/usr/lib/R/site-library/phangorn/NAMESPACE is in r-cran-phangorn 1.99.14-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 | 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)
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