export(cladelabels, collapse.to.star, collapseTree, contMap, cophylo, countSimmap, compute.mr)
export(edgelabels.cophylo, edgeProbs, estDiversity, evol.rate.mcmc, evol.vcv, evolvcv.lite, exhaustiveMP, expm, export.as.xml)
export(fancyTree, fastAnc, fastBM, fastDist, fastHeight, fastMRCA, findMRCA, fitBayes, fitMk, fitDiversityModel, fitPagel)
export(gammatest, genus.to.species.tree, genSeq, getCladesofSize, getDescendants, getExtant, getExtinct, getSisters, getStates)
export(threshBayes, threshDIC, threshState, tiplabels.cophylo, tipRotate, to.matrix, treeSlice)
importFrom(ape, consensus, compute.brlen, cophenetic.phylo, di2multi, dist.dna, dist.nodes, drop.tip, edgelabels, extract.clade)
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)

export(densityMap, densityTree, describe.simmap, di2multi.simmap, dot.legend, dotTree, drop.clade, drop.leaves)
export(phyl.vcv, phylo.heatmap, phylo.toBackbone,phylo.to.map, phylANOVA, phyloDesign, phylomorphospace, phylomorphospace3d, phylosig)
export(reroot, rerootingMethod, rescaleSimmap, rotateNodes, rootedge.to.singleton, roundBranches, roundPhylogram, rstate)
importFrom(graphics, strwidth, par, segments, locator, lines, text, strheight, symbols, plot, layout, plot.new, title, axis, points, plot.window, polygon, rect, curve, image)

export(anc.ML, anc.trend, ancThresh, applyBranchLengths, as.multiPhylo, ave.rates, averageTree)
export(backbone.toPhylo, bmPlot, bind.tip, bind.tree.simmap, biplot.phyl.pca, branching.diffusion, brownie.lite, brownieREML)
export(cladelabels, collapse.to.star, collapseTree, consensus.edges, contMap, cophylo, countSimmap, compute.mr)
export(ladderize.simmap, lambda.transform, likMlambda, locate.fossil, locate.yeti, 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, mrp.supertree, multi.mantel)
export(plotBranchbyTrait, plot.contMap, plot.cophylo, plot.densityMap, plot.fitMk, plot.fitPagel, plot.phylo.to.map, plot.gfit)
export(plotSimmap, plotThresh, plotTree, plotTree.singletons, plotTree.splits, plotTree.wBars, posterior.evolrate)
importFrom(ape, .PlotPhyloEnv, .uncompressTipLabel, ace, all.equal.phylo, as.DNAbin, as.phylo, bind.tree, branching.times, collapse.singles)
importFrom(phangorn, allTrees, Ancestors, as.phyDat, dist.hamming, midpoint, NJ, nni, optim.parsimony, parsimony, phyDat, pratchet, nnls.tree, treedist, RF.dist, KF.dist, path.dist)
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)