Reference manual

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install.packages("ape")

5.6-2 by Emmanuel Paradis, 3 months ago


http://ape-package.ird.fr/


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, tools, utils, parallel, Rcpp

Suggests gee, expm, igraph, phangorn

Linking to Rcpp


Imported by AnnotationBustR, BAT, BIEN, BPEC, BayesSPsurv, BoSSA, CALANGO, CNull, CommT, DAMOCLES, DCLEAR, DDD, DHARMa, EnvNJ, EpiModel, EvoPhylo, FishPhyloMaker, FossilSim, GOCompare, GUniFrac, HACSim, HMPTrees, HTSSIP, HierDpart, Hmsc, MACER, MAGNAMWAR, ML.MSBD, MultivariateAnalysis, NicheBarcoding, PBD, PCMBase, PCPS, PIGShift, POSTm, POUMM, PVR, PhySortR, PhyloMeasures, Plasmidprofiler, Quartet, RAINBOWR, RPS, RRPP, RRphylo, Rarefy, Revticulate, Rogue, Rtropical, SPARTAAS, STEPCAM, STraTUS, SeqFeatR, SigTree, TBRDist, TransPhylo, TreeDiagram, TreeDist, TreeSearch, TreeSimGM, aPCoA, abdiv, adaptiveGPCA, adegenet, adephylo, adiv, alakazam, beastier, beautier, betapart, bioseq, bite, bnpsd, brranching, coil, colordistance, concatipede, contact, covid19.analytics, dartR, debar, dowser, entropart, epm, evobiR, evolqg, evolvability, file2meco, fishtree, genBaRcode, geomedb, geomorph, ggmotif, ggmuller, ggrasp, glinvci, gquad, gromovlab, haplotypes, harrietr, hillR, hilldiv, homals, iCellR, idar, immunarch, indelmiss, insect, ipADMIXTURE, jackalope, liayson, mFD, markophylo, metacoder, microeco, msaR, msap, multilaterals, mvSLOUCH, nLTT, nodeSub, nodiv, oppr, outbreaker2, paco, pcmabc, perfectphyloR, phyext2, phylobase, phylocanvas, phylogram, phylopath, phyloregion, phylosignal, phyr, poolfstat, popkin, poppr, prewas, primerTree, prioritizr, rKOMICS, ratematrix, rhierbaps, rotl, rr2, secsse, sharpshootR, shazam, shinyTempSignal, sidier, slouch, spider, stylo, tapnet, taxize, tidytree, treeDA, treebalance, treedata.table, treeman, treenomial, treestructure, vcfR, yatah.

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

Suggested by ACDC, CongreveLamsdell2016, DAISIE, ENMTools, FinePop, GLSME, HSAUR, HSAUR2, HSAUR3, MVA, OptCirClust, Platypus, RVAideMemoire, Seurat, TextMiningGUI, TiPS, TotalCopheneticIndex, ade4, adespatial, aphid, aqp, asnipe, babette, brms, data.tree, dcGOR, dendextend, ecolottery, enveomics.R, fido, gamclass, ggimage, hagis, harmonicmeanp, hierfstat, igraph, kmer, lingtypology, mdendro, metadat, metafor, metagear, multicross, netdiffuseR, nosoi, occCite, ouch, outbreaks, outsider, pagoo, paleobuddy, phylocomr, phylotate, plotbb, polysat, rbiom, rdiversity, rehh, rncl, safedata, sand, scrm, shipunov, spiralize, spots, symmoments, taxlist, tidygraph, tidysq, tracerer, vhica, warbleR.

Enhanced by clue.


See at CRAN