Base Package for Phylogenetic Structures and Comparative Data

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Documentation for package ‘phylobase’ version 0.8.12

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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"