/usr/lib/R/site-library/phangorn/NAMESPACE is in r-cran-phangorn 2.4.0-1.
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 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | 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, as.alignment, di2multi, multi2di, .uncompressTipLabel,
.compressTipLabel, prop.part, Ntip, getMRCA, postprocess.prop.part,
speciesTree, plotPhyloCoor, cladogram.plot, phylogram.plot, has.singles,
node.depth.edgelength, drop.tip, stree, rtree, rcoal, rmtree,
is.ultrametric, .PlotPhyloEnv, nodelabels, edgelabels, BOTHlabels,
read.nexus.data, write.nexus.data, read.dna, write.dna, reorder.phylo,
dist.nodes, collapse.singles, rotate, prop.clades, fastme.bal, fastme.ols,
Nnode, image.DNAbin, ONEwise, as.AAbin, as.phyDat.AAbin, image.AAbin,
as.bitsplits, as.bitsplits.prop.part, arecompatible, is.compatible,
is.compatible.bitsplits, reorderRcpp)
importFrom(igraph, graph, graph_from_adjacency_matrix, layout_with_kk,
plot.igraph, shortest_paths, set.edge.attribute, set_edge_attr, decompose,
components, groups, vcount, graph.edgelist, graph_from_edgelist, topo_sort,
layout_nicely)
#layout.kamada.kawai, graph.adjacency, get.shortest.paths, topological.sort,
import(methods, Rcpp)
#importFrom(Rcpp,sourceCpp)
importFrom(magrittr,"%>%", "%<>%")
importFrom(Matrix, Matrix, sparseMatrix, spMatrix, crossprod, solve) #, %*%
importFrom(fastmatch, fmatch, "%fin%")
#importFrom(nnls, nnls)
#importFrom(parallel, mclapply, detectCores)
import(parallel)
importFrom(quadprog, solve.QP, solve.QP.compact)
#importFrom(rgl, open3d, segments3d, spheres3d, rgl.texts)
importFrom(stats, AIC, BIC, logLik, reorder, update, optim, optimize,
constrOptim, na.omit, cophenetic, hclust, as.dist, pchisq, reshape, qgamma,
pgamma, model.matrix, aggregate, lm.fit, xtabs, quantile, sd, runif)
importFrom(graphics, plot, plot.default, plot.new, plot.window, text, par,
abline, strwidth, axis, title, segments, points, image, matplot, legend,
hist, identify, locator)
importFrom(utils, read.table, download.file, stack,
installed.packages, write.table, combn, packageDescription)
importFrom(grDevices, rgb, rainbow, adjustcolor, col2rgb)
#importFrom(methods, hasArg, is)
#importFrom(Rcpp, evalCpp)
#importMethodsFrom(Biostrings,as.matrix)
#importFrom(Biostrings,DNAMultipleAlignment)
#importFrom(Biostrings,RNAMultipleAlignment)
#importFrom(Biostrings,AAMultipleAlignment)
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, allCircularSplits, fhm, distanceHadamard,
treedist, sankoff, fitch, h2st, h4st, dist.logDet, dist.hamming,
dist.ml, dist.p, unique.dist, upgma, wpgma, write.nexus.splits,
read.nexus.splits, read.nexus.networx, write.nexus.networx, write.splits,
write.nexus.dist, pmlPart, pmlCluster, pmlMix, pmlPen, read.aa, allTrees,
designTree, designSplits, nnls.tree, nnls.splits, nnls.phylo, nnls.networx,
neighborNet, pmlPart2multiPhylo, multiphyDat2pmlPart, splitsNetwork, simSeq,
SH.test, bootstrap.pml, bootstrap.phyDat, RF.dist, wRF.dist, KF.dist,
path.dist, sprdist, SPR.dist, mast, rNNI, rSPR, plotBS, Ancestors,
Descendants, allDescendants, 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, createLabel, SOWH.test,
presenceAbsence, as.networx.splits, addTrivialSplits, removeTrivialSplits,
phyDat2alignment, AICc, readDist, writeDist, discrete.gamma, matchSplits,
distinct.splits, c.splits, dna2codon, codon2dna, genlight2phyDat,
removeUndeterminedSites, phyDat2MultipleAlignment, delta.score,
maxCladeCred, as.MultipleAlignment, threshStateC, coords, add.tips,
map_duplicates)
# plot.networx, countCycles,
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(BIC, pml)
S3method(c, phyDat)
S3method(c, splits)
S3method(cbind, phyDat)
S3method(unique, phyDat)
S3method(unique, dist)
S3method(as.bitsplits, splits)
S3method(as.matrix, splits)
S3method(as.Matrix, splits)
S3method(as.networx, splits)
S3method(unique, splits)
S3method(as.networx, phylo)
#S3method(as.igraph, networx)
S3method(as.phyDat, DNAbin)
S3method(as.phyDat, alignment)
S3method(as.phyDat, character)
S3method(as.phyDat, data.frame)
S3method(as.phyDat, factor)
S3method(as.phyDat, matrix)
S3method(as.phyDat, MultipleAlignment)
S3method(as.MultipleAlignment, phyDat)
S3method(as.AAbin, phyDat)
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(identify, networx)
S3method(image, phyDat)
S3method(logLik, pml)
S3method(logLik, pmlPart)
S3method(logLik, pmlMix)
S3method(midpoint, phylo)
S3method(midpoint, multiPhylo)
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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