieREML . cladelabels . collapse.to.star . collapseTree . compare.chronograms . consensus.edges . contMap . cophylo . cospeciation . countSimmap . ctt . density.multiSimmap . densityMap . densityTree . describe.simmap . di2multi.simmap . dotTree . drop.clade . drop.leaves . drop.tip.contMap . drop.tip.multiSimmap . drop.tip.simmap . edge.widthMap . edgeProbs . estDiversity . evol.rate.mcmc . evol.vcv . evolvcv.lite . exhaustiveMP . expand.clade . export.as.xml . fancyTree . fastAnc . fastBM . fastMRCA . findMRCA . fit.bd . fitBayes . fitDiversityModel . fitMk . fitPagel . force.ultrametric . gamma_pruning . gammatest . genSeq . geo.legend . get.treepos . getCladesofSize . getDescendants . getExtant . getSisters . getStates . labelnodes . ladderize.simmap . lambda.transform . likMlambda . linklabels . locate.fossil . locate.yeti . ls.tree . ltt . ltt95 . make.era.map . make.simmap . map.overlap . map.to.singleton . mapped.states . markChanges . matchNodes . mergeMappedStates . midpoint.root . minRotate . minSplit . modified.Grafen . mrp.supertree . multi.mantel . multiC . multiRF . multirateBM . nodeHeights . nodelabels.cophylo . optim.phylo.ls . orderMappedEdge . paintSubTree . paste.tree . pbtree . pgls.Ives . phenogram . phyl.RMA . phyl.cca . phyl.pairedttest . phyl.pca . phyl.resid . phyl.vcv . phylANOVA . phylo.heatmap . phylo.impute . phylo.to.map . phylo.toBackbone . phyloDesign . phylomorphospace . phylomorphospace3d . phylosig . phytools-package . plot.backbonePhylo . plotBranchbyTrait . plotSimmap . plotThresh . plotTree.datamatrix . plotTree.errorbars . plotTree . plotTree.wBars . posterior.evolrate . posthoc . print.backbonePhylo . pscore . ratebystate . ratebytree . rateshift . read.newick . read.simmap . reorder.backbonePhylo . reorderSimmap . rep.phylo . reroot . rerootingMethod . rescale . rescaleSimmap . resolveNode . rotateNodes . roundBranches . roundPhylogram . rstate . sampleFrom . setMap . sim.corrs . sim.history . sim.ratebystate . sim.rates . simBMphylo . skewers . splitEdgeColor . splitTree . splitplotTree . starTree . strahlerNumber . threshBayes . threshDIC . threshState . to.matrix . tree.grow . treeSlice . untangle . vcvPhylo . write.simmap . writeAncestors . writeNexus .
Some associated R codes: Dtest.R . add.everywhere.R . add.random.R . add.species.to.genus.R . allFurcTrees.R . anc.Bayes.R . anc.ML.R . anc.trend.R . ancThresh.R . ansi_phylo.R . asr.R . backbonePhylo.R . bd.R . bmPlot.R . branching.diffusion.R . brownie.lite.R . brownieREML.R . collapseTree.R . compare.chronograms.R . consensus.edges.R . contMap.R . cophylo.R . cospeciation.R . cotangleplot.R . ctt.R . densityMap.R . densityTree.R . dotTree.R . drop.tip.simmap.R . estDiversity.R . evol.rate.mcmc.R . evol.vcv.R . evolvcv.lite.R . exhaustiveMP.R . export.as.xml.R . fancyTree.R . fastAnc.R . fastBM.R . fitBayes.R . fitBiogeog.R . fitDiversityModel.R . fitHRM.R . fitMk.R . fitMk.parallel.R . fitPagel.R . fitgammaMk.R . fitmultiMk.R . fitpolyMk.R . locate.fossil.R . locate.yeti.R . ls.consensus.R . ltt.R . ltt95.R . make.era.map.R . make.simmap.R . map.overlap.R . map.to.singleton.R . mcmcBM.R . mcmcBM.full.R . mcmcLambda.R . mcmcMk.R . mrp.supertree.R . multi.mantel.R . multiRF.R . multirateBM.R . optim.phylo.ls.R . paintSubTree.R . parsimony.R . pbtree.R . pgls.Ives.R . phenogram.R . phyl.RMA.R . phyl.cca.R . phyl.pairedttest.R . phyl.pca.R . phyl.resid.R . phylANOVA.R . phylo.heatmap.R . phylo.impute.R . phylo.to.map.R . phylomorphospace.R . phylomorphospace3d.R . phylosig.R . plotBranchbyTrait.R . plotSimmap.R . plotTree.datamatrix.R . plotTree.errorbars.R . plotTree.wBars.R . plotrix_fn.R . project.phylomorphospace.R . ratebystate.R . ratebytree.R . rateshift.R . read.newick.R . read.simmap.R . readNexus.R . rerootingMethod.R . resolveNodes.R . roundPhylogram.R . sim.corrs.R . sim.history.R . sim.rates.R . simBMphylo.R . skewers.R . splitplotTree.R . starTree.R . strahlerNumber.R . threshBayes.R . tree.grow.R . treeSlice.R . utilities.R . write.simmap.R . writeAncestors.R . writeNexus.R . Full phytools package functions and examples
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