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
phylobase documentation built on March 26, 2020, 7:44 p.m.