A C D E F G H I L M N O 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 |
| depthTips | edgeLength methods |
| depthTips,phylo4-methods | edgeLength methods |
| depthTips-method | edgeLength methods |
| descendants | Tree traversal and utility functions |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| MRCA | MRCA |
| MRCA-method | MRCA |
| multiPhylo-class | multiPhylo4 and extended classes |
| multiPhylo4-class | multiPhylo4 and extended classes |
| multiPhylo4d-class | multiPhylo4 and extended classes |
| 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 |
| owls4 | 'Owls' data from ape |
| 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 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" |
| 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. |
| 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 |
| 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 |
| [ | 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" |