phylobase-package	phylobase-package
addData	addData
addData,phylo4-method	addData
addData,phylo4d-method	addData
addData-methods	addData
ancestor	treewalk
ancestors	treewalk
as	as-methods
as,multiPhylo,multiPhylo4-method	as-methods
as,multiPhylo4,multiPhylo-method	as-methods
as,multiPhylo4d,multiPhylo-method	as-methods
as,phylo,phylo4-method	as-methods
as,phylo,phylo4d-method	as-methods
as,phylo4,data.frame-method	as-methods
as,phylo4,phylo-method	as-methods
as,phylo4,phylo4vcov-method	as-methods
as,phylo4d,data.frame-method	as-methods
as,phylo4d,phylo-method	as-methods
as,phylo4vcov,phylo4-method	as-methods
as-method	as-methods
as_phylo4vcov	phylomat-class
checkPhylo4	check.phylo4
checkPhylo4Data	check.phylo4
checkTree	check.phylo4
check_pdata	pdata
children	treewalk
coerce,multiPhylo,multiPhylo4-method	as-methods
coerce,multiPhylo4,multiPhylo-method	as-methods
coerce,multiPhylo4d,multiPhylo-method	as-methods
coerce,phylo,phylo4-method	as-methods
coerce,phylo,phylo4d-method	as-methods
coerce,phylo4,data.frame-method	as-methods
coerce,phylo4,phylo-method	as-methods
coerce,phylo4,phylo4vcov-method	as-methods
coerce,phylo4,phylog-method	phylog
coerce,phylo4d,data.frame-method	as-methods
coerce,phylo4d,phylo-method	as-methods
coerce,phylo4vcov,phylo4-method	as-methods
coerce-methods	as-methods
depthTips	phylo4-accessors
depthTips,phylo4-method	phylo4-accessors
depthTips,phylo4d-method	phylo4-accessors
depthTips-methods	phylo4-accessors
descendants	treewalk
edgeId	getNode
edgeId,phylo4-method	getNode
edgeLabels	phylo4-labels
edgeLabels,phylo4-method	phylo4-labels
edgeLabels-methods	phylo4-labels
edgeLabels<-	phylo4-labels
edgeLabels<-,phylo4,character-method	phylo4-labels
edgeLength	phylo4-accessors
edgeLength,phylo4-method	phylo4-accessors
edgeLength-methods	phylo4-accessors
edgeLength<-	phylo4-accessors
edgeLength<-,phylo4,ANY-method	phylo4-accessors
edgeLength<-,phylo4-method	phylo4-accessors
edgeOrder	phylo4-accessors
edgeOrder,phylo4-method	phylo4-accessors
edges	phylo4-accessors
edges,phylo4-method	phylo4-accessors
edges-methods	phylo4-accessors
extractTree	extract.tree
formatData	formatData
geospiza	geospiza
geospiza_raw	geospiza
getEdge	getNode
getNode	getNode
hasDuplicatedLabels	phylo4-labels
hasDuplicatedLabels,phylo4-method	phylo4-labels
hasDuplicatedLabels-methods	phylo4-labels
hasEdgeLabels	phylo4-labels
hasEdgeLabels,phylo4-method	phylo4-labels
hasEdgeLabels-methods	phylo4-labels
hasEdgeLength	phylo4-accessors
hasEdgeLength,phylo4-method	phylo4-accessors
hasEdgeLength-methods	phylo4-accessors
hasNodeData	phylo4d-hasData
hasNodeData,phylo4d-method	phylo4d-hasData
hasNodeData-methods	phylo4d-hasData
hasNodeLabels	phylo4-labels
hasNodeLabels,phylo4-method	phylo4-labels
hasNodeLabels-methods	phylo4-labels
hasPoly	hasSingles
hasRetic	hasSingles
hasSingle	hasSingles
hasTipData	phylo4d-hasData
hasTipData,phylo4d-method	phylo4d-hasData
hasTipData-methods	phylo4d-hasData
head,phylo4-method	phylo4-display
head,phylo4d-method	phylo4d-display
isRooted	phylo4-accessors
isRooted,phylo4-method	phylo4-accessors
isRooted-methods	phylo4-accessors
isUltrametric	phylo4-accessors
isUltrametric,phylo4-method	phylo4-accessors
isUltrametric-methods	phylo4-accessors
labels,phylo4-method	phylo4-labels
labels<-	phylo4-labels
labels<-,phylo4,ANY,ANY,character-method	phylo4-labels
labels<-,phylo4d,ANY,ANY,character-method	phylo4-labels
MRCA	treewalk
multiPhylo-class	multiPhylo-class
multiPhylo4-class	multiPhylo-class
multiPhylo4d-class	multiPhylo-class
na.omit,phylo4d-method	subset-methods
names,phylo4-method	phylo4-display
names,phylo4d-method	phylo4d-display
nData	phylo4d-nData
nData,phylo4d-method	phylo4d-nData
nEdges	phylo4-accessors
nEdges,phylo4-method	phylo4-accessors
nEdges-methods	phylo4-accessors
nNodes	phylo4-accessors
nNodes,phylo4-method	phylo4-accessors
nNodes-methods	phylo4-accessors
nodeData	tdata
nodeData,phylo4d-method	tdata
nodeData-method	tdata
nodeData<-	tdata
nodeData<-,phylo4d,ANY-method	tdata
nodeData<-,phylo4d-method	tdata
nodeDepth	phylo4-accessors
nodeDepth,phylo4-method	phylo4-accessors
nodeDepth-methods	phylo4-accessors
nodeId	getNode
nodeId,phylo4-method	getNode
nodeLabels	phylo4-labels
nodeLabels,phylo4-method	phylo4-labels
nodeLabels-methods	phylo4-labels
nodeLabels<-	phylo4-labels
nodeLabels<-,phylo4,character-method	phylo4-labels
nodeLabels<-,phylo4d,ANY-method	phylo4-labels
nodeType	phylo4-accessors
nodeType,phylo4-method	phylo4-accessors
nTips	phylo4-accessors
nTips,phylo-method	phylo4-accessors
nTips,phylo4-method	phylo4-accessors
nTips-methods	phylo4-accessors
owls4	owls4
pdata	pdata
pdata-class	pdata-class
phylo-class	phylo4-class
phylo4	phylo4
phylo4,matrix-method	phylo4
phylo4,phylo-method	phylo4
phylo4-class	phylo4-class
phylo4-methods	phylo4
phylo4d	phylo4d
phylo4d,matrix-method	phylo4d
phylo4d,phylo-method	phylo4d
phylo4d,phylo4-method	phylo4d
phylo4d,phylo4d-method	phylo4d
phylo4d-class	phylo4d-class
phylo4d-methods	phylo4d
phylo4vcov-class	phylomat-class
phylo4_orderings	phylo4-class
phylobase	phylobase-package
phylobase.options	phylobase.options
phylobubbles	phylobubbles
phylog-class	phylog
phyloXXYY	phyloXXYY
plot,ANY,ANY-method	treePlot-methods
plot,pdata,missing-method	treePlot-methods
plot,phylo4,missing-method	treePlot-methods
plotOneTree	plotOneTree
print,phylo4-method	phylo4-display
print,phylo4d-method	phylo4d-display
printphylo4	printphylo4
prune	subset-methods
prune,phylo4-method	subset-methods
prune,phylo4d-method	subset-methods
prune-methods	subset-methods
ptypes	pdata-class
readNCL	readNCL
readNewick	readNCL
readNexus	readNCL
reorder,phylo-method	reorder-methods
reorder,phylo4-method	reorder-methods
reorder,phylo4d-method	reorder-methods
reorder-methods	reorder-methods
rootEdge	phylo4-accessors
rootEdge,phylo4-method	phylo4-accessors
rootEdge-methods	phylo4-accessors
rootNode	phylo4-accessors
rootNode,phylo4-method	phylo4-accessors
rootNode-methods	phylo4-accessors
rootNode<-	phylo4-accessors
rootNode<-,phylo4-method	phylo4-accessors
shortestPath	treewalk
show,phylo4-method	phylo4-display
show,phylo4d-method	phylo4d-display
siblings	treewalk
subset,phylo4-method	subset-methods
subset,phylo4d-method	subset-methods
subset-methods	subset-methods
sumEdgeLength	treewalk
sumEdgeLength,phylo4-method	treewalk
summary,phylo4-method	phylo4-display
summary,phylo4d-method	phylo4d-display
tail,phylo4-method	phylo4-display
tail,phylo4d-method	phylo4d-display
tbind	multiPhylo-class
tdata	tdata
tdata,phylo4d-method	tdata
tdata-method	tdata
tdata<-	tdata
tdata<-,phylo4d,ANY-method	tdata
tdata<-,phylo4d-method	tdata
tip.data.plot	tip.data.plot
tipData	tdata
tipData,phylo4d-method	tdata
tipData-method	tdata
tipData<-	tdata
tipData<-,phylo4d,ANY-method	tdata
tipData<-,phylo4d-method	tdata
tipLabels	phylo4-labels
tipLabels,phylo4-method	phylo4-labels
tipLabels-methods	phylo4-labels
tipLabels<-	phylo4-labels
tipLabels<-,phylo4,character-method	phylo4-labels
tipLabels<-,phylo4d,character-method	phylo4-labels
treePlot	treePlot-methods
treePlot,phylo4,phylo4d-method	treePlot-methods
treePlot-method	treePlot-methods
[,pdata,ANY,ANY,ANY-method	pdata-class
[,pdata-method	pdata-class
[,phylo4,ANY,ANY,ANY-method	subset-methods
[,phylo4,character,missing,missing-method	subset-methods
[,phylo4,logical,missing,missing-method	subset-methods
[,phylo4,missing,missing,missing-method	subset-methods
[,phylo4,numeric,missing,missing-method	subset-methods
[,phylo4-method	subset-methods
[,phylo4d,ANY,character,missing-method	subset-methods
[,phylo4d,ANY,logical,missing-method	subset-methods
[,phylo4d,ANY,missing,missing-method	subset-methods
[,phylo4d,ANY,numeric,missing-method	subset-methods
[,phylo4d-method	subset-methods
[-methods	subset-methods
[<-,pdata-method	pdata-class
[[,pdata,ANY,ANY-method	pdata-class
[[,pdata,ANY,missing-method	pdata-class
[[,pdata-method	pdata-class
[[<-,pdata-method	pdata-class
