Package ‘phytools’ June 3, 2021 Version 0.7-80 Date 2021-6-02 Title Phylogenetic Tools for Comparative Biology (and Other Things) Author Liam J. Revell Maintainer Liam J. Revell <[email protected]> Depends R (>= 3.5.0), ape (>= 4.0), maps Imports clusterGeneration, coda, combinat, expm, graphics, grDevices, MASS, methods, mnormt, nlme, numDeriv, phangorn (>= 2.3.1), plotrix, scatterplot3d, stats, utils Suggests animation, geiger, RColorBrewer, rgl ZipData no Description A wide range of functions for phylogenetic analysis. Functionality is concentrated in phy- logenetic comparative biology, but also includes numerous methods for visualizing, manipulat- ing, reading or writing, and even inferring phylogenetic trees and data. Included among the func- tions in phylogenetic comparative biology are various for ancestral state reconstruction, model- fitting, simulation of phylogenies and data, and multivariate analy- sis. There are a broad range of plotting methods for phylogenies and comparative data which in- clude, but are not restricted to, methods for mapping trait evolution on trees, for project- ing trees into phenotypic space or a geographic map, and for visualizing correlated speciation be- tween trees. Finally, there are a number of functions for reading, writing, analyzing, infer- ring, simulating, and manipulating phylogenetic trees and comparative data not cov- ered by other packages. For instance, there are functions for randomly or non-randomly attach- ing species or clades to a phylogeny, for estimating supertrees or consensus phyloge- nies from a set, for simulating trees and phylogenetic data under a range of mod- els, and for a wide variety of other manipulations and analyses that phylogenetic biolo- gists might find useful in their research. License GPL (>= 2) URL https://github.com/liamrevell/phytools Repository CRAN Date/Publication 2021-06-03 11:10:02 UTC NeedsCompilation no 1 2 R topics documented: R topics documented: phytools-package . .5 add.arrow . .6 add.color.bar . .7 add.everywhere . .9 add.random . .9 add.simmap.legend . 11 add.species.to.genus . 12 aic.w . 13 allFurcTrees . 14 anc.Bayes . 15 anc.ML . 17 anc.trend . 18 ancThresh . 20 anoletree . 22 applyBranchLengths . 23 as.multiPhylo . 24 as.Qmatrix . 25 ave.rates . 26 averageTree . 27 bd.............................................. 27 bind.tip . 28 bind.tree.simmap . 30 bmPlot . 31 branching.diffusion . 32 brownie.lite . 33 brownieREML . 35 cladelabels . 36 collapse.to.star . 38 collapseTree . 38 compare.chronograms . 39 consensus.edges . 40 contMap . 41 cophylo . 43 cospeciation . 45 countSimmap . 46 ctt.............................................. 47 density.multiSimmap . 48 densityMap . 49 densityTree . 51 describe.simmap . 52 di2multi.simmap . 53 dotTree . 55 drop.clade . 56 drop.leaves . 57 drop.tip.contMap . 58 drop.tip.multiPhylo . 59 R topics documented: 3 drop.tip.simmap . 60 Dtest . 61 edge.widthMap . 62 edgeProbs . 63 estDiversity . 64 evol.rate.mcmc . 65 evol.vcv . 66 evolvcv.lite . 68 exhaustiveMP . 70 expand.clade . 71 export.as.xml . 72 fancyTree . 73 fastAnc . 75 fastBM . 76 fastMRCA . 78 findMRCA . 79 fit.bd . 80 fitBayes . 82 fitDiversityModel . 83 fitMk ............................................ 84 fitPagel . 88 force.ultrametric . 89 gammatest . 90 genSeq . 91 geo.legend . 92 get.treepos . 93 getCladesofSize . 94 getDescendants . 94 getExtant . 95 getSisters . 96 getStates . 97 labelnodes . 98 ladderize.simmap . 99 lambda.transform . 99 likMlambda . ..