/usr/lib/R/site-library/phangorn/help/AnIndex is in r-cran-phangorn 2.4.0-1.
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acctran parsimony
acgt2ry phyDat
add.tips add.tips
addConfidences addConfidences
addTrivialSplits as.splits
AICc modelTest
allCircularSplits as.splits
allDescendants Ancestors
allSitePattern phyDat
allSplits as.splits
allTrees allTrees
Ancestors Ancestors
ancestral.pars ancestral.pml
ancestral.pml ancestral.pml
as.AAbin.phyDat phyDat
as.bitsplits.splits as.splits
as.character.phyDat phyDat
as.data.frame.phyDat phyDat
as.DNAbin.phyDat phyDat
as.Matrix as.splits
as.Matrix.splits as.splits
as.matrix.splits as.splits
as.MultipleAlignment phyDat
as.MultipleAlignment.phyDat phyDat
as.networx as.networx
as.networx.phylo as.networx
as.networx.splits as.networx
as.phyDat phyDat
as.phyDat.alignment phyDat
as.phyDat.character phyDat
as.phyDat.data.frame phyDat
as.phyDat.DNAbin phyDat
as.phyDat.factor phyDat
as.phyDat.matrix phyDat
as.phyDat.MultipleAlignment phyDat
as.phylo.splits as.splits
as.prop.part.splits as.splits
as.splits as.splits
as.splits.multiPhylo as.splits
as.splits.networx as.splits
as.splits.phylo as.splits
bab bab
baseFreq phyDat
bootstrap.phyDat bootstrap.pml
bootstrap.pml bootstrap.pml
BranchAndBound bab
c.phyDat phyDat
c.splits as.splits
cbind.phyDat phyDat
Children Ancestors
chloroplast chloroplast
CI CI
cladePar cladePar
coalSpeciesTree coalSpeciesTree
codon2dna phyDat
compatible as.splits
consensusNet consensusNet
coords phangorn-internal
cophenetic.networx cophenetic.networx
cophenetic.splits cophenetic.networx
createLabel addConfidences
delta.score delta.score
densiTree densiTree
Descendants Ancestors
designSplits designTree
designTree designTree
dfactorial dfactorial
discrete.gamma pml.fit
dist.hamming dist.hamming
dist.logDet dist.hamming
dist.ml dist.hamming
dist.p dist.p
distanceHadamard distanceHadamard
distinct.splits as.splits
diversity getClans
dna2codon phyDat
edQt pml.fit
fhm hadamard
fitch parsimony
genlight2phyDat phyDat
getClans getClans
getClips getClans
getDiversity getClans
getRoot midpoint
getSlices getClans
h2st hadamard
h4st hadamard
hadamard hadamard
identify.networx identify.networx
image.phyDat phyDat
KF.dist treedist
Laurasiatherian Laurasiatherian
ldfactorial dfactorial
lento lento
lli pml.fit
map_duplicates phangorn-internal
mast mast
matchSplits as.splits
maxCladeCred maxCladeCred
midpoint midpoint
midpoint.multiPhylo midpoint
midpoint.phylo midpoint
modelTest modelTest
mrca.phylo Ancestors
multiphyDat2pmlPart pmlPart
neighborNet neighborNet
networx as.networx
NJ NJ
nni nni
nnls.networx designTree
nnls.phylo designTree
nnls.splits designTree
nnls.tree designTree
optim.parsimony parsimony
optim.pml pml
pace ancestral.pml
parsimony parsimony
path.dist treedist
phangorn phangorn-package
phangorn-internal phangorn-internal
phyDat phyDat
phyDat2alignment phyDat
phyDat2MultipleAlignment phyDat
plot.networx as.networx
plotAnc ancestral.pml
plotBS bootstrap.pml
pml pml
pml.control pml
pml.fit pml.fit
pml.free pml.fit
pml.init pml.fit
pmlCluster pmlCluster
pmlMix pmlMix
pmlPart pmlPart
pmlPart2multiPhylo pmlPart
pmlPen pmlMix
PNJ NJ
pratchet parsimony
presenceAbsence addConfidences
print.splits as.splits
pruneTree midpoint
random.addition parsimony
read.aa read.aa
read.nexus.networx read.nexus.splits
read.nexus.splits read.nexus.splits
read.phyDat phyDat
readDist writeDist
removeTrivialSplits as.splits
removeUndeterminedSites phyDat
RF.dist treedist
RI CI
rNNI nni
rSPR nni
sankoff parsimony
SH.test SH.test
Siblings Ancestors
simSeq simSeq
simSeq.phylo simSeq
simSeq.pml simSeq
SOWH.test SOWH.test
splits as.splits
splitsNetwork splitsNetwork
SPR.dist treedist
sprdist treedist
subset.phyDat phyDat
superTree superTree
threshStateC phangorn-internal
treedist treedist
unique.dist writeDist
unique.phyDat phyDat
unique.splits as.splits
UNJ NJ
upgma upgma
wpgma upgma
wRF.dist treedist
write.nexus.dist writeDist
write.nexus.networx read.nexus.splits
write.nexus.splits read.nexus.splits
write.phyDat phyDat
write.splits read.nexus.splits
writeDist writeDist
yeast yeast
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