/usr/lib/R/site-library/ape/NAMESPACE is in r-cran-ape 3.1-4-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 | useDynLib(ape, .registration = TRUE)
exportPattern("^[^\\.]")
export(.compressTipLabel, .uncompressTipLabel, .PlotPhyloEnv)
importFrom(graphics, arrows, identify, image.default, lines, plot,
plot.default, segments)
importFrom(lattice, xyplot, panel.lines, panel.points)
importFrom(nlme, corMatrix, Dim, getCovariate, getGroups,
getGroupsFormula, gls, Initialize)
importFrom(stats, as.hclust, biplot, coef, cophenetic, drop1, hclust,
mahalanobis, reorder)
importFrom(utils, setTxtProgressBar, txtProgressBar)
## Methods for the classes defined in ape, including for the generics
## defined in ape (see also below). Some methods are exported above.
S3method(AIC, ace)
S3method(anova, ace)
S3method(deviance, ace)
S3method(logLik, ace)
S3method(print, ace)
S3method(as.prop.part, bitsplits)
S3method(is.compatible, bitsplits)
S3method(print, bitsplits)
S3method(drop1, compar.gee)
S3method(predict, compar.gee)
S3method(print, compar.gee)
S3method("[", DNAbin)
S3method(as.character, DNAbin)
S3method(as.list, DNAbin)
S3method(as.matrix, DNAbin)
S3method(c, DNAbin)
S3method(cbind, DNAbin)
S3method(image, DNAbin)
S3method(labels, DNAbin)
S3method(makeLabel, DNAbin)
S3method(print, DNAbin)
S3method(rbind, DNAbin)
S3method(as.phylo, evonet)
S3method(plot, evonet)
S3method(print, evonet)
S3method("[", multiPhylo)
S3method("[<-", multiPhylo)
S3method("[[", multiPhylo)
S3method("[[<-", multiPhylo)
S3method("$", multiPhylo)
S3method("$<-", multiPhylo)
S3method(c, multiPhylo)
S3method(makeLabel, multiPhylo)
S3method(plot, multiPhylo)
S3method(print, multiPhylo)
S3method(str, multiPhylo)
S3method(unique, multiPhylo)
S3method("+", phylo)
S3method(all.equal, phylo)
S3method(as.hclust, phylo)
S3method(as.matching, phylo)
S3method(coalescent.intervals, phylo)
S3method(c, phylo)
S3method(cophenetic, phylo)
S3method(identify, phylo)
S3method(makeLabel, phylo)
S3method(plot, phylo)
S3method(print, phylo)
S3method(reorder, phylo)
S3method(skyline, phylo)
S3method(summary, phylo)
S3method(vcv, phylo)
S3method(plot, phymltest)
S3method(print, phymltest)
S3method(summary, phymltest)
S3method(lines, popsize)
S3method(plot, popsize)
S3method(as.bitsplits, prop.part)
S3method(plot, prop.part)
S3method(print, prop.part)
S3method(summary, prop.part)
S3method(lines, skyline)
S3method(plot, skyline)
## Methods for PGLS:
## methods of coef() from stats:
S3method(coef, corBlomberg)
S3method(coef, corBrownian)
S3method(coef, corGrafen)
S3method(coef, corMartins)
S3method(coef, corPagel)
## methods to work with nlme:
S3method(corMatrix, corBlomberg)
S3method(corMatrix, corBrownian)
S3method(corMatrix, corGrafen)
S3method(corMatrix, corMartins)
S3method(corMatrix, corPagel)
S3method(Initialize, corPhyl)
## Miscellaneous classes for which there is only one method:
S3method(biplot, pcoa)
S3method(plot, correlogram)
S3method(plot, correlogramList)
S3method(plot, mst)
S3method(plot, varcomp)
S3method(print, birthdeath)
S3method(print, bitsplits)
S3method(print, chronos)
S3method(print, lmorigin)
S3method(print, parafit)
## Other methods of the generics defined in ape:
S3method(as.DNAbin, alignment)
S3method(as.DNAbin, character)
S3method(as.DNAbin, list)
S3method(as.phylo, formula)
S3method(as.phylo, hclust)
S3method(as.phylo, matching)
S3method(as.phylo, phylog)
S3method(coalescent.intervals, default)
S3method(makeLabel, character)
S3method(skyline, coalescentIntervals)
S3method(skyline, collapsedIntervals)
S3method(vcv, corPhyl)
|