API for phylobase
Base package for phylogenetic structures and comparative data

Global functions
GetNCL 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,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
all_naC Source code
ancestor Man page Source code
ancestors Man page Source code
any_naC Source code
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 Source code
bubLegendGrob Source code
checkPhylo4 Man page Source code
checkPhylo4Data Man page Source code
checkTree Man page Source code
checkTreeCpp Source code
checkTreeOld Source code
check_pdata Man page Source code
children Man page Source code
chnumsort Source code
createEdge Source code
createLabels Source code
depthTips Man page
depthTips,phylo4-method Man page
depthTips,phylo4-methods Man page
descendants Man page Source code
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,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 Source code
formatData Man page Source code
genlab 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
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
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
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
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
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
onAttach Source code
orderIndex Source code
owls4 Man page
pdata Man page Source code
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
phylo4Data Source code
phylo4ToDataFrame Source code
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 Source code
phylobase Man page
phylobase-package Man page
phylobase.options Man page Source code
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 Source code
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
shortestPathInt Source code
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,character-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 May 31, 2017, 5:03 a.m.