A C D E F G H I L M N P R S T misc
phylobase-package | Utilities and Tools for Phylogenetics |
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 |
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 |
descendants | tree traversal and utility functions |
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 |
formatData | Format data for use in phylo4d objects |
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 |
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 |
isRooted | Methods for S4 phylogeny classes |
isRooted-method | Methods for S4 phylogeny classes |
isRooted-methods | Methods for S4 phylogeny classes |
labels-method | Labels for phylo4/phylo4d objects |
labels<- | Labels for phylo4/phylo4d objects |
labels<--method | Labels for phylo4/phylo4d objects |
MRCA | tree traversal and utility functions |
multiPhylo-class | multiPhylo4 and extended classes |
multiPhylo4-class | multiPhylo4 and extended classes |
multiPhylo4d-class | multiPhylo4 and extended classes |
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 |
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" |
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 |
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 |
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 |
[-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" |