addData |
Adding data to a phylo4 or a phylo4d object |
addData,phylo4-method |
Adding data to a phylo4 or a phylo4d object |
addData,phylo4d-method |
Adding data to a phylo4 or a phylo4d object |
addData-methods |
Adding data to a phylo4 or a phylo4d object |
ancestor |
tree traversal and utility functions |
ancestors |
tree traversal and utility functions |
as |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,multiPhylo,multiPhylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,multiPhylo4,multiPhylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,multiPhylo4d,multiPhylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo,phylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo,phylo4d-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4,data.frame-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4,phylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4,phylo4vcov-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4d,data.frame-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4d,phylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as,phylo4vcov,phylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
as_phylo4vcov |
matrix classes for phylobase |
checkPhylo4 |
Validity checking for phylo4 objects |
checkPhylo4Data |
Validity checking for phylo4 objects |
checkTree |
Validity checking for phylo4 objects |
check_pdata |
Constructor for pdata (phylogenetic data) class |
children |
tree traversal and utility functions |
coerce,multiPhylo,multiPhylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,multiPhylo4,multiPhylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,multiPhylo4d,multiPhylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo,phylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo,phylo4d-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4,data.frame-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4,phylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4,phylo4vcov-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4,phylog-method |
Class "phylog" |
coerce,phylo4d,data.frame-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4d,phylo-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce,phylo4vcov,phylo4-method |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
coerce-methods |
Converting between phylo4/phylo4d and other phylogenetic tree formats |
edgeId |
node and edge look-up functions |
edgeId,phylo4-method |
node and edge look-up functions |
edgeLabels |
Labels for phylo4/phylo4d objects |
edgeLabels,phylo4-method |
Labels for phylo4/phylo4d objects |
edgeLabels-methods |
Labels for phylo4/phylo4d objects |
edgeLabels<- |
Labels for phylo4/phylo4d objects |
edgeLabels<-,phylo4,character-method |
Labels for phylo4/phylo4d objects |
edgeLength |
Methods for S4 phylogeny classes |
edgeLength,phylo4-method |
Methods for S4 phylogeny classes |
edgeLength-methods |
Methods for S4 phylogeny classes |
edgeLength<- |
Methods for S4 phylogeny classes |
edgeLength<-,phylo4,ANY-method |
Methods for S4 phylogeny classes |
edgeLength<-,phylo4-method |
Methods for S4 phylogeny classes |
edgeOrder |
Methods for S4 phylogeny classes |
edgeOrder,phylo4-method |
Methods for S4 phylogeny classes |
edges |
Methods for S4 phylogeny classes |
edges,phylo4-method |
Methods for S4 phylogeny classes |
edges-methods |
Methods for S4 phylogeny classes |
extractTree |
Get tree from tree+data object |
hasEdgeLabels |
Labels for phylo4/phylo4d objects |
hasEdgeLabels,phylo4-method |
Labels for phylo4/phylo4d objects |
hasEdgeLabels-methods |
Labels for phylo4/phylo4d objects |
hasEdgeLength |
Methods for S4 phylogeny classes |
hasEdgeLength,phylo4-method |
Methods for S4 phylogeny classes |
hasEdgeLength-methods |
Methods for S4 phylogeny classes |
hasNodeData |
Tests for presence of data associated with trees stored as phylo4d objects |
hasNodeData,phylo4d-method |
Tests for presence of data associated with trees stored as phylo4d objects |
hasNodeData-methods |
Tests for presence of data associated with trees stored as phylo4d objects |
hasNodeLabels |
Labels for phylo4/phylo4d objects |
hasNodeLabels,phylo4-method |
Labels for phylo4/phylo4d objects |
hasNodeLabels-methods |
Labels for phylo4/phylo4d objects |
hasPoly |
Test trees for polytomies, inline nodes, or reticulation |
hasRetic |
Test trees for polytomies, inline nodes, or reticulation |
hasSingle |
Test trees for polytomies, inline nodes, or reticulation |
hasTipData |
Tests for presence of data associated with trees stored as phylo4d objects |
hasTipData,phylo4d-method |
Tests for presence of data associated with trees stored as phylo4d objects |
hasTipData-methods |
Tests for presence of data associated with trees stored as phylo4d objects |
head,phylo4-method |
Displaying phylo4 object |
head,phylo4d-method |
Display methods for phylo4d objects |
na.omit,phylo4d-method |
Methods for creating subsets of phylogenies |
names,phylo4-method |
Displaying phylo4 object |
names,phylo4d-method |
Display methods for phylo4d objects |
nEdges |
Methods for S4 phylogeny classes |
nEdges,phylo4-method |
Methods for S4 phylogeny classes |
nEdges-methods |
Methods for S4 phylogeny classes |
nNodes |
Methods for S4 phylogeny classes |
nNodes,phylo4-method |
Methods for S4 phylogeny classes |
nNodes-methods |
Methods for S4 phylogeny classes |
nodeData |
Retrieving or updating tip and node data in phylo4d objects |
nodeData,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
nodeData-method |
Retrieving or updating tip and node data in phylo4d objects |
nodeData<- |
Retrieving or updating tip and node data in phylo4d objects |
nodeData<-,phylo4d,ANY-method |
Retrieving or updating tip and node data in phylo4d objects |
nodeData<-,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
nodeId |
node and edge look-up functions |
nodeId,phylo4-method |
node and edge look-up functions |
nodeLabels |
Labels for phylo4/phylo4d objects |
nodeLabels,phylo4-method |
Labels for phylo4/phylo4d objects |
nodeLabels-methods |
Labels for phylo4/phylo4d objects |
nodeLabels<- |
Labels for phylo4/phylo4d objects |
nodeLabels<-,phylo4,character-method |
Labels for phylo4/phylo4d objects |
nodeLabels<-,phylo4d,ANY-method |
Labels for phylo4/phylo4d objects |
nodeType |
Methods for S4 phylogeny classes |
nodeType,phylo4-method |
Methods for S4 phylogeny classes |
nTips |
Methods for S4 phylogeny classes |
nTips,phylo-method |
Methods for S4 phylogeny classes |
nTips,phylo4-method |
Methods for S4 phylogeny classes |
nTips-methods |
Methods for S4 phylogeny classes |
pdata |
Constructor for pdata (phylogenetic data) class |
pdata-class |
Class "pdata" |
phylo-class |
The phylo4 class |
phylo4 |
Create a phylogenetic tree |
phylo4,matrix-method |
Create a phylogenetic tree |
phylo4,phylo-method |
Create a phylogenetic tree |
phylo4-class |
The phylo4 class |
phylo4-methods |
Create a phylogenetic tree |
phylo4d |
Combine a phylogenetic tree with data |
phylo4d,matrix-method |
Combine a phylogenetic tree with data |
phylo4d,phylo-method |
Combine a phylogenetic tree with data |
phylo4d,phylo4-method |
Combine a phylogenetic tree with data |
phylo4d,phylo4d-method |
Combine a phylogenetic tree with data |
phylo4d-class |
phylo4d class |
phylo4d-methods |
Combine a phylogenetic tree with data |
phylo4vcov-class |
matrix classes for phylobase |
phylo4_orderings |
The phylo4 class |
phylobase |
Utilities and Tools for Phylogenetics |
phylobubbles |
Bubble plots for phylo4d objects |
phylog-class |
Class "phylog" |
phyloXXYY |
Calculate node x and y coordinates |
plot,ANY,ANY-method |
Phylogeny plotting |
plot,pdata,missing-method |
Phylogeny plotting |
plot,phylo4,missing-method |
Phylogeny plotting |
plotOneTree |
Plot a phylo4 object |
print,phylo4-method |
Displaying phylo4 object |
print,phylo4d-method |
Display methods for phylo4d objects |
printphylo4 |
print a phylogeny |
prune |
Methods for creating subsets of phylogenies |
prune,phylo4-method |
Methods for creating subsets of phylogenies |
prune,phylo4d-method |
Methods for creating subsets of phylogenies |
prune-methods |
Methods for creating subsets of phylogenies |
ptypes |
Class "pdata" |
tail,phylo4-method |
Displaying phylo4 object |
tail,phylo4d-method |
Display methods for phylo4d objects |
tbind |
multiPhylo4 and extended classes |
tdata |
Retrieving or updating tip and node data in phylo4d objects |
tdata,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
tdata-method |
Retrieving or updating tip and node data in phylo4d objects |
tdata<- |
Retrieving or updating tip and node data in phylo4d objects |
tdata<-,phylo4d,ANY-method |
Retrieving or updating tip and node data in phylo4d objects |
tdata<-,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
tip.data.plot |
Plotting trees and associated data |
tipData |
Retrieving or updating tip and node data in phylo4d objects |
tipData,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
tipData-method |
Retrieving or updating tip and node data in phylo4d objects |
tipData<- |
Retrieving or updating tip and node data in phylo4d objects |
tipData<-,phylo4d,ANY-method |
Retrieving or updating tip and node data in phylo4d objects |
tipData<-,phylo4d-method |
Retrieving or updating tip and node data in phylo4d objects |
tipLabels |
Labels for phylo4/phylo4d objects |
tipLabels,phylo4-method |
Labels for phylo4/phylo4d objects |
tipLabels-methods |
Labels for phylo4/phylo4d objects |
tipLabels<- |
Labels for phylo4/phylo4d objects |
tipLabels<-,phylo4,character-method |
Labels for phylo4/phylo4d objects |
tipLabels<-,phylo4d,character-method |
Labels for phylo4/phylo4d objects |
treePlot |
Phylogeny plotting |
treePlot,phylo4,phylo4d-method |
Phylogeny plotting |
treePlot-method |
Phylogeny plotting |
[,pdata,ANY,ANY,ANY-method |
Class "pdata" |
[,pdata-method |
Class "pdata" |
[,phylo4,ANY,ANY,ANY-method |
Methods for creating subsets of phylogenies |
[,phylo4,character,missing,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4,logical,missing,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4,missing,missing,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4,numeric,missing,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4-method |
Methods for creating subsets of phylogenies |
[,phylo4d,ANY,character,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4d,ANY,logical,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4d,ANY,missing,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4d,ANY,numeric,missing-method |
Methods for creating subsets of phylogenies |
[,phylo4d-method |
Methods for creating subsets of phylogenies |
[-methods |
Methods for creating subsets of phylogenies |
[<-,pdata-method |
Class "pdata" |
[[,pdata,ANY,ANY-method |
Class "pdata" |
[[,pdata,ANY,missing-method |
Class "pdata" |
[[,pdata-method |
Class "pdata" |
[[<-,pdata-method |
Class "pdata" |