/usr/lib/R/site-library/phytools/help/AnIndex is in r-cran-phytools 0.6-44-1.
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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 | phytools-package phytools-package
add.arrow add.arrow
add.color.bar add.color.bar
add.everywhere add.everywhere
add.random add.random
add.simmap.legend add.simmap.legend
add.species.to.genus add.species.to.genus
aic.w aic.w
allFurcTrees allFurcTrees
allRotations rotateNodes
anc.Bayes anc.Bayes
anc.ML anc.ML
anc.trend anc.trend
ancThresh ancThresh
anoletree anoletree
applyBranchLengths applyBranchLengths
arc.cladelabels cladelabels
as.multiPhylo as.multiPhylo
as.multiPhylo.multiSimmap as.multiPhylo
as.multiPhylo.phylo as.multiPhylo
ave.rates ave.rates
averageTree averageTree
backbone.toPhylo phylo.toBackbone
bd bd
bind.tip bind.tip
bind.tree.simmap bind.tree.simmap
biplot.phyl.pca phyl.pca
bmPlot bmPlot
branching.diffusion branching.diffusion
brownie.lite brownie.lite
brownieREML brownieREML
cladelabels cladelabels
coef.phyl.RMA phyl.RMA
collapse.to.star collapse.to.star
collapseTree collapseTree
compare.chronograms compare.chronograms
compute.mr mrp.supertree
consensus.edges consensus.edges
contMap contMap
cophylo cophylo
cospeciation cospeciation
countSimmap countSimmap
density.multiSimmap density.multiSimmap
densityMap densityMap
densityTree densityTree
describe.simmap describe.simmap
di2multi.simmap di2multi.simmap
dot.legend dotTree
dotTree dotTree
drop.clade drop.clade
drop.leaves drop.leaves
drop.tip.contMap drop.tip.contMap
drop.tip.densityMap drop.tip.contMap
drop.tip.simmap drop.tip.simmap
drop.tip.singleton map.to.singleton
edgelabels.cophylo nodelabels.cophylo
edgeProbs edgeProbs
errorbar.contMap contMap
estDiversity estDiversity
evol.rate.mcmc evol.rate.mcmc
evol.vcv evol.vcv
evolvcv.lite evolvcv.lite
exhaustiveMP exhaustiveMP
expand.clade expand.clade
expm expm
export.as.xml export.as.xml
extract.clade.simmap drop.tip.simmap
extract.strahlerNumber strahlerNumber
fancyTree fancyTree
fastAnc fastAnc
fastBM fastBM
fastDist fastMRCA
fastHeight fastMRCA
fastMRCA fastMRCA
findMRCA findMRCA
fit.bd fit.bd
fit.yule fit.bd
fitBayes fitBayes
fitDiversityModel fitDiversityModel
fitMk fitMk
fitPagel fitPagel
force.ultrametric force.ultrametric
gammatest gammatest
genSeq genSeq
genus.to.species.tree add.species.to.genus
geo.legend geo.legend
get.treepos get.treepos
getCladesofSize getCladesofSize
getDescendants getDescendants
getExtant getExtant
getExtinct getExtant
getnode get.treepos
getParent getDescendants
getSisters getSisters
getStates getStates
labelnodes labelnodes
ladderize.simmap ladderize.simmap
lambda.transform lambda.transform
lik.bd fit.bd
likMlambda likMlambda
likSurface.rateshift rateshift
linklabels linklabels
locate.fossil locate.fossil
locate.yeti locate.yeti
ls.consensus averageTree
ls.tree ls.tree
ltt ltt
ltt95 ltt95
make.era.map make.era.map
make.simmap make.simmap
make.transparent densityTree
Map.Overlap map.overlap
map.overlap map.overlap
map.to.singleton map.to.singleton
mapped.states mapped.states
markChanges markChanges
matchLabels matchNodes
matchNodes matchNodes
mergeMappedStates mergeMappedStates
midpoint.root midpoint.root
minRotate minRotate
minSplit minSplit
minTreeDist averageTree
modified.Grafen modified.Grafen
mrp.supertree mrp.supertree
multi.mantel multi.mantel
multiC multiC
multiOU sim.rates
multiRF multiRF
node.paths modified.Grafen
nodeheight nodeHeights
nodeHeights nodeHeights
nodelabels.cophylo nodelabels.cophylo
optim.phylo.ls optim.phylo.ls
orderMappedEdge orderMappedEdge
paintBranches paintSubTree
paintSubTree paintSubTree
paste.tree paste.tree
pbtree pbtree
pgls.Ives pgls.Ives
pgls.SEy pgls.Ives
phenogram phenogram
phyl.cca phyl.cca
phyl.pairedttest phyl.pairedttest
phyl.pca phyl.pca
phyl.resid phyl.resid
phyl.RMA phyl.RMA
phyl.vcv phyl.vcv
phylANOVA phylANOVA
phylo.heatmap phylo.heatmap
phylo.to.map phylo.to.map
phylo.toBackbone phylo.toBackbone
phyloDesign phyloDesign
phylomorphospace phylomorphospace
phylomorphospace3d phylomorphospace3d
phylosig phylosig
phytools phytools-package
plot.backbonePhylo plot.backbonePhylo
plot.changesMap density.multiSimmap
plot.contMap contMap
plot.cophylo cophylo
plot.cospeciation cospeciation
plot.densityMap densityMap
plot.describe.simmap describe.simmap
plot.expand.clade expand.clade
plot.fitMk fitMk
plot.fitPagel fitPagel
plot.gfit fitMk
plot.ltt95 ltt95
plot.multiSimmap plotSimmap
plot.phyl.RMA phyl.RMA
plot.phylo.to.map phylo.to.map
plot.rateshift rateshift
plot.simmap plotSimmap
plotBranchbyTrait plotBranchbyTrait
plotSimmap plotSimmap
plotThresh plotThresh
plotTree plotTree
plotTree.barplot plotTree.wBars
plotTree.boxplot plotTree.wBars
plotTree.errorbars plotTree.errorbars
plotTree.singletons map.to.singleton
plotTree.splits splitplotTree
plotTree.wBars plotTree.wBars
posterior.evolrate posterior.evolrate
posthoc posthoc
posthoc.ratebytree ratebytree
print.backbonePhylo print.backbonePhylo
print.cospeciation cospeciation
print.fit.bd fit.bd
ratebystate ratebystate
ratebytree ratebytree
rateshift rateshift
read.newick read.newick
read.simmap read.simmap
reorder.backbonePhylo reorder.backbonePhylo
reorderSimmap reorderSimmap
rep.multiPhylo rep.phylo
rep.phylo rep.phylo
repPhylo rep.phylo
reroot reroot
rerootingMethod rerootingMethod
rescaleSimmap rescaleSimmap
resolveAllNodes resolveNode
resolveNode resolveNode
rootedge.to.singleton map.to.singleton
rotate.multi rotateNodes
rotateNodes rotateNodes
roundBranches roundBranches
roundPhylogram roundPhylogram
rstate rstate
sampleFrom sampleFrom
setMap setMap
sim.corrs sim.corrs
sim.history sim.history
sim.ratebystate sim.ratebystate
sim.rates sim.rates
skewers skewers
splitEdgeColor splitEdgeColor
splitplotTree splitplotTree
splitTree splitTree
starTree starTree
strahlerNumber strahlerNumber
summary.multiSimmap describe.simmap
summary.simmap describe.simmap
threshBayes threshBayes
threshDIC threshDIC
threshState threshState
tiplabels.cophylo nodelabels.cophylo
tipRotate minRotate
to.matrix to.matrix
treeSlice treeSlice
untangle untangle
vcvPhylo vcvPhylo
write.simmap write.simmap
writeAncestors writeAncestors
writeNexus writeNexus
|