export(add.color.bar, add.everywhere, add.random, add.simmap.legend, allFurcTrees, anc.Bayes, anc.ML, anc.trend, ancThresh)
export(applyBranchLengths, ave.rates)
export(backbone.toPhylo, bmPlot, bind.tip, branching.diffusion,brownie.lite, brownieREML)
export(collapse.to.star, contMap, countSimmap)
export(densityMap, describe.simmap, drop.clade, drop.leaves, drop.tip.simmap)
export(estDiversity, evol.rate.mcmc, evol.vcv, evolvcv.lite, exhaustiveMP, expm, export.as.xml, extract.clade.simmap)
export(extract.strahlerNumber)
export(fancyTree, fastAnc, fastBM, fastMRCA, findMRCA, fitBayes, fitDiversityModel)
export(gammatest, genSeq, getCladesofSize, getDescendants, getExtant, getExtinct, getSisters, getStates)
export(lambda.transform, likMlambda, ls.tree, ltt, ltt95)
export(make.era.map, make.simmap, map.overlap, map.to.singleton, matchNodes, mergeMappedStates, minRotate, minSplit, mrp.supertree)
export(multi.mantel, multiC, multiRF)
export(nodeHeights)
export(optim.phylo.ls, orderMappedEdge)
export(paintSubTree, paste.tree, pbtree, pgls.Ives,phenogram, phyl.cca, phyl.pairedttest, phyl.pca, phyl.resid, phyl.RMA, phyl.vcv)
export(phylo.toBackbone,phylo.to.map, phylANOVA, phyloDesign, phylomorphospace, phylomorphospace3d, phylosig, plotBranchbyTrait)
export(plot.contMap, plot.densityMap, plot.phylo.to.map, plotSimmap, plotThresh, plotTree, plotTree.singletons, posterior.evolrate)
export(ratebystate, read.newick, read.simmap, reorder.backbonePhylo, reorderSimmap, repPhylo, reroot, rerootingMethod)
export(rescaleSimmap, rotateNodes, roundBranches, rstate)
export(sampleFrom, sim.corrs, sim.history, sim.ratebystate, sim.rates, splitplotTree, splitTree, starTree, strahlerNumber)
export(threshBayes, threshDIC, threshState, to.matrix, treeSlice)
export(untangle)
export(vcvPhylo)
export(write.simmap, writeAncestors, writeNexus)
export(xkcdTree)

S3method(plot, densityMap)
S3method(plot, contMap)
S3method(plot, phylo.to.map)
S3method(plot, backbonePhylo)
S3method(reorder, backbonePhylo)
S3method(print, backbonePhylo)

importFrom(animation, ani.options, ani.record, ani.replay, saveVideo)
importFrom(ape, .PlotPhyloEnv, .uncompressTipLabel, ace, all.equal.phylo, as.DNAbin, bind.tree, branching.times, collapse.singles)
importFrom(ape, compute.brlen, cophenetic.phylo, di2multi, dist.dna, dist.nodes, drop.tip, extract.clade, is.binary.tree, is.rooted)
importFrom(ape, is.ultrametric, matexpo, mrca, multi2di, neworder_phylo, neworder_pruningwise, nodelabels, pic, plot.phylo, prop.part)
importFrom(ape, read.tree, reorder.phylo, root, rotate, rtree, stree, tiplabels, unroot, vcv, vcv.phylo, write.tree)
#importFrom(extrafont, embed_fonts, font_import, fonts, loadfonts)
importFrom(maps, map)
importFrom(mnormt, dmnorm)
importFrom(msm, MatrixExp)
importFrom(numDeriv, hessian)
importFrom(phangorn, allTrees, Ancestors, as.phyDat, dist.hamming, NJ, nni, optim.parsimony, parsimony, phyDat, pratchet)
importFrom(plotrix, draw.arc)
importFrom(rgl, lines3d, play3d, plot3d, r3dDefaults, segments3d, spheres3d, spin3d, text3d)
importFrom(scatterplot3d, scatterplot3d)
importFrom(stats, cophenetic, reorder)


