| 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" |