# Base package for phylogenetic structures and comparative data

## Documentation for package ‘phylobase’ version 0.6.3

- DESCRIPTION file.
- Overview of user guides and package vignettes; browse directory.
- Package NEWS.

## Help Pages

A C D E F G H I L M N P R S T misc

phylobase-package | Utilities and Tools for Phylogenetics

## -- A --

addData | Adding data to a phylo4 or a phylo4d object
addData-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-method | Converting between phylo4/phylo4d and other phylogenetic tree formats
as_phylo4vcov | matrix classes for phylobase

## -- C --

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-method | Converting between phylo4/phylo4d and other phylogenetic tree formats
coerce-method | Class "phylog"
coerce-methods | Converting between phylo4/phylo4d and other phylogenetic tree formats

## -- D --

depthTips | Methods for S4 phylogeny classes
depthTips-method | Methods for S4 phylogeny classes
depthTips-methods | Methods for S4 phylogeny classes
descendants | tree traversal and utility functions

## -- E --

edgeId | node and edge look-up functions
edgeId-method | node and edge look-up functions
edgeLabels | Labels for phylo4/phylo4d objects
edgeLabels-method | Labels for phylo4/phylo4d objects
edgeLabels-methods | Labels for phylo4/phylo4d objects
edgeLabels<- | Labels for phylo4/phylo4d objects
edgeLabels<--method | Labels for phylo4/phylo4d objects
edgeLength | Methods for S4 phylogeny classes
edgeLength-method | Methods for S4 phylogeny classes
edgeLength-methods | Methods for S4 phylogeny classes
edgeLength<- | Methods for S4 phylogeny classes
edgeLength<--method | Methods for S4 phylogeny classes
edgeOrder | Methods for S4 phylogeny classes
edgeOrder-method | Methods for S4 phylogeny classes
edges | Methods for S4 phylogeny classes
edges-method | Methods for S4 phylogeny classes
edges-methods | Methods for S4 phylogeny classes
extractTree | Get tree from tree+data object

## -- F --

formatData | Format data for use in phylo4d objects

## -- G --

geospiza | Data from Darwin's finches
geospiza_raw | Data from Darwin's finches
getEdge | node and edge look-up functions
getNode | node and edge look-up functions

## -- H --

hasDuplicatedLabels | Labels for phylo4/phylo4d objects
hasDuplicatedLabels-method | Labels for phylo4/phylo4d objects
hasDuplicatedLabels-methods | Labels for phylo4/phylo4d objects
hasEdgeLabels | Labels for phylo4/phylo4d objects
hasEdgeLabels-method | Labels for phylo4/phylo4d objects
hasEdgeLabels-methods | Labels for phylo4/phylo4d objects
hasEdgeLength | Methods for S4 phylogeny classes
hasEdgeLength-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-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-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-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-method | Displaying phylo4 object
head-method | Display methods for phylo4d objects

## -- I --

isRooted | Methods for S4 phylogeny classes
isRooted-method | Methods for S4 phylogeny classes
isRooted-methods | Methods for S4 phylogeny classes
isUltrametric | Methods for S4 phylogeny classes
isUltrametric-method | Methods for S4 phylogeny classes
isUltrametric-methods | Methods for S4 phylogeny classes

## -- L --

labels-method | Labels for phylo4/phylo4d objects
labels<- | Labels for phylo4/phylo4d objects
labels<--method | Labels for phylo4/phylo4d objects

## -- M --

MRCA | tree traversal and utility functions
multiPhylo-class | multiPhylo4 and extended classes
multiPhylo4-class | multiPhylo4 and extended classes
multiPhylo4d-class | multiPhylo4 and extended classes

## -- N --

na.omit-method | Methods for creating subsets of phylogenies
names-method | Displaying phylo4 object
names-method | Display methods for phylo4d objects
nData | Retrieves the number of datasets in phylo4d objects
nData-method | Retrieves the number of datasets in phylo4d objects
nEdges | Methods for S4 phylogeny classes
nEdges-method | Methods for S4 phylogeny classes
nEdges-methods | Methods for S4 phylogeny classes
nNodes | Methods for S4 phylogeny classes
nNodes-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-method | Retrieving or updating tip and node data in phylo4d objects
nodeData<- | Retrieving or updating tip and node data in phylo4d objects
nodeData<--method | Retrieving or updating tip and node data in phylo4d objects
nodeDepth | Methods for S4 phylogeny classes
nodeDepth-method | Methods for S4 phylogeny classes
nodeDepth-methods | Methods for S4 phylogeny classes
nodeId | node and edge look-up functions
nodeId-method | node and edge look-up functions
nodeLabels | Labels for phylo4/phylo4d objects
nodeLabels-method | Labels for phylo4/phylo4d objects
nodeLabels-methods | Labels for phylo4/phylo4d objects
nodeLabels<- | Labels for phylo4/phylo4d objects
nodeLabels<--method | Labels for phylo4/phylo4d objects
nodeType | Methods for S4 phylogeny classes
nodeType-method | Methods for S4 phylogeny classes
nTips | Methods for S4 phylogeny classes
nTips-method | Methods for S4 phylogeny classes
nTips-methods | Methods for S4 phylogeny classes

## -- P --

pdata | Constructor for pdata (phylogenetic data) class
pdata-class | Class "pdata"
phylo-class | The phylo4 class
phylo4 | Create a phylogenetic tree
phylo4-class | The phylo4 class
phylo4-method | Create a phylogenetic tree
phylo4-methods | Create a phylogenetic tree
phylo4d | Combine a phylogenetic tree with data
phylo4d-class | phylo4d class
phylo4d-method | Combine a phylogenetic tree with data
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
phylobase.options | Set or return options of phylobase
phylobubbles | Bubble plots for phylo4d objects
phylog-class | Class "phylog"
phyloXXYY | Calculate node x and y coordinates
plot-method | Phylogeny plotting
plotOneTree | Plot a phylo4 object
print-method | Displaying phylo4 object
print-method | Display methods for phylo4d objects
printphylo4 | print a phylogeny
prune | Methods for creating subsets of phylogenies
prune-method | Methods for creating subsets of phylogenies
prune-methods | Methods for creating subsets of phylogenies
ptypes | Class "pdata"

## -- R --

readNCL | Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file
readNewick | Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file
readNexus | Create a phylo4, phylo4d or data.frame object from a Nexus or a Newick file
reorder-method | reordering trees within phylobase objects
reorder-methods | reordering trees within phylobase objects
rootEdge | Methods for S4 phylogeny classes
rootEdge-method | Methods for S4 phylogeny classes
rootEdge-methods | Methods for S4 phylogeny classes
rootNode | Methods for S4 phylogeny classes
rootNode-method | Methods for S4 phylogeny classes
rootNode-methods | Methods for S4 phylogeny classes
rootNode<- | Methods for S4 phylogeny classes
rootNode<--method | Methods for S4 phylogeny classes

## -- S --

shortestPath | tree traversal and utility functions
show-method | Displaying phylo4 object
show-method | Display methods for phylo4d objects
siblings | tree traversal and utility functions
subset-method | Methods for creating subsets of phylogenies
subset-methods | Methods for creating subsets of phylogenies
sumEdgeLength | tree traversal and utility functions
sumEdgeLength-method | tree traversal and utility functions
summary-method | Displaying phylo4 object
summary-method | Display methods for phylo4d objects

## -- T --

tail-method | Displaying phylo4 object
tail-method | Display methods for phylo4d objects
tbind | multiPhylo4 and extended classes
tdata | 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<--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-method | Retrieving or updating tip and node data in phylo4d objects
tipData<- | Retrieving or updating tip and node data in phylo4d objects
tipData<--method | Retrieving or updating tip and node data in phylo4d objects
tipLabels | Labels for phylo4/phylo4d objects
tipLabels-method | Labels for phylo4/phylo4d objects
tipLabels-methods | Labels for phylo4/phylo4d objects
tipLabels<- | Labels for phylo4/phylo4d objects
tipLabels<--method | Labels for phylo4/phylo4d objects
treePlot | Phylogeny plotting
treePlot-method | Phylogeny plotting

## -- misc --

[-method | Class "pdata"
[-method | Methods for creating subsets of phylogenies
[-methods | Methods for creating subsets of phylogenies
[<--method | Class "pdata"
[[-method | Class "pdata"
[[<--method | Class "pdata"