# Base Package for Phylogenetic Structures and Comparative Data

## Documentation for package ‘phylobase’ version 0.8.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D E F G H I L M N O 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

## -- D --

depthTips | edgeLength methods
depthTips,phylo4-methods | edgeLength methods
depthTips-method | edgeLength methods
descendants | Tree traversal and utility functions

## -- E --

edgeId | nodeId methods
edgeId-method | nodeId methods
edgeLabels | Labels for phylo4/phylo4d objects
edgeLabels-method | Labels for phylo4/phylo4d objects
edgeLabels<- | Labels for phylo4/phylo4d objects
edgeLabels<--method | Labels for phylo4/phylo4d objects
edgeLength | edgeLength methods
edgeLength-method | edgeLength methods
edgeLength<- | edgeLength methods
edgeLength<--method | edgeLength methods
edgeOrder | Edges accessors
edgeOrder-method | Edges accessors
edges | Edges accessors
edges-method | Edges accessors
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
getEdge-method | Node and Edge look-up functions
getEdge-methods | Node and Edge look-up functions
getNode | Node and Edge look-up functions
getNode-method | Node and Edge look-up functions

## -- H --

hasDuplicatedLabels | Labels for phylo4/phylo4d objects
hasDuplicatedLabels-method | Labels for phylo4/phylo4d objects
hasEdgeLabels | Labels for phylo4/phylo4d objects
hasEdgeLabels-method | Labels for phylo4/phylo4d objects
hasEdgeLength | edgeLength methods
hasEdgeLength-method | edgeLength methods
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
hasPoly | Test trees for polytomies, inline nodes (singletons), or reticulation
hasPoly-method | Test trees for polytomies, inline nodes (singletons), or reticulation
hasRetic | Test trees for polytomies, inline nodes (singletons), or reticulation
hasRetic-method | Test trees for polytomies, inline nodes (singletons), or reticulation
hasSingle | Test trees for polytomies, inline nodes (singletons), or reticulation
hasSingle-method | Test trees for polytomies, inline nodes (singletons), 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-method-method | Tests for presence of data associated with trees stored as phylo4d objects
head | print a phylogeny
head-method | print a phylogeny

## -- I --

Import Nexus and Newick files | Create a 'phylo4', 'phylo4d' or 'data.frame' object from a NEXUS or a Newick file
internalEdges | Edges accessors
internalEdges-method | Edges accessors
isRooted | Methods to test, access (and modify) the root of a phylo4 object.
isRooted-method | Methods to test, access (and modify) the root of a phylo4 object.
isUltrametric | edgeLength methods
isUltrametric-method | edgeLength methods

## -- L --

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

## -- M --

MRCA | MRCA
MRCA-method | MRCA
multiPhylo-class | multiPhylo4 and extended classes
multiPhylo4-class | multiPhylo4 and extended classes
multiPhylo4d-class | multiPhylo4 and extended classes

## -- N --

names | print a phylogeny
names-method | print a phylogeny
nData | Tests for presence of data associated with trees stored as phylo4d objects
nData-method | Tests for presence of data associated with trees stored as phylo4d objects
nEdges | nTips, nNodes, nEdges
nEdges-method | nTips, nNodes, nEdges
nexml-method | Create a phylogenetic tree
nexml-method | Combine a phylogenetic tree with data
nNodes | nTips, nNodes, nEdges
nNodes-method | nTips, nNodes, nEdges
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 | edgeLength methods
nodeDepth-method | edgeLength methods
nodeHeight | edgeLength methods
nodeHeight-method | edgeLength methods
nodeId | nodeId methods
nodeId-method | nodeId methods
nodeLabels | Labels for phylo4/phylo4d objects
nodeLabels-method | Labels for phylo4/phylo4d objects
nodeLabels<- | Labels for phylo4/phylo4d objects
nodeLabels<--method | Labels for phylo4/phylo4d objects
nodeType | Summary for phylo4/phylo4d objects
nodeType-method | Summary for phylo4/phylo4d objects
nTips | nTips, nNodes, nEdges
nTips-method | nTips, nNodes, nEdges

## -- O --

owls4 | 'Owls' data from ape

## -- P --

pdata | Constructor for pdata (phylogenetic data) class
pdata-class | Class "pdata"
phylo4 | Create a phylogenetic tree
phylo4-class | The phylo4 class
phylo4-labels | Labels for phylo4/phylo4d objects
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 | Create a phylogenetic tree
phylobase | Utilities and Tools for Phylogenetics
phylobase.options | Set or return options of phylobase
phylobubbles | Bubble plots for phylo4d objects
phylomat-class | matrix classes for phylobase
phylomat-setAs | matrix classes for phylobase
phyloXXYY | Calculate node x and y coordinates
plot | Phylogeny plotting
plot-method | Phylogeny plotting
plotOneTree | Plot a phylo4 object
print | print a phylogeny
print-method | print a phylogeny
prune | Methods for creating subsets of phylogenies
prune-method | 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 | reordering trees within phylobase objects
reorder-method | reordering trees within phylobase objects
reorder-methods | reordering trees within phylobase objects
rootNode | Methods to test, access (and modify) the root of a phylo4 object.
rootNode-method | Methods to test, access (and modify) the root of a phylo4 object.
rootNode<- | Methods to test, access (and modify) the root of a phylo4 object.
rootNode<--method | Methods to test, access (and modify) the root of a phylo4 object.

## -- S --

setAs | Converting between phylo4/phylo4d and other phylogenetic tree formats
setAs-method | matrix classes for phylobase
setAs-method | Converting between phylo4/phylo4d and other phylogenetic tree formats
shortestPath | shortestPath-methods
shortestPath-method | shortestPath-methods
shortestPath-phylo | shortestPath-methods
shortestPath-phylo4 | shortestPath-methods
show | print a phylogeny
show-method | print a phylogeny
siblings | Tree traversal and utility functions
subset | Methods for creating subsets of phylogenies
subset-method | Methods for creating subsets of phylogenies
subset-methods | Methods for creating subsets of phylogenies
sumEdgeLength | edgeLength methods
sumEdgeLength-method | edgeLength methods
summary | Summary for phylo4/phylo4d objects
summary-method | Summary for phylo4/phylo4d objects
summary-methods | Summary for phylo4/phylo4d objects

## -- T --

tail | print a phylogeny
tail-method | print a phylogeny
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
terminalEdges | Edges accessors
terminalEdges-method | Edges accessors
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<- | Labels for phylo4/phylo4d objects
tipLabels<--method | Labels for phylo4/phylo4d objects
treePlot | Phylogeny plotting
treePlot-method | Phylogeny plotting
treePlot-methods | Phylogeny plotting

## -- misc --

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