Reference manual

It appears you don't have a PDF plugin for this browser. You can click here to download the reference manual.

install.packages("ape")

5.7-1 by Emmanuel Paradis, a year ago


http://ape-package.ird.fr/, https://github.com/emmanuelparadis/ape


Report a bug at https://github.com/emmanuelparadis/ape/issues


Browse source code at https://github.com/cran/ape


Authors: Emmanuel Paradis [aut, cre, cph] , Simon Blomberg [aut, cph] , Ben Bolker [aut, cph] , Joseph Brown [aut, cph] , Santiago Claramunt [aut, cph] , Julien Claude [aut, cph] , Hoa Sien Cuong [aut, cph] , Richard Desper [aut, cph] , Gilles Didier [aut, cph] , Benoit Durand [aut, cph] , Julien Dutheil [aut, cph] , RJ Ewing [aut, cph] , Olivier Gascuel [aut, cph] , Thomas Guillerme [aut, cph] , Christoph Heibl [aut, cph] , Anthony Ives [aut, cph] , Bradley Jones [aut, cph] , Franz Krah [aut, cph] , Daniel Lawson [aut, cph] , Vincent Lefort [aut, cph] , Pierre Legendre [aut, cph] , Jim Lemon [aut, cph] , Guillaume Louvel [aut, cph] , Eric Marcon [aut, cph] , Rosemary McCloskey [aut, cph] , Johan Nylander [aut, cph] , Rainer Opgen-Rhein [aut, cph] , Andrei-Alin Popescu [aut, cph] , Manuela Royer-Carenzi [aut, cph] , Klaus Schliep [aut, cph] , Korbinian Strimmer [aut, cph] , Damien de Vienne [aut, cph]


Documentation:   PDF Manual  


GPL-2 | GPL-3 license


Imports nlme, lattice, graphics, methods, stats, utils, parallel, Rcpp, digest

Suggests gee, expm, igraph, phangorn

Linking to Rcpp


Imported by AnnotationBustR, Apoderoides, BAT, BIEN, BoSSA, CALANGO, CRABS, DAISIEprep, DAMOCLES, DCLEAR, DDD, DHARMa, EnvNJ, EpiModel, EvoPhylo, FishPhyloMaker, FossilSim, FuncDiv, GIFT, GOCompare, GUniFrac, GaMaBioMD, HACSim, HMPTrees, HTSSIP, Hmsc, HybridMicrobiomes, MACER, MAGNAMWAR, ML.MSBD, MLVSBM, MiscMetabar, MultivariateAnalysis, NST, NicheBarcoding, OpenTreeChronograms, PBD, PCMBase, PCPS, POMS, POSTm, POUMM, PVR, PhyInsight, PhySortR, Plasmidprofiler, Quartet, RAINBOWR, RRPP, RRphylo, RevGadgets, Revticulate, Rogue, Rtropical, SPARTAAS, STEPCAM, STraTUS, SeqFeatR, SiPhyNetwork, SigTree, Sysrecon, TBRDist, TML, TransPhylo, TreeDiagram, TreeDist, TreeSearch, TreeSimGM, aPCoA, abdiv, adaptiveGPCA, adegenet, adephylo, adiv, alakazam, arakno, autoGO, beastier, beautier, betapart, bioregion, bioseq, bite, bnpsd, canaper, chemodiv, cloneRate, coil, colordistance, concatipede, copyseparator, covid19.analytics, dartR, dartR.base, datelife, ddtlcm, debar, dowser, ecoregime, entropart, epm, evobiR, evolqg, evolvability, file2meco, fishtree, funspace, genBaRcode, geneHapR, geomorph, ggmuller, ggrasp, glinvci, gquad, gromovlab, haplotypes, harrietr, hillR, hilldiv, homals, iCAMP, iCellR, iNEXT.3D, iNEXT.beta3D, idar, immunarch, indelmiss, insect, ipADMIXTURE, itol.toolkit, jackalope, mFD, markophylo, metacoder, microeco, mmodely, msaR, multilaterals, mvSLOUCH, nLTT, nodiv, numbat, ontophylo, oppr, outbreaker2, paco, palaeoverse, pcmabc, phyext2, phylobase, phylocanvas, phylogram, phylopath, phyloraster, phyloregion, phylosem, phylosignal, phylter, phyr, poolfstat, popkin, poppr, primerTree, prioritizr, rKOMICS, rapidphylo, ratematrix, refdb, restez, rhierbaps, rotl, rr2, rrnni, scistreer, secsse, sharpshootR, shazam, shinyTempSignal, sidier, slendr, slouch, spider, stylo, tapnet, taxize, tidytree, treeDA, treebalance, treedata.table, treenomial, treesliceR, treestats, treestructure, vcfR, yatah.

Depended on by Anaconda, BAMMtools, BarcodingR, Canopy, Claddis, FD, JNplots, MCMCglmm, MCMCtreeR, MPSEM, MSCquartets, MSCsimtester, MiSPU, MonoPhy, OUwie, PhylogeneticEM, RNeXML, RPANDA, Rphylopars, StructFDR, TESS, TreeSim, TreeTools, VDJgermlines, admtools, apex, aphylo, caper, cati, cauphy, coalescentMCMC, convevol, corHMM, ctpm, dispRity, distory, diversitree, geiger, hisse, ips, jrich, motmot, mvMORPH, nichevol, nodeSub, paleoDiv, paleotree, pegas, perspectev, pez, phangorn, phyclust, phyloTop, phyloclim, phylolm, phylotools, phytools, picante, quiddich, recluster, rwty, sensiPhy, strap, surface, treats, treebase, treedater, treespace, treestartr, windex.

Suggested by CTNote, CongreveLamsdell2016, DAISIE, ENMTools, FinePop, GLSME, HSAUR, HSAUR2, HSAUR3, MVA, OptCirClust, Platypus, RVAideMemoire, Seurat, SoilTaxonomy, TextMiningGUI, TiPS, TotalCopheneticIndex, ade4, adespatial, aphid, aqp, asnipe, brms, castor, changeRangeR, data.tree, deeptime, dendextend, divraster, dynamicSDM, ecolottery, ecospat, ecotraj, enveomics.R, fido, ggimage, hagis, harmonicmeanp, hierfstat, igraph, jSDM, kmer, lingtypology, mdendro, meconetcomp, mecoturn, metadat, metafor, metagear, netdiffuseR, nosoi, occCite, ouch, outbreaks, pagoo, paleobuddy, phylocomr, phylotate, plotbb, polysat, rbiom, rdiversity, rehh, rncl, rphylopic, safedata, sand, scrm, shipunov, spiralize, supportR, symmoments, taxlist, tidygraph, tidysq, tracerer, vhica, warbleR.

Enhanced by clue.


See at CRAN