File: NAMESPACE

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r-cran-phangorn 1.99.14-1~bpo8+1
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useDynLib(phangorn, .registration=TRUE)

importFrom(ape, as.DNAbin, as.phylo, plot.phylo, as.prop.part, nj,old2new.phylo, dist.dna,
    new2old.phylo, cophenetic.phylo, is.rooted, unroot, root, is.binary.tree, as.alignment,
    di2multi, multi2di, .uncompressTipLabel, .compressTipLabel, prop.part, 
    postprocess.prop.part, speciesTree, plotPhyloCoor, cladogram.plot, phylogram.plot,
    node.depth.edgelength, drop.tip, stree, rtree, is.ultrametric, .PlotPhyloEnv,
    nodelabels, edgelabels, BOTHlabels, read.nexus.data, write.nexus.data, 
    read.dna, write.dna, reorder.phylo, dist.nodes, collapse.singles, rotate)
importFrom(igraph, graph, graph.adjacency, layout.kamada.kawai, plot.igraph,
    get.shortest.paths, set.edge.attribute, vcount, graph.edgelist, topological.sort) 
importFrom(Matrix, Matrix, sparseMatrix, spMatrix, crossprod, solve) #, %*%
#importFrom(fastmatch, fmatch)
importFrom(nnls, nnls)
importFrom(parallel, mclapply)
importFrom(quadprog, solve.QP, solve.QP.compact)
#importFrom(rgl, open3d, segments3d, spheres3d, rgl.texts)
#importFrom(Rcpp, evalCpp)
importFrom(stats, AIC, logLik, reorder, update, optim, optimize, constrOptim, na.omit, 
           cophenetic, hclust, as.dist, pchisq, reshape, qgamma, pgamma, model.matrix,
           aggregate, lm.fit, xtabs, quantile) 
importFrom(graphics, plot.new, plot.window, text, par, plot, abline, strwidth, axis, title, segments, 
           points, image, matplot, legend, hist) 
importFrom(utils, read.table, download.file, citation, stack, installed.packages, write.table) 
importFrom(grDevices, rgb, rainbow, adjustcolor)
importFrom(methods, hasArg)

export(pml, optim.pml, pml.control, parsimony, optim.parsimony, pratchet, NJ, UNJ, PNJ, 
    phyDat, cbind.phyDat, read.phyDat, write.phyDat, as.Matrix, as.phyDat, as.splits, as.networx,
    dfactorial, ldfactorial, hadamard, nni, allSitePattern, allSplits, fhm, 
    distanceHadamard, treedist, sankoff, fitch, h2st, h4st, dist.logDet, dist.hamming, 
    dist.ml, dist.p, upgma, wpgma, write.nexus.splits, read.nexus.splits, write.splits, pmlPart, 
    pmlCluster, pmlMix, pmlPen, read.aa, allTrees, designTree, designSplits, nnls.tree,
    nnls.splits, nnls.phylo, nnls.networx, neighborNet, pmlPart2multiPhylo,
    splitsNetwork, simSeq, SH.test, bootstrap.pml, bootstrap.phyDat, RF.dist, rNNI, 
    rSPR, plotBS, Ancestors, Descendants, mrca.phylo, Children, Siblings, pace, modelTest, 
    lento, compatible, acgt2ry, ancestral.pars, ancestral.pml, CI, RI, getClans, getSlices,
    getClips, getDiversity, midpoint, pruneTree, acctran, getRoot, plotAnc, consensusNet, 
    bab, random.addition, diversity, baseFreq, densiTree, superTree, coalSpeciesTree, 
    pml.fit, pml.init, pml.free, edQt, lli, cladePar, addConfidences, countCycles, 
    SOWH.test, plot.networx, presenceAbsence, as.networx.splits, addTrivialSplits,
    phyDat2alignment, AICc, readDist, writeDist, discrete.gamma)

S3method('[', splits)          
S3method(addConfidences, phylo)
S3method(addConfidences, splits)
S3method(addConfidences, networx)
S3method(AICc, pml)
S3method(as.character, phyDat)
S3method(as.data.frame, phyDat)
S3method(anova, pml)
S3method(c, phyDat)
S3method(c, splits)
S3method(cbind, phyDat)
S3method(unique, phyDat) 
S3method(as.matrix, splits)
S3method(as.Matrix, splits) 
S3method(as.networx, splits)
#S3method(as.igraph, networx)
S3method(as.phyDat, DNAbin)
S3method(as.phyDat, alignment)
S3method(as.phyDat, data.frame)
S3method(as.phyDat, matrix)
S3method(as.DNAbin, phyDat)
S3method(as.phylo, splits)
S3method(as.splits, phylo)
S3method(as.splits, multiPhylo)
S3method(as.splits, prop.part)
S3method(as.splits, networx)
S3method(as.prop.part, splits)
S3method(cophenetic, networx)
S3method(cophenetic, splits)
S3method(logLik, pml)
S3method(logLik, pmlPart)
S3method(logLik, pmlMix)
S3method(plot, pml)
S3method(plot, pmlPart)
S3method(plot, networx)
S3method(plot, pmlCluster)
S3method(print, phyDat)
S3method(print, pml)
S3method(print, pmlMix)
S3method(print, pmlPart)
S3method(print, splits)
S3method(print, summary.clanistics)
S3method(print, SOWH)
S3method(reorder, networx)
#S3method(reorder, splits)
S3method(simSeq, phylo)
S3method(simSeq, pml)
S3method(subset, phyDat)
S3method(summary, clanistics)
S3method(summary, SOWH)
S3method(update, pml)
S3method(vcov, pml)