API for phylobase
Base Package for Phylogenetic Structures and Comparative Data

Global functions
.bubLegendGrob	Source code
.chnumsort	Source code
.createEdge	Source code
.createLabels	Source code
.genlab	Source code
.onAttach	Source code
.phylo4Data	Source code
.phylo4ToDataFrame	Source code
.shortestPathInt	Source code
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,logical,missing,missing-method	Man page
[,phylo4,missing,missing,missing-method	Man page
[,phylo4,numeric,missing,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
`treePlot`	Source code
addData	Man page
addData,phylo4-method	Man page
addData,phylo4d-method	Man page
addData-methods	Man page
all_naC	Source code
ancestor	Man page Source code
ancestors	Man page
any_naC	Source code
as	Man page
as,nexml,phylo4-method	Man page
as,nexml,phylo4d-method	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 Source code
checkPhylo4	Man page Source code
checkPhylo4Data	Man page Source code
checkTree	Man page Source code
checkTreeCpp	Source code
check_pdata	Man page Source code
children	Man page Source code
depthTips	Man page
depthTips,phylo4-method	Man page
depthTips,phylo4-methods	Man page
descendants	Man page
drawDetails.bubLegend	Source code
edgeId	Man page
edgeId,phylo4-method	Man page
edgeIdCpp	Source code
edgeLabels	Man page
edgeLabels,phylo4-method	Man page
edgeLabels<-	Man page
edgeLabels<-,phylo4-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 Source code
formatData	Man page Source code
geospiza	Man page
geospiza_raw	Man page
getAllNodesFast	Source code
getAllNodesSafe	Source code
getEdge	Man page
getEdge,phylo4-method	Man page
getEdge-methods	Man page
getNode	Man page
getNode,phylo4-method	Man page
getRange	Source code
get_edge_length	Source code
get_edge_matrix	Source code
hasDuplicatedLabels	Man page
hasDuplicatedLabels,phylo4,ANY-method	Man page
hasDuplicatedLabels,phylo4-method	Man page
hasDuplicatedLabelsCpp	Source code
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
hasPolytomy	Source code
hasRetic	Man page
hasRetic,phylo4-method	Man page
hasSingle	Man page
hasSingle,phylo4-method	Man page
hasSingleton	Source code
hasTipData	Man page
hasTipData,phylo4d-method	Man page
hasTipData-method,phylo4d-method	Man page
has_node_labels	Source code
head	Man page
head,phylo4-method	Man page
internalEdges	Man page
internalEdges,phylo4-method	Man page
isLabelName	Source code
isRooted	Man page
isRooted,phylo4-method	Man page
isUltrametric	Man page
isUltrametric,phylo4-method	Man page
is_rooted	Source code
label_to_data	Source code
labels	Man page
labels,phylo4-method	Man page
labels<-	Man page
labels<-,phylo4-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
nRoots	Source code
nTips	Man page
nTips,phylo-method	Man page
nTips,phylo4-method	Man page
nTipsFastCpp	Source code
nTipsSafe	Source code
names	Man page
names,phylo4-method	Man page
nb_naC	Source code
nexml,phylo4-method	Man page
nexml,phylo4d-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
nodeHeight	Man page
nodeHeight,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-method	Man page
nodeType	Man page
nodeType,phylo4-method	Man page
orderIndex	Source code
owls4	Man page
pdata	Man page Source code
pdata-class	Man page
phylo4	Man page
phylo4,matrix-method	Man page
phylo4,nexml-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,nexml-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
phylo4d-methods	Man page
phylo4vcov-class	Man page
phyloXXYY	Man page Source code
phylobase	Man page
phylobase-package	Man page
phylobase.options	Man page
phylobubbles	Man page Source code
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 Source code
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 Source code
readNewick	Man page Source code
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 Source code
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
tabulateTips	Source code
tail	Man page
tail,phylo4-method	Man page
tbind	Man page Source code
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
testEqInt	Source code
tip.data.plot	Man page Source code
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-method	Man page
tipsFast	Source code
tipsSafe	Source code
treePlot	Man page
treePlot,phylo4,phylo4d-method	Man page
treePlot-method	Man page
treePlot-methods	Man page