API for phylobase
Base package for phylogenetic structures and comparative data

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