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