importFrom(grDevices, colorRampPalette, dev.new, rgb, pdf, dev.off, col2rgb, dev.size)
importFrom(stats, density, coef, cmdscale, AIC)
importFrom(utils, flush.console, head, installed.packages, str, capture.output, combn)

export(ratebystate, ratebytree, rateshift, read.newick, read.simmap, readNexus)
export(reorder.backbonePhylo, reorderSimmap, rep.multiPhylo, rep.phylo, repPhylo, reroot)
export(rerootingMethod, rescaleSimmap, resolveAllNodes, resolveNode, rootedge.to.singleton)
export(rotate.multi, rotateNodes, roundBranches, roundPhylogram, rstate)
importFrom(ape, multi2di, nodelabels, Ntip, pic, plot.phylo, prop.part, read.nexus, read.tree)
importFrom(grDevices, colorRamp, colorRampPalette, dev.new, rgb, pdf, dev.off, col2rgb, dev.size)

export(consensus.edges, contMap, cophylo, countSimmap, compute.mr, cotangleplot, cospeciation)

export(as.princomp, as.princomp.phyl.pca, as.Qmatrix, ave.rates, averageTree)

export(fit.yule, fitBayes, fitHRM, fitMk, fitMk.parallel, fitmultiMk, fitpolyMk, fitDiversityModel)
export(ls.consensus, ls.tree, ltt, ltt95, ltt.multiPhylo, ltt.multiSimmap, ltt.phylo, ltt.simmap)
export(sampleFrom, scores, scores.phyl.pca, setMap, sigmoidPhylogram, sim.corrs, sim.ctt)
export(sim.history, sim.Mk, sim.multiCtt, sim.multiMk, sim.ratebystate, sim.rates)
export(simBMphylo, skewers, splitEdgeColor, splitplotTree, splitTree, starTree)

importFrom(stats, coef, coefficients, fitted, fitted.values, vcov, logLik)
#import(  limma, OCplus)  #convest and tMixture respectively

## added using K. Hornik's code since 3.3.0
importFrom("graphics", "abline", "axis", "box", "curve", "hist", "lines", "mtext", "par", "persp", "points", "rug", "title")
importFrom("grDevices", "nclass.FD", "nclass.Sturges", "nclass.scott", "trans3d", "dev.new")
importFrom("stats", "aggregate", "approx", "approxfun", "dchisq", "df", "dnorm", "dt", "integrate", "make.link", "nlminb", "optim", "optimize", "pnorm", "pt", "qchisq", "qnorm", "qt", "quantile", "rnorm", "sd", "start", "var", "constrOptim", "nobs")