r-cran-phytools 0.6-44-1 / usr / lib / R / site-library / phytools / NAMESPACE

export(add.arrow, add.color.bar, add.everywhere, add.random, add.simmap.legend, add.species.to.genus, aic.w, allFurcTrees)
export(allRotations, anc.Bayes, anc.ML, anc.trend, ancThresh, applyBranchLengths, arc.cladelabels, as.multiPhylo, ave.rates, averageTree)
export(backbone.toPhylo, bd, bmPlot, bind.tip, bind.tree.simmap, biplot.phyl.pca, branching.diffusion, brownie.lite, brownieREML)
export(cladelabels, coef.phyl.RMA, collapse.to.star, collapseTree, compare.chronograms, consensus.edges, contMap, cophylo, countSimmap)
export(compute.mr, cospeciation)
export(density.multiSimmap, densityMap, densityTree, describe.simmap, di2multi.simmap, dot.legend, dotTree, drop.clade, drop.leaves)
export(drop.tip.contMap, drop.tip.densityMap, drop.tip.simmap, drop.tip.singleton)
export(edgelabels.cophylo, edgeProbs, errorbar.contMap, estDiversity, evol.rate.mcmc, evol.vcv, evolvcv.lite, exhaustiveMP)
export(expand.clade, expm, export.as.xml, extract.clade.simmap, extract.strahlerNumber)
export(fancyTree, fastAnc, fastBM, fastDist, fastHeight, fastMRCA, findMRCA, fit.bd, fit.yule, fitBayes, fitMk, fitDiversityModel, fitPagel)
export(force.ultrametric)
export(gammatest, genus.to.species.tree, genSeq, geo.legend, get.treepos, getCladesofSize, getDescendants, getExtant, getExtinct, getnode)
export(getParent, getSisters, getStates)
export(labelnodes, ladderize.simmap, lambda.transform, lik.bd, likMlambda, likSurface.rateshift, linklabels, locate.fossil, locate.yeti)
export(ls.consensus, ls.tree, ltt, ltt95)
export(make.era.map, make.simmap, make.transparent, map.overlap, Map.Overlap, map.to.singleton, mapped.states, markChanges)
export(matchLabels, matchNodes, mergeMappedStates, midpoint.root, minRotate, minSplit, minTreeDist, modified.Grafen)
export(mrp.supertree, multi.mantel, multiC, multiOU, multiRF)
export(nodeheight, nodeHeights, nodelabels.cophylo, node.paths)
export(optim.phylo.ls, orderMappedEdge)
export(paintBranches, paintSubTree, paste.tree, pbtree, pgls.Ives, pgls.SEy, phenogram, phyl.cca, phyl.pairedttest, phyl.pca, phyl.resid, phyl.RMA)
export(phyl.vcv, phylo.heatmap, phylo.toBackbone, phylo.to.map, phylANOVA, phyloDesign, phylomorphospace, phylomorphospace3d, phylosig)
export(plot.changesMap, plot.contMap, plot.cophylo, plot.densityMap, plot.fitMk, plot.fitPagel, plot.phyl.RMA, plot.phylo.to.map, plot.gfit)
export(plotBranchbyTrait, plotSimmap, plotThresh, plotTree, plotTree.barplot, plotTree.boxplot, plotTree.errorbars, plotTree.singletons)
export(plotTree.splits, plotTree.wBars, posterior.evolrate, posthoc, posthoc.ratebytree)
export(ratebystate, ratebytree, rateshift, read.newick, read.simmap, reorder.backbonePhylo, reorderSimmap, rep.multiPhylo, rep.phylo)
export(repPhylo, reroot, rerootingMethod, rescaleSimmap, resolveAllNodes, resolveNode, rotate.multi, rotateNodes, rootedge.to.singleton)
export(roundBranches, roundPhylogram, rstate)
export(sampleFrom, setMap, sim.corrs, sim.history, sim.ratebystate, sim.rates, skewers, splitEdgeColor, splitplotTree)
export(splitTree, starTree, strahlerNumber)
export(threshBayes, threshDIC, threshState, tiplabels.cophylo, tipRotate, to.matrix, treeSlice)
export(untangle)
export(vcvPhylo)
export(write.simmap, writeAncestors, writeNexus)

S3method(plot, densityMap)
S3method(plot, contMap)
S3method(plot, phylo.to.map)
S3method(plot, backbonePhylo)
S3method(reorder, backbonePhylo)
S3method(print, backbonePhylo)
S3method(print, phyl.pca)
S3method(summary, phyl.pca)
S3method(biplot, phyl.pca)
S3method(print, brownie.lite)
S3method(print, densityMap)
S3method(print, contMap)
S3method(print, rateshift)
S3method(logLik, rateshift)
S3method(print, evol.vcv)
S3method(plot, ltt95)
S3method(print, ltt95)
S3method(plot, describe.simmap)
S3method(print, describe.simmap)
S3method(rep, phylo)
S3method(rep, multiPhylo)
S3method(print, fitPagel)
S3method(print, ltt)
S3method(print, multiLtt)
S3method(plot, ltt)
S3method(plot, multiLtt)
S3method(plot, cophylo)
S3method(print, cophylo)
S3method(plot, simmap)
S3method(print, simmap)
S3method(summary, simmap)
S3method(plot, multiSimmap)
S3method(print, multiSimmap)
S3method(summary, multiSimmap)
S3method(reorder, simmap)
S3method(plot, rateshift)
S3method(print, fastAnc)
S3method(print, anc.ML)
S3method(print, fitMk)
S3method(summary, fitMk)
S3method(logLik, fitMk)
S3method(print, brownieREML)
S3method(AIC, fitMk)
S3method(print, phylo.to.map)
S3method(as.phylo, simmap)
S3method(as.multiPhylo, multiSimmap)
S3method(as.multiPhylo, phylo)
S3method(plot, fitPagel)
S3method(plot, fitMk)
S3method(plot, gfit)
S3method(plot, phyl.pca)
S3method(summary, cophylo)
S3method(print, multiCophylo)
S3method(plot, multiCophylo)
S3method(logLik, simmap)
S3method(logLik, multiSimmap)
S3method(plot, cospeciation)
S3method(print, cospeciation)
S3method(density, multiSimmap)
S3method(plot, changesMap)
S3method(print, changesMap)
S3method(plot, phyloScattergram)
S3method(print, phyloScattergram)
S3method(di2multi, simmap)
S3method(print, aic.w)
S3method(print, phyl.RMA)
S3method(coef, phyl.RMA)
S3method(residuals, phyl.RMA)
S3method(plot, phyl.RMA)
S3method(print, ratebytree)
S3method(print, evolvcv.lite)
S3method(print, expand.clade)
S3method(plot, expand.clade)
S3method(posthoc, ratebytree)
S3method(print, posthoc.ratebytree)
S3method(AIC, ratebytree)
S3method(print, fit.bd)
S3method(logLik, fit.bd)
S3method(print, anc.trend)
S3method(logLik, anc.trend)
S3method(print, ancThresh)
S3method(plot, ancThresh)
S3method(print, evol.rate.mcmc)
S3method(print, threshBayes)
S3method(plot, threshBayes)
S3method(print, rerootingMethod)
S3method(plot, rerootingMethod)
S3method(logLik, rerootingMethod)
S3method(print, fitBayes)
S3method(plot, fitBayes)
S3method(print, ratebystate)
S3method(print, phylANOVA)
S3method(print, pgls.Ives)
S3method(logLik, pgls.Ives)
S3method(print, phyl.cca)
S3method(print, anc.Bayes)
S3method(plot, anc.Bayes)

importFrom(animation, ani.options, ani.record, ani.replay, saveVideo)
importFrom(ape, .PlotPhyloEnv, .uncompressTipLabel, ace, all.equal.phylo, as.DNAbin, as.phylo, bind.tree, branching.times, collapse.singles)
importFrom(ape, consensus, compute.brlen, cophenetic.phylo, corBrownian, di2multi, dist.dna, dist.nodes, drop.tip, edgelabels, extract.clade)
importFrom(ape, getMRCA, is.binary.tree)
importFrom(ape, is.monophyletic, is.rooted, is.ultrametric, ladderize, matexpo, mrca, multi2di, neworder_phylo, neworder_pruningwise)
importFrom(ape, nodelabels, Ntip, pic, plot.phylo, prop.part, read.tree, reorder.phylo, root, rotate, rtree, stree, tiplabels)
importFrom(ape, unroot, vcv, vcv.phylo, write.tree)
importFrom(clusterGeneration, genPositiveDefMat)
importFrom(maps, map)
importFrom(mnormt, dmnorm, pd.solve)
importFrom(msm, MatrixExp)
importFrom(numDeriv, hessian)
importFrom(phangorn, allTrees, Ancestors, as.phyDat, dist.hamming, midpoint, NJ, nni, nnls.tree, optim.parsimony, parsimony, phyDat, pratchet, treedist, RF.dist, KF.dist, path.dist, SPR.dist, Children, Descendants, threshStateC)
importFrom(plotrix, arctext, draw.arc, draw.circle, draw.ellipse, textbox)
importFrom(scatterplot3d, scatterplot3d)
importFrom(stats, cophenetic, reorder, runif, setNames, optim, dexp, dnorm, rnorm, var, nlminb, biplot, pchisq, rexp, optimize, logLik, as.dist, pnorm, median, cor, aggregate, rgamma, dgamma, lm, rbinom, rgeom, pt, anova, p.adjust, screeplot, rchisq, optimHess, rmultinom, sd, dunif, dist, plogis, density, coef, cmdscale)
importFrom(methods, hasArg)
importFrom(graphics, strwidth, par, segments, locator, lines, text, strheight, symbols, plot, layout, plot.new, title, axis, points, plot.window, polygon, rect, curve, image, mtext, arrows, barplot, boxplot, contour, hist, abline, legend, grid)
importFrom(utils, flush.console, installed.packages, str, capture.output)
importFrom(grDevices, palette, colors, dev.hold, dev.flush, rainbow, heat.colors, gray, colorRampPalette, dev.new, rgb,
pdf, dev.off, col2rgb)
importFrom(combinat, permn)
importFrom(coda, HPDinterval)
importFrom(nlme, gls, varFixed)
importFrom(MASS, ginv)