Base package for phylogenetic structures and comparative data


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Documentation for package ‘phylobase’ version 0.5

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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 --

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 --

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

-- 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
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
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
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 --

read.nexustreestring Read Nexus tree string
readNexus Create a phylo4 or a phylo4d object from a Nexus 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"